Search results for query "look through"

527 messages

Re: [phenixbb] AUTOSOL for MAD data with error message-'Need a symfile for solve'

by Thomas C. Terwilliger

Hi again Frank and Graeme and Mohan, This is now fixed and should be available in tomorrow's build of PHENIX. Most setting should now be available in Autosol (this bug only affected Autosol, not Autobuild or any other PHENIX routines). Thanks for pointing out the problem (and Mohan if this does not solve it in your case, please let me know and I'll continue to fix it). All the best, Tom T >> Hi Frank and Graeme and Mohan, >> >> Yes, P 2 21 21 should be allowed in autosol. I see that it doesn't work >> and I'll fix that. >> >> All the best, >> Tom T >> >> >>>> Um, this one has been hacked to death on ccp4bb: there is in fact >>>> nothing wrong or "non-standard" with that setting. If the program >>>> won't >>>> handle it, email the authors and ask them to fix it. >>>> >>>> Reindexing is an almighty pain in the butt. >>>> >>>> That said: it sounds like you may be pointing at an out-of-date >>>> symmetry operator file; I forget which environment variable it is, >>>> check the manual, but point it to an up-to-date ccp4 installation, and >>>> I >>>> suspect it will be fine. >>>> >>>> phx >>>> >>>> >>>> >>>> >>>> On 02/02/2010 13:49, Graeme Winter wrote: >>>>> Hi Mohan, >>>>> >>>>> P22121 is not the standard setting for this spacegroup - in >>>>> International Tables the convention is to have the spacegroup's unique >>>>> axis as C, e.g. P21212 in this case. If you run this reflection file >>>>> through reindex as follows: >>>>> >>>>> reindex hklin in.mtz hklout out.mtz<< eof >>>>> reindex k,l,h >>>>> eof >>>>> >>>>> Then it should work just fine. An alternative would be to compose a >>>>> solve "symm" file and put this in the right place. This would look >>>>> something like: >>>>> >>>>> 4 Equiv positions, P22121 SG # 3018 >>>>> X,Y,Z >>>>> X,-Y,-Z >>>>> -X,1/2+Y,1/2-Z >>>>> -X,1/2-Y,1/2+Z >>>>> >>>>> (copied from spacegroup #3018 in the CCP4 symop.lib) which would need >>>>> to >>>>> go in >>>>> >>>>> phenix-1.6-289/solve_resolve/ext_ref_files >>>>> >>>>> On balance, reindexing is probably easiest! >>>>> >>>>> Best wishes, >>>>> >>>>> Graeme >>>>> >>>>> On 2 February 2010 13:38,<m.b.rajasekaran(a)reading.ac.uk> wrote: >>>>> >>>>>> >>>>>> Dear all, >>>>>> I have a query regarding the Autosol option in the >>>>>> PHENIX-1.6-289 version. We are trying to process a MAD data for a >>>>>> zinc >>>>>> bound >>>>>> protein crystal with AuTOSOL. We uploaded the scaled files, sequence >>>>>> and all >>>>>> other details and started running AUTOSOL. But the program stopped >>>>>> with >>>>>> the >>>>>> following error message pasted below mentioning some missing of >>>>>> symfile. We >>>>>> were not able to locate any parameters file on the installation >>>>>> directory. >>>>>> It would be helpful if we get some useful suggestions on this. >>>>>> >>>>>> Thanks in advance, >>>>>> Mohan >>>>>> *********************************************************** >>>>>> >>>>>> PHENIX AutoSol Tue Feb 2 12:37:41 2010 >>>>>> >>>>>> ************************************************************ >>>>>> >>>>>> Working directory: /home/sar06mbr/30JanDiamondI02/107/107_php22121 >>>>>> PHENIX VERSION: 1.6 of 29-01-2010 PHENIX RELEASE_TAG : 289 PHENIX >>>>>> MTYPE >>>>>> : >>>>>> intel-linux-2.6 PHENIX MVERSION : suse AutoSol_start AutoSol Run 2 >>>>>> Tue >>>>>> Feb 2 >>>>>> 12:37:41 2010 INPUT FILE LIST: >>>>>> ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz', >>>>>> '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz', >>>>>> '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz'] >>>>>> >>>>>> Copied /home/sar06mbr/30JanDiamondI02/107/107_php22121/result.seq to >>>>>> /home/sar06mbr/30JanDiamondI02/107/107_php22121/AutoSol_run_2_/sequence_autosol.dat >>>>>> >>>>>> Setting chain_type to PROTEIN Setting defaults for data_quality >>>>>> moderate >>>>>> Setting thorough_denmod to Yes Settin fix_xyz_after_denmod to False >>>>>> Setting >>>>>> max_ha_iterations to 2 Setting fixscattfactors to No Settin defaults >>>>>> for >>>>>> thoroughness quick Setting best_of_n_hyss_always to 1 Setting >>>>>> max_extra_unique_solutions to 0 Settin ha_iteration to No Setting >>>>>> max_choices to 1 Setting number_of_models to 1 Setting >>>>>> number_of_builds >>>>>> to 1 >>>>>> Setting test_mask_type to No Setting n_cycle_build to 0 Setting >>>>>> thorough_loop_fit to Setting create_scoring_table to No Not >>>>>> truncating >>>>>> ha >>>>>> sites at start of resolve as this is not PHASER SAD phasing >>>>>> >>>>>> Trying to guess refinement file for later use from >>>>>> ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz', >>>>>> '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz', >>>>>> '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz'] >>>>>> >>>>>> Choosing guess of refinement file for later use from all files: >>>>>> ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz', >>>>>> '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz', >>>>>> '/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz'] >>>>>> >>>>>> FILE TYPE ccp4_mtz >>>>>> >>>>>> COLUMN LABELS: ['H', 'K', 'L', 'FreeR_flag', 'F_107_2re', >>>>>> 'SIGF_107_2re', >>>>>> 'F_107_2re(+)', 'SIGF_107_2re(+)', 'F_107_2re(-)', 'SIGF_107_2re(-)', >>>>>> 'DANO_107_2re', 'SIGDANO_107_2re', 'IMEAN_107_2re', >>>>>> 'SIGIMEAN_107_2re', >>>>>> 'I_107_2re(+)', 'SIGI_107_2re(+)', 'I_107_2re(-)', 'SIGI_107_2re(-)'] >>>>>> >>>>>> GUESS FILE TYPE MERGE TYPE mtz premerged TARGET LABELS ['F1', >>>>>> 'SIGF1', >>>>>> 'DANO1', 'SIGDANO1'] Unit cell: (34.79, 108.92, 134.88, 90, 90, 90) >>>>>> Space >>>>>> group: P 2 21 21 (No. 18) CONTENTS: >>>>>> ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz', >>>>>> 'mtz', 'premerged', 'P 2 21 21', [34.790000915527344, >>>>>> 108.92009735107422, >>>>>> 134.8800048828125, 90.0, 90.0, 90.0], 2.4890566908055836, ['F1', >>>>>> 'SIGF1', >>>>>> 'DANO1', 'SIGDANO1']] >>>>>> >>>>>> File >>>>>> /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz >>>>>> RES: 2.5 >>>>>> >>>>>> FILE TYPE ccp4_mtz COLUMN LABELS: ['H', 'K', 'L', 'FreeR_flag', >>>>>> 'F_107_3re', >>>>>> 'SIGF_107_3re', 'F_107_3re(+)', 'SIGF_107_3re(+)', 'F_107_3re(-)', >>>>>> 'SIGF_107_3re(-)', 'DANO_107_3re', 'SIGDANO_107_3re', >>>>>> 'IMEAN_107_3re', >>>>>> 'SIGIMEAN_107_3re', 'I_107_3re(+)', 'SIGI_107_3re(+)', >>>>>> 'I_107_3re(-)', >>>>>> 'SIGI_107_3re(-)'] >>>>>> >>>>>> GUESS FILE TYPE MERGE TYPE mtz premerged TARGET LABELS ['F1', >>>>>> 'SIGF1', >>>>>> 'DANO1', 'SIGDANO1'] Unit cell: (34.85, 109.18, 135.27, 90, 90, 90) >>>>>> Space >>>>>> group: P 2 21 21 (No. 18) CONTENTS: >>>>>> ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz', >>>>>> 'mtz', 'premerged', 'P 2 21 21', [34.849998474121094, >>>>>> 109.18000030517578, >>>>>> 135.26980590820312, 90.0, 90.0, 90.0], 2.4889952912293629, ['F1', >>>>>> 'SIGF1', >>>>>> 'DANO1', 'SIGDANO1']] >>>>>> >>>>>> File >>>>>> /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz >>>>>> RES: 2.5 >>>>>> >>>>>> FILE TYPE ccp4_mtz COLUMN LABELS: ['H', 'K', 'L', 'FreeR_flag', >>>>>> 'F_107_4re', >>>>>> 'SIGF_107_4re', 'F_107_4re(+)', 'SIGF_107_4re(+)', 'F_107_4re(-)', >>>>>> 'SIGF_107_4re(-)', 'DANO_107_4re', 'SIGDANO_107_4re', >>>>>> 'IMEAN_107_4re', >>>>>> 'SIGIMEAN_107_4re', 'I_107_4re(+)', 'SIGI_107_4re(+)', >>>>>> 'I_107_4re(-)', >>>>>> 'SIGI_107_4re(-)'] >>>>>> >>>>>> GUESS FIL TARGET LABELS ['F1', 'SIGF1', 'DANO1', 'SIGDANO1'] Unit >>>>>> cell: >>>>>> (34.87, 109.2, 135.33, 90, 90, 90) Space group: P 2 21 21 (No. 18) >>>>>> CONTENTS: >>>>>> ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz', >>>>>> 'mtz', 'premerged', 'P 2 21 21', [34.869998931884766, >>>>>> 109.19999694824219, >>>>>> 135.32989501953125, 90.0, 90.0, 90.0], 2.4890134311310943, ['F1', >>>>>> 'SIGF1', >>>>>> 'DANO1', 'SIGDANO1']] >>>>>> >>>>>> File >>>>>> /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_4_P22121_scala2.mtz >>>>>> RES: 2.5 >>>>>> >>>>>> Guess of datafile for refinement: >>>>>> /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz >>>>>> >>>>>> Using >>>>>> /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz >>>>>> for refinement >>>>>> >>>>>> Specify >>>>>> input_refinement_file=/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_3_P22121_scala2.mtz >>>>>> to change this >>>>>> >>>>>> HKLIN ENTRY: >>>>>> /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz >>>>>> >>>>>> FILE TYPE ccp4_mtz >>>>>> >>>>>> COLUMN LABELS: ['H', 'K', 'L', 'FreeR_flag', 'F_107_2re', >>>>>> 'SIGF_107_2re', >>>>>> 'F_107_2re(+)', 'SIGF_107_2re(+)', 'F_107_2re(-)', 'SIGF_107_2re(-)', >>>>>> 'DANO_107_2re', 'SIGDANO_107_2re', 'IMEAN_107_2re', >>>>>> 'SIGIMEAN_107_2re', >>>>>> 'I_107_2re(+)', 'SIGI_107_2re(+)', 'I_107_2re(-)', 'SIGI_107_2re(-)'] >>>>>> >>>>>> GUESS FILE TYPE MERGE TYPE mtz premerged TARGET LABELS ['F1', >>>>>> 'SIGF1', >>>>>> 'DANO1', 'SIGDANO1'] Unit cell: (34.79, 108.92, 134.88, 90, 90, 90) >>>>>> Space >>>>>> group: P 2 21 21 (No. 18) CONTENTS: >>>>>> ['/home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz', >>>>>> 'mtz', 'premerged', 'P 2 21 21', [34.790000915527344, >>>>>> 108.92009735107422, >>>>>> 134.8800048828125, 90.0, 90.0, 90.0], 2.4890566908055836, ['F1', >>>>>> 'SIGF1', >>>>>> 'DANO1', 'SIGDANO1']] >>>>>> >>>>>> Inverse hand of space group: P 2 21 21 Creating sg entry from >>>>>> /home/sar06mbr/30JanDiamondI02/107/107_php22121/M75_Zn_107_2_P22121_scala2.mtz >>>>>> Unit cell: (34.79, 108.92, 134.88, 90, 90, 90) Space group: P 2 21 21 >>>>>> (No. >>>>>> 18) Space group name is: P 2 21 21 symbol is: p22121 >>>>>> >>>>>> **************************************** >>>>>> >>>>>> AutoSol Input failed >>>>>> >>>>>> Need a symfile for solve >>>>>> >>>>>> **************************************** >>>>>> >>>>>> _______________________________________________ >>>>>> phenixbb mailing list >>>>>> phenixbb(a)phenix-online.org >>>>>> http://phenix-online.org/mailman/listinfo/phenixbb >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> phenixbb mailing list >>>>> phenixbb(a)phenix-online.org >>>>> http://phenix-online.org/mailman/listinfo/phenixbb >>>>> >>>> _______________________________________________ >>>> phenixbb mailing list >>>> phenixbb(a)phenix-online.org >>>> http://phenix-online.org/mailman/listinfo/phenixbb >>>> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

16 years

Re: [cctbxbb] some thoughts on cctbx and pip

by Gergely Katona

Dear Billy, I did some tests installing in my base conda was not troublefree in python 3.8. Running iotbx.fetch_pdb --all --mtz 1kp8 resulted in boost related error when converting to mtz. Installing into a test environment went fine with iotbx.fetch_pdb --all --mtz 1kp8 running successfully. I could add pymc3, jupyter and seaborn and iotbx still did not break. My LIBTBX_BUILD is not set however in the test environment, which breaks miller when I was trying to import it. Manually setting the LIBTBX_BUILD to CONDA_PREFIX (setenv LIBTBX_BUILD $CONDA_PREFIX) fixes this and one of my script works fine! I will come back if I find some problems with my other scripts, but so far this looks promising! Happy new year! Gergely On Fri, Dec 20, 2019 at 8:16 PM Billy Poon <BKPoon(a)lbl.gov> wrote: > > Hi everyone, > > I updated the conda packages on the cctbx-dev channel and there are also now packages for macOS. The old packages have been removed so you can create a new environment with > > conda create -n test -c cctbx-dev cctbx python=2.7 > conda activate test > > where "test" is the environment name and 2.7 is the python version. For the python version, you can also pick 3.6, 3.7, or 3.8. I think the latest conda will install 3.8 as the default python if the python argument is not provided. Or install into an existing environment (with python already installed) with the same command as before, > > conda install -c cctbx-dev cctbx > > Again, your .condarc file should have conda-forge as the first channel so that dependencies can be pulled correctly. > > The dispatchers should work now and $LIBTBX_BUILD will be set on activation of an environment (and unset on environment deactivation) or after installing into an existing environment, so you can do more interesting things like > > iotbx.fetch_pdb --all --mtz 1kp8 > > However, this package does not install databases, so > > molprobity.molprobity 1kp8.pdb 1kp8.mtz > > will fail because the database is not available (also probe and reduce are not built). > > Some known issues in no particular order, > > 1) You can run "libtbx.run_tests_parallel module=cctbx nproc=Auto" to run tests, but not all the test files were copied, so I got 30 failures here. The final package will probably not have the test files. > 2) The other python dispatchers, like "cctbx.python", were not updated, so those will fail. But you can just run "python" in the active environment. > 3) Parts of mmtbx still need to be updated for Python 3. > 4) The LIBTBX_BUILD variable should be set for sh and csh shells. Let me know if it's not working for your shell (i.e. "echo $LIBTBX_BUILD" should show the same thing as $CONDA_PREFIX). > 5) One future step is to enable building other CCTBX-like modules with this conda package. This will require some bookkeeping updates so that modules in the conda environment and the modules being built are tracked properly. Also, making sure that all the necessary headers exist in $PREFIX/include. > > Gergely, let me know if your scripts are working. > > Happy holidays! > > -- > Billy K. Poon > Research Scientist, Molecular Biophysics and Integrated Bioimaging > Lawrence Berkeley National Laboratory > 1 Cyclotron Road, M/S 33R0345 > Berkeley, CA 94720 > Tel: (510) 486-5709 > Fax: (510) 486-5909 > Web: https://phenix-online.org > > > On Wed, Dec 18, 2019 at 11:25 AM Billy Poon <BKPoon(a)lbl.gov> wrote: >> >> Hi Gergely, >> >> That's the other information that hasn't been updated yet in the conda package. :) >> >> For LIBTBX_BUILD, I can set up environment variables sort of how the conda gcc package sets up environment variables. I have to double check to see if they're set after installation of the package and after activation of an environment. The variable will just be a copy of $CONDA_PREFIX. >> >> The libtbx_env file is a file that exists in $LIBTBX_BUILD that basically stores configuration information. I'll have to modify the contents to update the locations of the different modules since the conda package will not have a "modules" directory. >> >> -- >> Billy K. Poon >> Research Scientist, Molecular Biophysics and Integrated Bioimaging >> Lawrence Berkeley National Laboratory >> 1 Cyclotron Road, M/S 33R0345 >> Berkeley, CA 94720 >> Tel: (510) 486-5709 >> Fax: (510) 486-5909 >> Web: https://phenix-online.org >> >> >> On Wed, Dec 18, 2019 at 2:08 AM Gergely Katona <gkatona(a)gmail.com> wrote: >>> >>> Hi Billy, >>> >>> Conda install went fine with your instructions after rearranging the >>> channels by putting cctbx last. I removed all environmental variables >>> and previous build of cctbx. >>> >>> import sys >>> print (sys.path, sys.prefix) >>> >>> ['/home/gergely/anaconda3/lib/python36.zip', >>> '/home/gergely/anaconda3/lib/python3.6', >>> '/home/gergely/anaconda3/lib/python3.6/lib-dynload', '', >>> '/home/gergely/anaconda3/lib/python3.6/site-packages', >>> '/home/gergely/anaconda3/lib/python3.6/site-packages/IPython/extensions', >>> '/home/gergely/.ipython'] /home/gergely/anaconda3 >>> >>> Many imports went fine including pymc3, but I encountered problems >>> with these three: >>> >>> from cctbx import miller >>> import iotbx.pdb >>> from iotbx import reflection_file_reader, mtz >>> >>> >>> I also got type error when handling space groups. >>> >>> >>> >>> --------------------------------------------------------------------------- >>> KeyError Traceback (most recent call last) >>> <ipython-input-5-cedbd4f84f3d> in <module> >>> 25 from cctbx import uctbx >>> 26 from cctbx import sgtbx >>> ---> 27 from cctbx import miller >>> 28 #from iotbx import reflection_file_reader, mtz >>> 29 sns.set_context("poster") >>> >>> ~/anaconda3/lib/python3.6/site-packages/cctbx/miller/__init__.py in <module> >>> 11 >>> 12 from cctbx import crystal >>> ---> 13 from cctbx import maptbx >>> 14 from cctbx import sgtbx >>> 15 from cctbx.sgtbx import lattice_symmetry >>> >>> ~/anaconda3/lib/python3.6/site-packages/cctbx/maptbx/__init__.py in <module> >>> 15 from libtbx import adopt_init_args >>> 16 from libtbx.utils import Sorry >>> ---> 17 import libtbx.load_env >>> 18 import math >>> 19 import sys, os >>> >>> ~/anaconda3/lib/python3.6/site-packages/libtbx/load_env.py in <module> >>> 3 import libtbx.env_config >>> 4 import os >>> ----> 5 libtbx.env = libtbx.env_config.unpickle() >>> 6 libtbx.env.set_os_environ_all_dist() >>> 7 libtbx.env.dispatcher_name = os.environ.get("LIBTBX_DISPATCHER_NAME") >>> >>> ~/anaconda3/lib/python3.6/site-packages/libtbx/env_config.py in unpickle() >>> 2603 >>> 2604 def unpickle(): >>> -> 2605 build_path = os.environ["LIBTBX_BUILD"] >>> 2606 set_preferred_sys_prefix_and_sys_executable(build_path=build_path) >>> 2607 libtbx_env = open(op.join(build_path, "libtbx_env"), "rb") >>> >>> ~/anaconda3/lib/python3.6/os.py in __getitem__(self, key) >>> 667 except KeyError: >>> 668 # raise KeyError with the original key value >>> --> 669 raise KeyError(key) from None >>> 670 return self.decodevalue(value) >>> 671 >>> >>> KeyError: 'LIBTBX_BUILD' >>> >>> >>> >>> --------------------------------------------------------------------------- >>> ArgumentError Traceback (most recent call last) >>> <ipython-input-7-2acd3a9ce26a> in <module> >>> 26 return ms,msnam,mscent,msacent,msnamacent,msnamcent,msnamacent_dstar >>> 27 >>> ---> 28 ms,msnam,mscent,msacent,msnamacent,msnamcent,msnamacent_dstar=initializecrystal() >>> >>> <ipython-input-7-2acd3a9ce26a> in initializecrystal() >>> 11 uc = uctbx.unit_cell(unit_cell) >>> 12 wavelength = 1.54980 >>> ---> 13 xtal_symm = crystal.symmetry(unit_cell=unit_cell, >>> space_group_symbol="P 43 21 2") >>> 14 >>> 15 ms = >>> miller.build_set(crystal_symmetry=xtal_symm,anomalous_flag=True, >>> d_min=1.61) >>> >>> ~/anaconda3/lib/python3.6/site-packages/cctbx/crystal/__init__.py in >>> __init__(self, unit_cell, space_group_symbol, space_group_info, >>> space_group, correct_rhombohedral_setting_if_necessary, >>> assert_is_compatible_unit_cell, raise_sorry_if_incompatible_unit_cell, >>> force_compatible_unit_cell) >>> 74 if (space_group_symbol is not None): >>> 75 self._space_group_info = sgtbx.space_group_info( >>> ---> 76 symbol=space_group_symbol) >>> 77 elif (space_group is not None): >>> 78 if (isinstance(space_group, sgtbx.space_group)): >>> >>> ~/anaconda3/lib/python3.6/site-packages/cctbx/sgtbx/__init__.py in >>> __init__(self, symbol, table_id, group, number, space_group_t_den) >>> 100 assert group is None >>> 101 if (table_id is None): >>> --> 102 symbols = space_group_symbols(symbol) >>> 103 else: >>> 104 if (isinstance(symbol, int)): symbol = str(symbol) >>> >>> ArgumentError: Python argument types in >>> space_group_symbols.__init__(space_group_symbols, str) >>> did not match C++ signature: >>> __init__(_object*, int space_group_number) >>> __init__(_object*, int space_group_number, >>> std::__cxx11::basic_string<char, std::char_traits<char>, >>> std::allocator<char> > extension='') >>> __init__(_object*, int space_group_number, >>> std::__cxx11::basic_string<char, std::char_traits<char>, >>> std::allocator<char> > extension='', std::__cxx11::basic_string<char, >>> std::char_traits<char>, std::allocator<char> > table_id='') >>> __init__(_object*, std::__cxx11::basic_string<char, >>> std::char_traits<char>, std::allocator<char> > symbol) >>> __init__(_object*, std::__cxx11::basic_string<char, >>> std::char_traits<char>, std::allocator<char> > symbol, >>> std::__cxx11::basic_string<char, std::char_traits<char>, >>> std::allocator<char> > table_id='') >>> >>> >>> When I tried to set LIBTBX_BUILD to /home/gergely/anaconda3 (this is >>> sys.prefix on my system), I got other problems when importing. Can >>> LIBTBX_BUILD be set in the conda package? >>> >>> >>> >>> --------------------------------------------------------------------------- >>> FileNotFoundError Traceback (most recent call last) >>> <ipython-input-1-7e2b144826cc> in <module> >>> 26 from cctbx import sgtbx >>> 27 #from cctbx import miller >>> ---> 28 from iotbx import reflection_file_reader, mtz >>> 29 sns.set_context("poster") >>> 30 plt.rcParams.update({'figure.autolayout': True}) >>> >>> ~/anaconda3/lib/python3.6/site-packages/iotbx/reflection_file_reader.py >>> in <module> >>> 53 >>> 54 from __future__ import absolute_import, division, print_function >>> ---> 55 from iotbx import mtz >>> 56 from iotbx.scalepack import merge as scalepack_merge >>> 57 from iotbx.scalepack import no_merge_original_index as >>> scalepack_no_merge >>> >>> ~/anaconda3/lib/python3.6/site-packages/iotbx/mtz/__init__.py in <module> >>> 9 import iotbx_mtz_ext as ext >>> 10 >>> ---> 11 from iotbx.mtz import extract_from_symmetry_lib >>> 12 from cctbx import xray >>> 13 import cctbx.xray.observation_types >>> >>> ~/anaconda3/lib/python3.6/site-packages/iotbx/mtz/extract_from_symmetry_lib.py >>> in <module> >>> 1 from __future__ import absolute_import, division, print_function >>> 2 from cctbx import sgtbx >>> ----> 3 import libtbx.load_env >>> 4 import os.path as op >>> 5 from six.moves import range >>> >>> ~/anaconda3/lib/python3.6/site-packages/libtbx/load_env.py in <module> >>> 3 import libtbx.env_config >>> 4 import os >>> ----> 5 libtbx.env = libtbx.env_config.unpickle() >>> 6 libtbx.env.set_os_environ_all_dist() >>> 7 libtbx.env.dispatcher_name = os.environ.get("LIBTBX_DISPATCHER_NAME") >>> >>> ~/anaconda3/lib/python3.6/site-packages/libtbx/env_config.py in unpickle() >>> 2605 build_path = os.environ["LIBTBX_BUILD"] >>> 2606 set_preferred_sys_prefix_and_sys_executable(build_path=build_path) >>> -> 2607 libtbx_env = open(op.join(build_path, "libtbx_env"), "rb") >>> 2608 env = pickle.load(libtbx_env) >>> 2609 if (env.python_version_major_minor != sys.version_info[:2]): >>> >>> FileNotFoundError: [Errno 2] No such file or directory: >>> '/home/gergely/anaconda3/libtbx_env' >>> >>> On Wed, Dec 18, 2019 at 9:10 AM Billy Poon <BKPoon(a)lbl.gov> wrote: >>> > >>> > Hi Gergely, >>> > >>> > I've uploaded linux packages to a new channel, cctbx-dev, and you can install it with >>> > >>> > conda install -c cctbx-dev cctbx >>> > >>> > in your current environment. You should set your ~/.condarc file to pull the other dependencies from the conda-forge channel first, so put conda-forge above cctbx. Mine looks like >>> > >>> > channels: >>> > - conda-forge >>> > - defaults >>> > - cctbx >>> > >>> > Do you need dxtbx for your scripts? This package does not build that part. I think the plan is to build a separate conda package for dxtbx so that it can be updated more frequently. I can rebuild the packages to include it for testing, but the one being submitted to conda-forge will not have it. >>> > >>> > Also, your error message is probably due to version of HDF5 that the development build installs. The bootstrap.py script will install 1.10.4, but your other dependency is looking for 1.10.5. Installing this cctbx conda package should install 1.10.5, which should fix the issue. Also, I'm updating those environments and 1.10.5 will be the new default version. >>> > >>> > Lastly, the dispatchers will not work in these packages because the old paths during the build process are still in them and many of them expect some additional information that has not been updated in the packages yet. I'm in the process of doing that and will update the cctbx-dev channel when that's done. However, by starting python, you can import cctbx modules. So you can run commands like >>> > >>> > from scitbx.array_family import flex >>> > a = flex.random_double(1000000) >>> > b = flex.min_max_mean_double(a) >>> > b.min >>> > b.max >>> > b.mean >>> > >>> > Thanks! >>> > >>> > -- >>> > Billy K. Poon >>> > Research Scientist, Molecular Biophysics and Integrated Bioimaging >>> > Lawrence Berkeley National Laboratory >>> > 1 Cyclotron Road, M/S 33R0345 >>> > Berkeley, CA 94720 >>> > Tel: (510) 486-5709 >>> > Fax: (510) 486-5909 >>> > Web: https://phenix-online.org >>> > >>> > >>> > On Tue, Dec 17, 2019 at 5:39 AM Gergely Katona <gkatona(a)gmail.com> wrote: >>> >> >>> >> Dear Billy, >>> >> >>> >> Thank you for the detailed explanation, I look forward to do further >>> >> testing! I aim to pool all modules under the same environment, if >>> >> there are conflicts then I just try to reshuffle the order of imports. >>> >> So far this did not cause problems for me even when I was using system >>> >> python, but of course it is not the most prudent thing to do. With >>> >> anaconda everything is much more standardized and isolated already and >>> >> without being superuser I can have my familiar environment at any >>> >> synchrotron based cluster. It is great that cctbx will be an integral >>> >> part of this ecosystem and this was also the last thing holding me >>> >> back from adopting python3. About hdf5, pymc3 requires it and >>> >> importing causes a kernel restart with the following error messages, >>> >> curiously if I import h5py first this can be avoided. >>> >> >>> >> Best wishes, >>> >> >>> >> Gergely >>> >> >>> >> import pymc3 as pm >>> >> >>> >> Warning! ***HDF5 library version mismatched error*** >>> >> The HDF5 header files used to compile this application do not match >>> >> the version used by the HDF5 library to which this application is linked. >>> >> Data corruption or segmentation faults may occur if the application continues. >>> >> This can happen when an application was compiled by one version of HDF5 but >>> >> linked with a different version of static or shared HDF5 library. >>> >> You should recompile the application or check your shared library related >>> >> settings such as 'LD_LIBRARY_PATH'. >>> >> You can, at your own risk, disable this warning by setting the environment >>> >> variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'. >>> >> Setting it to 2 or higher will suppress the warning messages totally. >>> >> Headers are 1.10.4, library is 1.10.5 >>> >> SUMMARY OF THE HDF5 CONFIGURATION >>> >> ================================= >>> >> >>> >> General Information: >>> >> ------------------- >>> >> HDF5 Version: 1.10.5 >>> >> Configured on: Tue Oct 22 12:02:13 UTC 2019 >>> >> Configured by: conda@16247e67ecd5 >>> >> Host system: x86_64-conda_cos6-linux-gnu >>> >> Uname information: Linux 16247e67ecd5 4.15.0-1059-azure >>> >> #64-Ubuntu SMP Fri Sep 13 17:02:44 UTC 2019 x86_64 x86_64 x86_64 >>> >> GNU/Linux >>> >> Byte sex: little-endian >>> >> Installation point: /home/gergely/anaconda3 >>> >> >>> >> Compiling Options: >>> >> ------------------ >>> >> Build Mode: production >>> >> Debugging Symbols: no >>> >> Asserts: no >>> >> Profiling: no >>> >> Optimization Level: high >>> >> >>> >> Linking Options: >>> >> ---------------- >>> >> Libraries: static, shared >>> >> Statically Linked Executables: >>> >> LDFLAGS: -Wl,-O2 -Wl,--sort-common >>> >> -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags >>> >> -Wl,--gc-sections -Wl,-rpath,/home/gergely/anaconda3/lib >>> >> -Wl,-rpath-link,/home/gergely/anaconda3/lib >>> >> -L/home/gergely/anaconda3/lib >>> >> H5_LDFLAGS: >>> >> AM_LDFLAGS: -L/home/gergely/anaconda3/lib >>> >> Extra libraries: -lrt -lpthread -lz -ldl -lm >>> >> Archiver: >>> >> /home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/_build_env/bin/x86_64-conda_cos6-linux-gnu-ar >>> >> AR_FLAGS: cr >>> >> Ranlib: >>> >> /home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/_build_env/bin/x86_64-conda_cos6-linux-gnu-ranlib >>> >> >>> >> Languages: >>> >> ---------- >>> >> C: yes >>> >> C Compiler: >>> >> /home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc >>> >> CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 >>> >> -I/home/gergely/anaconda3/include >>> >> H5_CPPFLAGS: -D_GNU_SOURCE >>> >> -D_POSIX_C_SOURCE=200809L -DNDEBUG -UH5_DEBUG_API >>> >> AM_CPPFLAGS: -I/home/gergely/anaconda3/include >>> >> C Flags: -march=nocona -mtune=haswell >>> >> -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 >>> >> -ffunction-sections -pipe -I/home/gergely/anaconda3/include >>> >> -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/work=/usr/local/src/conda/hdf5_split-1.10.5 >>> >> -fdebug-prefix-map=/home/gergely/anaconda3=/usr/local/src/conda-prefix >>> >> H5 C Flags: -std=c99 -pedantic -Wall -Wextra >>> >> -Wbad-function-cast -Wc++-compat -Wcast-align -Wcast-qual -Wconversion >>> >> -Wdeclaration-after-statement -Wdisabled-optimization -Wfloat-equal >>> >> -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-declarations >>> >> -Wmissing-include-dirs -Wmissing-prototypes -Wnested-externs >>> >> -Wold-style-definition -Wpacked -Wpointer-arith -Wredundant-decls >>> >> -Wshadow -Wstrict-prototypes -Wswitch-default -Wswitch-enum -Wundef >>> >> -Wunused-macros -Wunsafe-loop-optimizations -Wwrite-strings >>> >> -finline-functions -s -Wno-inline -Wno-aggregate-return >>> >> -Wno-missing-format-attribute -Wno-missing-noreturn -O >>> >> AM C Flags: >>> >> Shared C Library: yes >>> >> Static C Library: yes >>> >> >>> >> >>> >> Fortran: yes >>> >> Fortran Compiler: >>> >> /home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/_build_env/bin/x86_64-conda_cos6-linux-gnu-gfortran >>> >> Fortran Flags: >>> >> H5 Fortran Flags: -pedantic -Wall -Wextra -Wunderflow >>> >> -Wimplicit-interface -Wsurprising -Wno-c-binding-type -s -O2 >>> >> AM Fortran Flags: >>> >> Shared Fortran Library: yes >>> >> Static Fortran Library: yes >>> >> >>> >> C++: yes >>> >> C++ Compiler: >>> >> /home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/_build_env/bin/x86_64-conda_cos6-linux-gnu-c++ >>> >> C++ Flags: -fvisibility-inlines-hidden >>> >> -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell >>> >> -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 >>> >> -ffunction-sections -pipe -I/home/gergely/anaconda3/include >>> >> -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/work=/usr/local/src/conda/hdf5_split-1.10.5 >>> >> -fdebug-prefix-map=/home/gergely/anaconda3=/usr/local/src/conda-prefix >>> >> H5 C++ Flags: -pedantic -Wall -W -Wundef -Wshadow >>> >> -Wpointer-arith -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion >>> >> -Wredundant-decls -Winline -Wsign-promo -Woverloaded-virtual >>> >> -Wold-style-cast -Weffc++ -Wreorder -Wnon-virtual-dtor >>> >> -Wctor-dtor-privacy -Wabi -finline-functions -s -O >>> >> AM C++ Flags: >>> >> Shared C++ Library: yes >>> >> Static C++ Library: yes >>> >> >>> >> Java: no >>> >> >>> >> >>> >> Features: >>> >> --------- >>> >> Parallel HDF5: no >>> >> Parallel Filtered Dataset Writes: no >>> >> Large Parallel I/O: no >>> >> High-level library: yes >>> >> Threadsafety: yes >>> >> Default API mapping: v110 >>> >> With deprecated public symbols: yes >>> >> I/O filters (external): deflate(zlib) >>> >> MPE: no >>> >> Direct VFD: no >>> >> dmalloc: no >>> >> Packages w/ extra debug output: none >>> >> API tracing: no >>> >> Using memory checker: yes >>> >> Memory allocation sanity checks: no >>> >> Function stack tracing: no >>> >> Strict file format checks: no >>> >> Optimization instrumentation: no >>> >> >>> >> On Tue, Dec 17, 2019 at 8:35 AM Billy Poon <BKPoon(a)lbl.gov> wrote: >>> >> > >>> >> > Hi Gergely, >>> >> > >>> >> > Let me build the test package tomorrow. All the gritty details for building with conda is being finalized and the official documentation will be updated to describe the steps. It would be too confusing to keep changing the documentation as the process evolves. You do have the general process, though, which is summarized as follows. >>> >> > >>> >> > 1) Installing dependencies. The cctbx_dependencies metapackage was an initial approach for managing the CCTBX dependencies, but after contacting the conda-forge folks, they recommended using the --only-deps flag. So when the CCTBX conda package is available, you'll be able to get a set of dependencies with, >>> >> > >>> >> > conda install -c conda-forge --only-deps cctbx >>> >> > >>> >> > By default, the bootstrap.py file will automatically install a set of dependencies in the "conda_base" directory (and a conda installation if one is not found). It just uses standard conda environment files located in libtbx/auto_build/conda_envs, so you do not need to install cctbx_dependencies as a separate step. The environment files avoid channel issues by explicitly defining the channel to pull the packages from and the cctbx channel just stores copies of packages from conda-forge. There were issues earlier where the conda-forge packages would sometimes be moved to a different label. The --use-conda flag also accepts a path to $CONDA_PREFIX if you want to use a specific environment for testing. >>> >> > >>> >> > 2) Building. The bootstrap.py file handles that with SCons. >>> >> > >>> >> > 3) Running. After building, there should be a setpaths.sh (and .csh) file that adds build/bin to your path. The build/bin directory has our dispatchers, which are just scripts that set up the environment variables for you. This prevents other programs from loading our libraries, whose versions may conflict. You should see that there is a "python" dispatcher, which is a convenience for developers. Otherwise, you can use libtbx.python, which will be able to import CCTBX modules. >>> >> > >>> >> > The running part is where the conda package for CCTBX will be different than this build. Since our Python files and extensions modules will be in the "site-packages" directory for Python, the PYTHONPATH variable will not be needed (and conda suggests that that variable not be set). The other CCTBX libraries will be in $CONDA_PREFIX/lib, so LD_LIBRARY_PATH is not needed. In an active environment, PATH will already be modified. And then our LIBTBX_BUILD directory can be set to sys.prefix. >>> >> > >>> >> > So with the conda package, you would only need to activate your conda environment and CCTBX should integrate with other conda packages. What is the conflict with hdf5? That's something that should be fixed. Thanks! >>> >> > >>> >> > -- >>> >> > Billy K. Poon >>> >> > Research Scientist, Molecular Biophysics and Integrated Bioimaging >>> >> > Lawrence Berkeley National Laboratory >>> >> > 1 Cyclotron Road, M/S 33R0345 >>> >> > Berkeley, CA 94720 >>> >> > Tel: (510) 486-5709 >>> >> > Fax: (510) 486-5909 >>> >> > Web: https://phenix-online.org >>> >> > >>> >> > >>> >> > On Mon, Dec 16, 2019 at 2:53 AM Gergely Katona <gkatona(a)gmail.com> wrote: >>> >> >> >>> >> >> Dear Billy, >>> >> >> >>> >> >> Thank you for this update and for your efforts! I found a solution and >>> >> >> indeed most things already work in anaconda3. The steps I took (even >>> >> >> if these instructions will have short expiry date): >>> >> >> >>> >> >> Modified .condarc with: >>> >> >> channels: >>> >> >> - cctbx >>> >> >> - conda-forge >>> >> >> - defaults >>> >> >> >>> >> >> run >>> >> >> conda conda install cctbx_dependencies python=3.6 >>> >> >> >>> >> >> I expect this will work without python=3.6 in the near future. >>> >> >> >>> >> >> Then compiling cctbx with anaconda3 python went without any problem >>> >> >> when using these flags: >>> >> >> python bootstrap.py --use-conda --python3 --nproc=12 >>> >> >> >>> >> >> Then I probably did the unorthodox thing and sourced these directories: >>> >> >> >>> >> >> setenv LIBTBX_BUILD /home/gergely/cctbx/build >>> >> >> setenv PATH ${PATH}:/home/gergely/cctbx/build/bin >>> >> >> setenv PYTHONPATH >>> >> >> /home/gergely/cctbx/modules/cctbx_project:/home/gergely/cctbx/modules:/home/gergely/cctbx/modules/cctbx_project/boost_adaptbx:/home/gergely/cctbx/build/lib:/home/gergely/cctbx/conda_base/lib/python3.6/site-packages:$PYTHONPATH >>> >> >> setenv LD_LIBRARY_PATH >>> >> >> /home/gergely/cctbx/conda_base/lib:/home/gergely/cctbx/build/lib:$LD_LIBRARY_PATH >>> >> >> >>> >> >> There is probably a better way to put this into conda environment. >>> >> >> With these steps I could run one of my scripts depending on cctbx. The >>> >> >> only problem I found is that hdf5 library had conflict with another >>> >> >> package in conda, but I does not find this as a showstopper. >>> >> >> >>> >> >> Best wishes, >>> >> >> >>> >> >> Gergely >>> >> >> >>> >> >> >>> >> >> >>> >> >> >>> >> >> >>> >> >> >>> >> >> On Fri, Dec 13, 2019 at 7:23 PM Billy Poon <BKPoon(a)lbl.gov> wrote: >>> >> >> > >>> >> >> > Hi Gergely, >>> >> >> > >>> >> >> > It's still a work in progress. I'm sorting out some Windows issues right now. I can probably build a test package on a separate channel for people that want to test it (let's say next week?). I'll provide instructions, but basically, the test conda package will be in its own separate channel and the dependencies will be pulled from the conda-forge channel. I want most things to be working correctly on Python 2.7, 3.6, 3.7, and 3.8 on all 3 platforms. >>> >> >> > >>> >> >> > Thanks! >>> >> >> > >>> >> >> > -- >>> >> >> > Billy K. Poon >>> >> >> > Research Scientist, Molecular Biophysics and Integrated Bioimaging >>> >> >> > Lawrence Berkeley National Laboratory >>> >> >> > 1 Cyclotron Road, M/S 33R0345 >>> >> >> > Berkeley, CA 94720 >>> >> >> > Tel: (510) 486-5709 >>> >> >> > Fax: (510) 486-5909 >>> >> >> > Web: https://phenix-online.org >>> >> >> > >>> >> >> > >>> >> >> > On Fri, Dec 13, 2019 at 5:44 AM Gergely Katona <gkatona(a)gmail.com> wrote: >>> >> >> >> >>> >> >> >> Dear Billy, >>> >> >> >> >>> >> >> >> This sounds very promising and exciting. I am not sure if cctbx is >>> >> >> >> already functional as a conda package in anaconda3 (Linux) or this is >>> >> >> >> still work in progress. My technical expertise does not allow me to >>> >> >> >> tell the difference. What I tried: >>> >> >> >> >>> >> >> >> Fresh install of anaconda3. Adding - cctbx and - conda-forge to >>> >> >> >> .condarc . Installing pyside2 with conda. Running conda install >>> >> >> >> conda_dependencies . I get a lot package version conflict, and I >>> >> >> >> cannot import cctbx or iotbx to anaconda python. Am I following the >>> >> >> >> right instructions? Or it is too early to expect that cctbx works when >>> >> >> >> installed through conda? >>> >> >> >> >>> >> >> >> Best wishes, >>> >> >> >> >>> >> >> >> Gergely >>> >> >> >> >>> >> >> >> On Wed, Nov 27, 2019 at 3:56 PM Billy Poon <BKPoon(a)lbl.gov> wrote: >>> >> >> >> > >>> >> >> >> > Hi all, >>> >> >> >> > >>> >> >> >> > For a brief update, I have submitted a recipe for cctbxlite to conda-forge (https://github.com/conda-forge/staged-recipes/pull/10021) and support for Python 3.7 and 3.8 is being added (https://github.com/cctbx/cctbx_project/pull/409). With some fixes for Windows (https://github.com/cctbx/cctbx_project/pull/416), all platforms (macOS, linux, and Windows) can build for Python 2.7, 3.6, 3.7, and 3.8. Some additional changes will be needed to get Windows to work with Python 3 and for tests to pass with Boost 1.70.0. That will enable the conda-forge recipe to build for all platforms and for all supported versions of Python. >>> >> >> >> > >>> >> >> >> > Currently, the conda-forge recipe will install into the conda python and cctbx imports can be done without sourcing the environment scripts. It looks like a lot of the environment variables being set in the dispatchers can be removed since the Python files and C++ extensions are in the right places. I'll update the libtbx_env file so that commands that load the environment can work correctly. >>> >> >> >> > >>> >> >> >> > -- >>> >> >> >> > Billy K. Poon >>> >> >> >> > Research Scientist, Molecular Biophysics and Integrated Bioimaging >>> >> >> >> > Lawrence Berkeley National Laboratory >>> >> >> >> > 1 Cyclotron Road, M/S 33R0345 >>> >> >> >> > Berkeley, CA 94720 >>> >> >> >> > Tel: (510) 486-5709 >>> >> >> >> > Fax: (510) 486-5909 >>> >> >> >> > Web: https://phenix-online.org >>> >> >> >> > >>> >> >> >> > >>> >> >> >> > On Sun, Aug 25, 2019 at 2:33 PM Tristan Croll <tic20(a)cam.ac.uk> wrote: >>> >> >> >> >> >>> >> >> >> >> Hi Luc, >>> >> >> >> >> >>> >> >> >> >> That sounds promising. From there, I’d need to work out how to make a fully-packaged installer (basically a modified wheel file) for the ChimeraX ToolShed - the aim is for the end user to not have to worry about any of this. That adds a couple of complications - e.g. $LIBTBX_BUILD would need to be set dynamically before first import - but doesn’t seem insurmountable. >>> >> >> >> >> >>> >> >> >> >> Thanks, >>> >> >> >> >> >>> >> >> >> >> Tristan >>> >> >> >> >> >>> >> >> >> >> >>> >> >> >> >> >>> >> >> >> >> Tristan Croll >>> >> >> >> >> Research Fellow >>> >> >> >> >> Cambridge Institute for Medical Research >>> >> >> >> >> University of Cambridge CB2 0XY >>> >> >> >> >> >>> >> >> >> >> >>> >> >> >> >> >>> >> >> >> >> >>> >> >> >> >> > On 25 Aug 2019, at 18:31, Luc Bourhis <luc_j_bourhis(a)mac.com> wrote: >>> >> >> >> >> > >>> >> >> >> >> > Hi Tristan, >>> >> >> >> >> > >>> >> >> >> >> > cctbx could be built to use your ChimeraX python, now that cctbx is moving to Python 3. The option —with-python is there for that with the bootstrap script. The specific environment setup boil down to setting two environment variable LIBTBX_BUILD and either LD_LIBRARY_PATH on Linux, PATH on Win32, or DYLIB_LIBRARY_PATH on MacOS. If you work within a framework such as ChimeraX, that should not be difficult to ensure those two variables are set. >>> >> >> >> >> > >>> >> >> >> >> > Best wishes, >>> >> >> >> >> > >>> >> >> >> >> > Luc >>> >> >> >> >> > >>> >> >> >> >> > >>> >> >> >> >> >> On 23 Aug 2019, at 19:02, Tristan Croll <tic20(a)cam.ac.uk> wrote: >>> >> >> >> >> >> >>> >> >> >> >> >> To add my two cents on this: probably the second-most common question I've had about ISOLDE's implementation is, "why didn't you use CCTBX?". The honest answer to that is, "I didn't know how." >>> >> >> >> >> >> >>> >> >> >> >> >> Still don't, really - although the current developments are rather promising. The problem I've faced is that CCTBX was designed as its own self-contained Python (2.7, until very recently) environment, with its own interpreter and a lot of very specific environment setup. Meanwhile I'm developing ISOLDE in ChimeraX, which is *also* its own self-contained Python (3.7) environment. To plug one into the other in that form... well, I don't think I'm a good enough programmer to really know where to start. >>> >> >> >> >> >> >>> >> >> >> >> >> The move to Conda and a more modular CCTBX architecture should make a lot more possible in that direction. Pip would be even better for me personally (ChimeraX can install directly from the PyPI, but doesn't interact with Conda) - but I understand pretty well the substantial challenge that would amount to (not least being that the PyPI imposes a limit - around 100MB from memory? - on the size of an individual package). >>> >> >> >> >> >> >>> >> >> >> >> >> Best regards, >>> >> >> >> >> >> >>> >> >> >> >> >> Tristan >>> >> >> >> >> >> >>> >> >> >> >> >>> On 2019-08-23 09:28, Luc Bourhis wrote: >>> >> >> >> >> >>> Hi Graeme, >>> >> >> >> >> >>> Yes, I know. But “black" is a program doing a very particular task >>> >> >> >> >> >>> (code formatting from the top of my head). Requiring to use a wrapper >>> >> >> >> >> >>> for python itself is another level. But ok, I think I am mellowing to >>> >> >> >> >> >>> the idea after all! Talking with people around me, and extrapolating, >>> >> >> >> >> >>> I would bet that, right now, a great majority of people interested by >>> >> >> >> >> >>> cctbx in pip have already used the cctbx, so they know about the >>> >> >> >> >> >>> Python wrapper, and they would not be too sanguine about that. My >>> >> >> >> >> >>> concern is for the future, when pip will be the first time some people >>> >> >> >> >> >>> use cctbx. Big fat warning notices on PyPI page and a better error >>> >> >> >> >> >>> message when cctbx fails because LIBTBX_BUILD is not set would be >>> >> >> >> >> >>> needed but that could be all right. >>> >> >> >> >> >>> If we do a pip installer, we should aim at a minimal install: cctbx, >>> >> >> >> >> >>> iotbx and their dependencies, and that’s it. >>> >> >> >> >> >>> Best wishes, >>> >> >> >> >> >>> Luc >>> >> >> >> >> >>>> On 23 Aug 2019, at 07:17, Graeme.Winter(a)Diamond.ac.uk <Graeme.Winter(a)diamond.ac.uk> wrote: >>> >> >> >> >> >>>> Without discussing the merits of this or whether we _choose_ to make the move to supporting PIP, I am certain it would be _possible_ - many other packages make dispatcher scripts when you pip install them e.g. >>> >> >> >> >> >>>> Silver-Surfer rescale_f2 :) $ which black; cat $(which black) >>> >> >> >> >> >>>> /Library/Frameworks/Python.framework/Versions/3.6/bin/black >>> >> >> >> >> >>>> #!/Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6 >>> >> >> >> >> >>>> # -*- coding: utf-8 -*- >>> >> >> >> >> >>>> import re >>> >> >> >> >> >>>> import sys >>> >> >> >> >> >>>> from black import main >>> >> >> >> >> >>>> if __name__ == '__main__': >>> >> >> >> >> >>>> sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0]) >>> >> >> >> >> >>>> sys.exit(main()) >>> >> >> >> >> >>>> So we _could_ work around the absence of LIBTBX_BUILD etc. in the system. Whether or not we elect to do the work is a different question, and it seems clear that here are very mixed opinions on this. >>> >> >> >> >> >>>> Best wishes Graeme >>> >> >> >> >> >>>> On 23 Aug 2019, at 01:21, Luc Bourhis <luc_j_bourhis(a)mac.com<mailto:[email protected]>> wrote: >>> >> >> >> >> >>>> Hi, >>> >> >> >> >> >>>> Even if we managed to ship our the boost dynamic libraries with pip, it would still not be pip-like, as we would still need our python wrappers to set LIBTBX_BUILD and LD_LIBRARY_PATH. Normal pip packages work with the standard python exe. LD_LIBRARY_PATH, we could get around that by changing the way we compile, using -Wl,-R, which is the runtime equivalent of build time -L. That’s a significant change that would need to be tested. But there is no way around setting LIBTBX_BUILD right now. Leaving that to the user is horrible. Perhaps there is a way to hack libtbx/env_config.py so that we can hardwire LIBTBX_BUILD in there when pip installs? >>> >> >> >> >> >>>> Best wishes, >>> >> >> >> >> >>>> Luc >>> >> >> >> >> >>>> On 16 Aug 2019, at 22:47, Luc Bourhis <luc_j_bourhis(a)mac.com<mailto:[email protected]>> wrote: >>> >> >> >> >> >>>> Hi, >>> >> >> >> >> >>>> I did look into that many years ago, and even toyed with building a pip installer. What stopped me is the exact conclusion you reached too: the user would not have the pip experience he expects. You are right that it is a lot of effort but is it worth it? Considering that remark, I don’t think so. Now, Conda was created specifically to go beyond pip pure-python-only support. Since cctbx has garnered support for Conda, the best avenue imho is to go the extra length to have a package on Anaconda.org<http://anaconda.org/>, and then to advertise it hard to every potential user out there. >>> >> >> >> >> >>>> Best wishes, >>> >> >> >> >> >>>> Luc >>> >> >> >> >> >>>> On 16 Aug 2019, at 21:45, Aaron Brewster <asbrewster(a)lbl.gov<mailto:[email protected]>> wrote: >>> >> >> >> >> >>>> Hi, to avoid clouding Dorothee's documentation email thread, which I think is a highly useful enterprise, here's some thoughts about putting cctbx into pip. Pip doesn't install non-python dependencies well. I don't think boost is available as a package on pip (at least the package version we use). wxPython4 isn't portable through pip (https://wiki.wxpython.org/How%20to%20install%20wxPython#Installing_wxPython…). MPI libraries are system dependent. If cctbx were a pure python package, pip would be fine, but cctbx is not. >>> >> >> >> >> >>>> All that said, we could build a manylinux1 version of cctbx and upload it to PyPi (I'm just learning about this). For a pip package to be portable (which is a requirement for cctbx), it needs to conform to PEP513, the manylinux1 standard (https://www.python.org/dev/peps/pep-0513/). For example, numpy is built according to this standard (see https://pypi.org/project/numpy/#files, where you'll see the manylinux1 wheel). Note, the manylinux1 standard is built with Centos 5.11 which we no longer support. >>> >> >> >> >> >>>> There is also a manylinux2010 standard, which is based on Centos 6 (https://www.python.org/dev/peps/pep-0571/). This is likely a more attainable target (note though by default C++11 is not supported on Centos 6). >>> >> >> >> >> >>>> If we built a manylinuxX version of cctbx and uploaded it to PyPi, the user would need all the non-python dependencies. There's no way to specify these in pip. For example, cctbx requires boost 1.63 or better. The user will need to have it in a place their python can find it, or we could package it ourselves and supply it, similar to how the pip h5py package now comes with an hd5f library, or how the pip numpy package includes an openblas library. We'd have to do the same for any packages we depend on that aren't on pip using the manylinux standards, such as wxPython4. >>> >> >> >> >> >>>> Further, we need to think about how dials and other cctbx-based packages interact. If pip install cctbx is set up, how does pip install dials work, such that any dials shared libraries can find the cctbx libraries? Can shared libraries from one pip package link against libraries in another pip package? Would each package need to supply its own boost? Possibly this is well understood in the pip field, but not by me :) >>> >> >> >> >> >>>> Finally, there's the option of providing a source pip package. This would require the full compiler toolchain for any given platform (macOS, linux, windows). These are likely available for developers, but not for general users. >>> >> >> >> >> >>>> Anyway, these are some of the obstacles. Not saying it isn't possible, it's just a lot of effort. >>> >> >> >> >> >>>> Thanks, >>> >> >> >> >> >>>> -Aaron >>> >> >> >> >> >>>> _______________________________________________ >>> >> >> >> >> >>>> cctbxbb mailing list >>> >> >> >> >> >>>> cctbxbb(a)phenix-online.org<mailto:[email protected]> >>> >> >> >> >> >>>> http://phenix-online.org/mailman/listinfo/cctbxbb >>> >> >> >> >> >>>> _______________________________________________ >>> >> >> >> >> >>>> cctbxbb mailing list >>> >> >> >> >> >>>> cctbxbb(a)phenix-online.org<mailto:[email protected]> >>> >> >> >> >> >>>> http://phenix-online.org/mailman/listinfo/cctbxbb >>> >> >> >> >> >>>> _______________________________________________ >>> >> >> >> >> >>>> cctbxbb mailing list >>> >> >> >> >> >>>> cctbxbb(a)phenix-online.org<mailto:[email protected]> >>> >> >> >> >> >>>> http://phenix-online.org/mailman/listinfo/cctbxbb >>> >> >> >> >> >>>> -- >>> >> >> >> >> >>>> This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. >>> >> >> >> >> >>>> Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. >>> >> >> >> >> >>>> Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. >>> >> >> >> >> >>>> Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom >>> >> >> >> >> >>>> _______________________________________________ >>> >> >> >> >> >>>> cctbxbb mailing list >>> >> >> >> >> >>>> cctbxbb(a)phenix-online.org >>> >> >> >> >> >>>> http://phenix-online.org/mailman/listinfo/cctbxbb >>> >> >> >> >> >>> _______________________________________________ >>> >> >> >> >> >>> cctbxbb mailing list >>> >> >> >> >> >>> cctbxbb(a)phenix-online.org >>> >> >> >> >> >>> http://phenix-online.org/mailman/listinfo/cctbxbb >>> >> >> >> >> >> >>> >> >> >> >> >> >>> >> >> >> >> >> _______________________________________________ >>> >> >> >> >> >> cctbxbb mailing list >>> >> >> >> >> >> cctbxbb(a)phenix-online.org >>> >> >> >> >> >> http://phenix-online.org/mailman/listinfo/cctbxbb >>> >> >> >> >> > >>> >> >> >> >> > >>> >> >> >> >> > _______________________________________________ >>> >> >> >> >> > cctbxbb mailing list >>> >> >> >> >> > cctbxbb(a)phenix-online.org >>> >> >> >> >> > http://phenix-online.org/mailman/listinfo/cctbxbb >>> >> >> >> >> >>> >> >> >> >> >>> >> >> >> >> _______________________________________________ >>> >> >> >> >> cctbxbb mailing list >>> >> >> >> >> cctbxbb(a)phenix-online.org >>> >> >> >> >> http://phenix-online.org/mailman/listinfo/cctbxbb >>> >> >> >> > >>> >> >> >> > _______________________________________________ >>> >> >> >> > cctbxbb mailing list >>> >> >> >> > cctbxbb(a)phenix-online.org >>> >> >> >> > http://phenix-online.org/mailman/listinfo/cctbxbb >>> >> >> >> >>> >> >> >> >>> >> >> >> >>> >> >> >> -- >>> >> >> >> Gergely Katona, PhD >>> >> >> >> Associate Professor >>> >> >> >> Department of Chemistry and Molecular Biology, University of Gothenburg >>> >> >> >> Box 462, 40530 Göteborg, Sweden >>> >> >> >> Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910 >>> >> >> >> Web: http://katonalab.eu, Email: gergely.katona(a)gu.se >>> >> >> >> >>> >> >> >> _______________________________________________ >>> >> >> >> cctbxbb mailing list >>> >> >> >> cctbxbb(a)phenix-online.org >>> >> >> >> http://phenix-online.org/mailman/listinfo/cctbxbb >>> >> >> > >>> >> >> > _______________________________________________ >>> >> >> > cctbxbb mailing list >>> >> >> > cctbxbb(a)phenix-online.org >>> >> >> > http://phenix-online.org/mailman/listinfo/cctbxbb >>> >> >> >>> >> >> >>> >> >> >>> >> >> -- >>> >> >> Gergely Katona, PhD >>> >> >> Associate Professor >>> >> >> Department of Chemistry and Molecular Biology, University of Gothenburg >>> >> >> Box 462, 40530 Göteborg, Sweden >>> >> >> Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910 >>> >> >> Web: http://katonalab.eu, Email: gergely.katona(a)gu.se >>> >> >> >>> >> >> _______________________________________________ >>> >> >> cctbxbb mailing list >>> >> >> cctbxbb(a)phenix-online.org >>> >> >> http://phenix-online.org/mailman/listinfo/cctbxbb >>> >> > >>> >> > _______________________________________________ >>> >> > cctbxbb mailing list >>> >> > cctbxbb(a)phenix-online.org >>> >> > http://phenix-online.org/mailman/listinfo/cctbxbb >>> >> >>> >> >>> >> >>> >> -- >>> >> Gergely Katona, PhD >>> >> Associate Professor >>> >> Department of Chemistry and Molecular Biology, University of Gothenburg >>> >> Box 462, 40530 Göteborg, Sweden >>> >> Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910 >>> >> Web: http://katonalab.eu, Email: gergely.katona(a)gu.se >>> >> >>> >> _______________________________________________ >>> >> cctbxbb mailing list >>> >> cctbxbb(a)phenix-online.org >>> >> http://phenix-online.org/mailman/listinfo/cctbxbb >>> > >>> > _______________________________________________ >>> > cctbxbb mailing list >>> > cctbxbb(a)phenix-online.org >>> > http://phenix-online.org/mailman/listinfo/cctbxbb >>> >>> >>> >>> -- >>> Gergely Katona, PhD >>> Associate Professor >>> Department of Chemistry and Molecular Biology, University of Gothenburg >>> Box 462, 40530 Göteborg, Sweden >>> Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910 >>> Web: http://katonalab.eu, Email: gergely.katona(a)gu.se >>> >>> _______________________________________________ >>> cctbxbb mailing list >>> cctbxbb(a)phenix-online.org >>> http://phenix-online.org/mailman/listinfo/cctbxbb > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb -- Gergely Katona, Professor Department of Chemistry and Molecular Biology, University of Gothenburg Box 462, 40530 Göteborg, Sweden Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910 Web: http://katonalab.eu, Email: gergely.katona(a)gu.se

6 years, 1 month

Re: [cctbxbb] Boost Python 1.56

by Billy Poon

Hi Graeme, I hope Markus's commands were helpful. The only tricky thing was the deletion of the build directory. If you had set up the cctbx environment, then python would have pointed to something in the build directory. You would have need to explicitly use ./base/bin/python or the system python with bootstrap.py instead. Also, I stripped extraneous stuff from the Boost tarball according to how earlier boost tarballs were built. This will improve download times and fix the Windows installation. Basically, only the following things are kept, LICENSE_1_0.txt boost/ libs/date_time libs/detail libs/filesystem libs/program_options libs/python libs/system libs/thread It's available now if you use authenticated access (--cciuser flag for bootstrap.py) and will propagate for unauthenticated access ( http://cci.lbl.gov/repositories) by 9:30 pm Pacific time (or 5:30 am UK time). Let me know of any issues. Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org On Thu, Apr 13, 2017 at 8:02 AM, R.D. Oeffner <rdo20(a)cam.ac.uk> wrote: > Sorry this was to Billy only. Please ignore. > > > > Rob > > > > > > On 13/04/2017 16:00, R.D. Oeffner wrote: > > Hi Billy, > > As you'll know the Windows builds failed with the new boost libraries. > this is due to some filenames exceeding the 255 char limit on Windows. It > worked fine on my nightly build because the build folder isn't as deeply > nested as on pulse and flux. On pulse and flux it dies in > tarfile.TarFile._extract_member() which I have made a monkey patch for > which appears to work by ignoring the offending files. > > However, as all the long filenames seem to come from html folders within > boost presumably these are just documentation and it would be better to > exclude these altogether in the cci subset of boost. People can always go > online if they want to read up on the documentation for boost. Besides > bootstrap.py is already quite bloated. > > Let me know what you think, > > Rob > > > > On 12/04/2017 21:47, Billy Poon wrote: > > Hi everyone, > > Boost 1.56 is now available and the tests have been updated. To update an > existing installtion, you have to delete the "build" directory first. If > you don't, I guess some files are not recompiled with the new Boost > headers, which will cause cctbx_project/scitbx/random/tests/tst_random.py > to expect the old values. Then run bootstrap.py with hot, update, and build > to rebuild. > > cd <installation directory> > rm -fr build > python bootstrap.py hot update build --builder=cctbx > > Let me know if there are any issues. Thanks! > > > -- > Billy K. Poon > Research Scientist, Molecular Biophysics and Integrated Bioimaging > Lawrence Berkeley National Laboratory > 1 Cyclotron Road, M/S 33R0345 > Berkeley, CA 94720 > Tel: (510) 486-5709 > Fax: (510) 486-5909 > Web: https://phenix-online.org > > On Fri, Apr 7, 2017 at 1:08 PM, Billy Poon <bkpoon(a)lbl.gov> wrote: > >> I can do the switch to Boost 1.56 next Wednesday now that Dials 1.5 has >> been released. I'm just double-checking some other Phenix tests. >> >> Once the update is live, bootstrap.py should delete the existing >> modules/boost directory and replace it with the new one. And then scons >> should recompile anything that depends on boost. If in doubt, you can >> manually delete the module/boost and build directories. >> >> -- >> Billy K. Poon >> Research Scientist, Molecular Biophysics and Integrated Bioimaging >> Lawrence Berkeley National Laboratory >> 1 Cyclotron Road, M/S 33R0345 >> Berkeley, CA 94720 >> Tel: (510) 486-5709 >> Fax: (510) 486-5909 >> Web: https://phenix-online.org >> On Thu, Apr 6, 2017 at 9:32 AM, Billy Poon <bkpoon(a)lbl.gov> wrote: >> >>> Hi James, >>> >>> I agree with Graeme's tests and I would add >>> >>> cctbx_regression.test_nightly >>> >>> That command is a shortcut for running the test modules for libtbx, >>> boost_adaptbx, scitbx, cctbx, iotbx, dxtbx, and smtbx. The mmtbx module is >>> also tested if chem_data is available. Should we add rstbx to the shortcut >>> (cctbx_project/cctbx/command_line/cctbx_test_nightly.py)? >>> >>> -- >>> Billy K. Poon >>> Research Scientist, Molecular Biophysics and Integrated Bioimaging >>> Lawrence Berkeley National Laboratory >>> 1 Cyclotron Road, M/S 33R0345 >>> Berkeley, CA 94720 >>> Tel: (510) 486-5709 >>> Fax: (510) 486-5909 >>> Web: https://phenix-online.org >>> On Thu, Apr 6, 2017 at 1:37 AM, <richard.gildea(a)diamond.ac.uk> wrote: >>> >>>> I've made a start on transcribing this document here: >>>> >>>> https://github.com/cctbx/cctbx_project/wiki/cctbx-Developer-Guidance >>>> >>>> It probably still needs cleaning up a bit (e.g. I couldn't figure out >>>> quickly how to do 3-level list nesting, 1.a.i etc.) and updating to reflect >>>> current practice (e.g. git not svn). >>>> >>>> Cheers, >>>> >>>> Richard >>>> >>>> Dr Richard Gildea >>>> Data Analysis Scientist >>>> Tel: +441235 77 8078 >>>> >>>> Diamond Light Source Ltd. >>>> Diamond House >>>> Harwell Science & Innovation Campus >>>> Didcot >>>> Oxfordshire >>>> OX11 0DE >>>> >>>> ________________________________________ >>>> From: cctbxbb-bounces(a)phenix-online.org [cctbxbb-bounces@phenix- >>>> online.org] on behalf of Pavel Afonine [pafonine(a)lbl.gov] >>>> Sent: 06 April 2017 09:07 >>>> To: cctbx mailing list >>>> Subject: Re: [cctbxbb] Boost Python 1.56 >>>> >>>> Hi Graeme, >>>> >>>> hm.. this is a good question. We've been through back-and-forth >>>> iterations of editing this file and I think the latest I have is from >>>> Paul. But I can't find a non-PDF version of it. Paul: do you have an >>>> editable version of this file? >>>> >>>> Thanks, >>>> Pavel >>>> >>>> On 4/6/17 13:45, Graeme.Winter(a)diamond.ac.uk wrote: >>>> > Hi Pavel >>>> > >>>> > These all seem sensible >>>> > >>>> > If you have the original non pdf document it may be easier to >>>> transcribe this over.. >>>> > >>>> > I also note that it lacks the actual detail on how to run tests! >>>> However would be happy to add this once on wiki >>>> > >>>> > Best wishes Graeme >>>> > >>>> > On 6 Apr 2017, at 04:00, Pavel Afonine <pafonine(a)lbl.gov<mailto:pafon >>>> ine(a)lbl.gov>> wrote: >>>> > >>>> > Not sure if that answers your questions but once upon a time we here >>>> at Berkeley tried to write a some sort of document that was supposed to >>>> answer questions like this. Attached. By no means it is complete, >>>> up-to-date, etc, but it might be worth reading for anyone who contributes >>>> to cctbx. (Even not sure if I'm sending the latest version). >>>> > Unfortunately, nobody bothered to put it in some central place. >>>> > >>>> > Pavel >>>> > >>>> > On 4/6/17 10:51, James Holton wrote: >>>> > Hey Billy, >>>> > >>>> > On a related note. How do I run these regression tests before >>>> committing something into Git? Is there a document on dials regression >>>> testing I can't find? >>>> > >>>> > -James >>>> > >>>> > On Apr 5, 2017, at 3:38 PM, Billy Poon <bkpoon(a)lbl.gov<mailto:bkpoon@ >>>> lbl.gov>> wrote: >>>> > >>>> > Hi all, >>>> > >>>> > I tested Boost 1.56 on our buildbot servers and got some new test >>>> failures with >>>> > >>>> > cctbx_project/scitbx/array_family/boost_python/tst_flex.py >>>> > cctbx_project/scitbx/random/tests/tst_random.py >>>> > >>>> > The full log for CentOS 6 can be found at >>>> > >>>> > http://cci-vm-6.lbl.gov:8010/builders/phenix-nightly-intel- >>>> linux-2.6-x86_64-centos6/builds/601/steps/test%20cctbx_ >>>> regression.test_nightly/logs/stdio >>>> > >>>> > It looks like the errors are related to random number generation. For >>>> a given seed, would the sequence of numbers change when Boost is changed? I >>>> did a diff between Boost 1.56 and the current Boost and could not see any >>>> changes that immediately stood out as being related to random numbers. >>>> > >>>> > Are these tests failing for others as well? >>>> > >>>> > -- >>>> > Billy K. Poon >>>> > Research Scientist, Molecular Biophysics and Integrated Bioimaging >>>> > Lawrence Berkeley National Laboratory >>>> > 1 Cyclotron Road, M/S 33R0345 >>>> > Berkeley, CA 94720 >>>> > Tel: (510) 486-5709 >>>> > Fax: (510) 486-5909 >>>> > Web: https://phenix-online.org<https://phenix-online.org/> >>>> > >>>> > On Wed, Apr 5, 2017 at 8:12 AM, Charles Ballard < >>>> charles.ballard(a)stfc.ac.uk<mailto:[email protected]>> wrote: >>>> > FYI, we (CCP4) have been using 1.56 for building cctbx/phaser/dials >>>> for the last while with no issues. Don't know about 1.60, but 1.59 causes >>>> issues with the boost python make_getter and make_setter (initialisation of >>>> none const reference if the passed type is a temporary). >>>> > >>>> > Charles >>>> > >>>> > On 3 Apr 2017, at 14:31, Luc Bourhis wrote: >>>> > >>>> > Hi all, >>>> > >>>> > everybody seemed to agree but then it was proposed to move straight >>>> to Boost 1.60, and this caused troubles. Could we consider again to move to >>>> at least 1.56? As far as I can tell, this does not cause any issue and as >>>> stated one year ago, it would help me and Olex 2. >>>> > >>>> > Thanks, >>>> > >>>> > Luc >>>> > >>>> > On 10 Feb 2016, at 15:17, Nicholas Sauter <nksauter(a)lbl.gov<mailto: >>>> nksauter(a)lbl.gov>> wrote: >>>> > >>>> > Nigel, Billy & Aaron, >>>> > >>>> > I completely endorse this move to Boost 1.56. Can we update our >>>> build? >>>> > >>>> > Nick >>>> > >>>> > Nicholas K. Sauter, Ph. D. >>>> > Computer Staff Scientist, Molecular Biophysics and Integrated >>>> Bioimaging Division >>>> > Lawrence Berkeley National Laboratory >>>> > 1 Cyclotron Rd., Bldg. 33R0345 >>>> > Berkeley, CA 94720 >>>> > (510) 486-5713<tel:%28510%29%20486-5713> >>>> > >>>> > On Wed, Feb 10, 2016 at 2:41 PM, Luc Bourhis <luc_j_bourhis(a)mac.com >>>> <mailto:[email protected]>> wrote: >>>> > Hi, >>>> > >>>> > I have improvements to the smtbx on their way to be committed which >>>> require Boost version 1.56. This is related to Boost.Threads, whose support >>>> I re-activated a few months ago on Nick's request. I need the function >>>> boost::thread::physical_concurrency which returns the number of >>>> physical cores on the machine, as opposed to virtual cores when >>>> hyperthreading is enabled (which it is by default on any Intel machine). >>>> That function is not available in Boost 1.55 which is the version currently >>>> used in the nightly tests: it appeared in 1.56. >>>> > >>>> > So, would it be possible to move to Boost 1.56? Otherwise, I will >>>> need to backport that function. Not too difficult but not thrilling. >>>> > >>>> > Best wishes, >>>> > >>>> > Luc >>>> > >>>> > >>>> > _______________________________________________ >>>> > cctbxbb mailing list >>>> > cctbxbb(a)phenix-online.org<mailto:[email protected]> >>>> > http://phenix-online.org/mailman/listinfo/cctbxbb >>>> > >>>> > _______________________________________________ >>>> > cctbxbb mailing list >>>> > cctbxbb(a)phenix-online.org<mailto:[email protected]> >>>> > http://phenix-online.org/mailman/listinfo/cctbxbb >>>> > >>>> > _______________________________________________ >>>> > cctbxbb mailing list >>>> > cctbxbb(a)phenix-online.org<mailto:[email protected]> >>>> > http://phenix-online.org/mailman/listinfo/cctbxbb >>>> > >>>> > >>>> > _______________________________________________ >>>> > cctbxbb mailing list >>>> > cctbxbb(a)phenix-online.org<mailto:[email protected]> >>>> > http://phenix-online.org/mailman/listinfo/cctbxbb >>>> > >>>> > >>>> > _______________________________________________ >>>> > cctbxbb mailing list >>>> > cctbxbb(a)phenix-online.org<mailto:[email protected]> >>>> > http://phenix-online.org/mailman/listinfo/cctbxbb >>>> > >>>> > >>>> > >>>> > _______________________________________________ >>>> > cctbxbb mailing list >>>> > cctbxbb(a)phenix-online.org<mailto:[email protected]> >>>> > http://phenix-online.org/mailman/listinfo/cctbxbb >>>> > >>>> > >>>> > <cctbx-developer-guidance-08-2015.pdf>_____________________ >>>> __________________________ >>>> > cctbxbb mailing list >>>> > cctbxbb(a)phenix-online.org<mailto:[email protected]> >>>> > http://phenix-online.org/mailman/listinfo/cctbxbb >>>> > >>>> > >>>> >>>> _______________________________________________ >>>> cctbxbb mailing list >>>> cctbxbb(a)phenix-online.org >>>> http://phenix-online.org/mailman/listinfo/cctbxbb >>>> >>>> -- >>>> This e-mail and any attachments may contain confidential, copyright and >>>> or privileged material, and are for the use of the intended addressee only. >>>> If you are not the intended addressee or an authorised recipient of the >>>> addressee please notify us of receipt by returning the e-mail and do not >>>> use, copy, retain, distribute or disclose the information in or attached to >>>> the e-mail. >>>> Any opinions expressed within this e-mail are those of the individual >>>> and not necessarily of Diamond Light Source Ltd. >>>> Diamond Light Source Ltd. cannot guarantee that this e-mail or any >>>> attachments are free from viruses and we cannot accept liability for any >>>> damage which you may sustain as a result of software viruses which may be >>>> transmitted in or with the message. >>>> Diamond Light Source Limited (company no. 4375679). Registered in >>>> England and Wales with its registered office at Diamond House, Harwell >>>> Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom >>>> >>>> >>>> _______________________________________________ >>>> cctbxbb mailing list >>>> cctbxbb(a)phenix-online.org >>>> http://phenix-online.org/mailman/listinfo/cctbxbb >>>> >>> > _______________________________________________ > cctbxbb mailing [email protected]://phenix-online.org/mailman/listinfo/cctbxbb > > > > > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb > >

8 years, 9 months

Re: [cctbxbb] some thoughts on cctbx and pip

by Billy Poon

Hi everyone, I updated the conda packages on the cctbx-dev channel and there are also now packages for macOS. The old packages have been removed so you can create a new environment with conda create -n test -c cctbx-dev cctbx python=2.7 conda activate test where "test" is the environment name and 2.7 is the python version. For the python version, you can also pick 3.6, 3.7, or 3.8. I think the latest conda will install 3.8 as the default python if the python argument is not provided. Or install into an existing environment (with python already installed) with the same command as before, conda install -c cctbx-dev cctbx Again, your .condarc file should have conda-forge as the first channel so that dependencies can be pulled correctly. The dispatchers should work now and $LIBTBX_BUILD will be set on activation of an environment (and unset on environment deactivation) or after installing into an existing environment, so you can do more interesting things like iotbx.fetch_pdb --all --mtz 1kp8 However, this package does not install databases, so molprobity.molprobity 1kp8.pdb 1kp8.mtz will fail because the database is not available (also probe and reduce are not built). Some known issues in no particular order, 1) You can run "libtbx.run_tests_parallel module=cctbx nproc=Auto" to run tests, but not all the test files were copied, so I got 30 failures here. The final package will probably not have the test files. 2) The other python dispatchers, like "cctbx.python", were not updated, so those will fail. But you can just run "python" in the active environment. 3) Parts of mmtbx still need to be updated for Python 3. 4) The LIBTBX_BUILD variable should be set for sh and csh shells. Let me know if it's not working for your shell (i.e. "echo $LIBTBX_BUILD" should show the same thing as $CONDA_PREFIX). 5) One future step is to enable building other CCTBX-like modules with this conda package. This will require some bookkeeping updates so that modules in the conda environment and the modules being built are tracked properly. Also, making sure that all the necessary headers exist in $PREFIX/include. Gergely, let me know if your scripts are working. Happy holidays! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org On Wed, Dec 18, 2019 at 11:25 AM Billy Poon <BKPoon(a)lbl.gov> wrote: > Hi Gergely, > > That's the other information that hasn't been updated yet in the conda > package. :) > > For LIBTBX_BUILD, I can set up environment variables sort of how the conda > gcc package sets up environment variables. I have to double check to see if > they're set after installation of the package and after activation of an > environment. The variable will just be a copy of $CONDA_PREFIX. > > The libtbx_env file is a file that exists in $LIBTBX_BUILD that basically > stores configuration information. I'll have to modify the contents to > update the locations of the different modules since the conda package will > not have a "modules" directory. > > -- > Billy K. Poon > Research Scientist, Molecular Biophysics and Integrated Bioimaging > Lawrence Berkeley National Laboratory > 1 Cyclotron Road, M/S 33R0345 > Berkeley, CA 94720 > Tel: (510) 486-5709 > Fax: (510) 486-5909 > Web: https://phenix-online.org > > > On Wed, Dec 18, 2019 at 2:08 AM Gergely Katona <gkatona(a)gmail.com> wrote: > >> Hi Billy, >> >> Conda install went fine with your instructions after rearranging the >> channels by putting cctbx last. I removed all environmental variables >> and previous build of cctbx. >> >> import sys >> print (sys.path, sys.prefix) >> >> ['/home/gergely/anaconda3/lib/python36.zip', >> '/home/gergely/anaconda3/lib/python3.6', >> '/home/gergely/anaconda3/lib/python3.6/lib-dynload', '', >> '/home/gergely/anaconda3/lib/python3.6/site-packages', >> '/home/gergely/anaconda3/lib/python3.6/site-packages/IPython/extensions', >> '/home/gergely/.ipython'] /home/gergely/anaconda3 >> >> Many imports went fine including pymc3, but I encountered problems >> with these three: >> >> from cctbx import miller >> import iotbx.pdb >> from iotbx import reflection_file_reader, mtz >> >> >> I also got type error when handling space groups. >> >> >> >> >> --------------------------------------------------------------------------- >> KeyError Traceback (most recent call >> last) >> <ipython-input-5-cedbd4f84f3d> in <module> >> 25 from cctbx import uctbx >> 26 from cctbx import sgtbx >> ---> 27 from cctbx import miller >> 28 #from iotbx import reflection_file_reader, mtz >> 29 sns.set_context("poster") >> >> ~/anaconda3/lib/python3.6/site-packages/cctbx/miller/__init__.py in >> <module> >> 11 >> 12 from cctbx import crystal >> ---> 13 from cctbx import maptbx >> 14 from cctbx import sgtbx >> 15 from cctbx.sgtbx import lattice_symmetry >> >> ~/anaconda3/lib/python3.6/site-packages/cctbx/maptbx/__init__.py in >> <module> >> 15 from libtbx import adopt_init_args >> 16 from libtbx.utils import Sorry >> ---> 17 import libtbx.load_env >> 18 import math >> 19 import sys, os >> >> ~/anaconda3/lib/python3.6/site-packages/libtbx/load_env.py in <module> >> 3 import libtbx.env_config >> 4 import os >> ----> 5 libtbx.env = libtbx.env_config.unpickle() >> 6 libtbx.env.set_os_environ_all_dist() >> 7 libtbx.env.dispatcher_name = >> os.environ.get("LIBTBX_DISPATCHER_NAME") >> >> ~/anaconda3/lib/python3.6/site-packages/libtbx/env_config.py in unpickle() >> 2603 >> 2604 def unpickle(): >> -> 2605 build_path = os.environ["LIBTBX_BUILD"] >> 2606 >> set_preferred_sys_prefix_and_sys_executable(build_path=build_path) >> 2607 libtbx_env = open(op.join(build_path, "libtbx_env"), "rb") >> >> ~/anaconda3/lib/python3.6/os.py in __getitem__(self, key) >> 667 except KeyError: >> 668 # raise KeyError with the original key value >> --> 669 raise KeyError(key) from None >> 670 return self.decodevalue(value) >> 671 >> >> KeyError: 'LIBTBX_BUILD' >> >> >> >> >> --------------------------------------------------------------------------- >> ArgumentError Traceback (most recent call >> last) >> <ipython-input-7-2acd3a9ce26a> in <module> >> 26 return >> ms,msnam,mscent,msacent,msnamacent,msnamcent,msnamacent_dstar >> 27 >> ---> 28 >> ms,msnam,mscent,msacent,msnamacent,msnamcent,msnamacent_dstar=initializecrystal() >> >> <ipython-input-7-2acd3a9ce26a> in initializecrystal() >> 11 uc = uctbx.unit_cell(unit_cell) >> 12 wavelength = 1.54980 >> ---> 13 xtal_symm = crystal.symmetry(unit_cell=unit_cell, >> space_group_symbol="P 43 21 2") >> 14 >> 15 ms = >> miller.build_set(crystal_symmetry=xtal_symm,anomalous_flag=True, >> d_min=1.61) >> >> ~/anaconda3/lib/python3.6/site-packages/cctbx/crystal/__init__.py in >> __init__(self, unit_cell, space_group_symbol, space_group_info, >> space_group, correct_rhombohedral_setting_if_necessary, >> assert_is_compatible_unit_cell, raise_sorry_if_incompatible_unit_cell, >> force_compatible_unit_cell) >> 74 if (space_group_symbol is not None): >> 75 self._space_group_info = sgtbx.space_group_info( >> ---> 76 symbol=space_group_symbol) >> 77 elif (space_group is not None): >> 78 if (isinstance(space_group, sgtbx.space_group)): >> >> ~/anaconda3/lib/python3.6/site-packages/cctbx/sgtbx/__init__.py in >> __init__(self, symbol, table_id, group, number, space_group_t_den) >> 100 assert group is None >> 101 if (table_id is None): >> --> 102 symbols = space_group_symbols(symbol) >> 103 else: >> 104 if (isinstance(symbol, int)): symbol = str(symbol) >> >> ArgumentError: Python argument types in >> space_group_symbols.__init__(space_group_symbols, str) >> did not match C++ signature: >> __init__(_object*, int space_group_number) >> __init__(_object*, int space_group_number, >> std::__cxx11::basic_string<char, std::char_traits<char>, >> std::allocator<char> > extension='') >> __init__(_object*, int space_group_number, >> std::__cxx11::basic_string<char, std::char_traits<char>, >> std::allocator<char> > extension='', std::__cxx11::basic_string<char, >> std::char_traits<char>, std::allocator<char> > table_id='') >> __init__(_object*, std::__cxx11::basic_string<char, >> std::char_traits<char>, std::allocator<char> > symbol) >> __init__(_object*, std::__cxx11::basic_string<char, >> std::char_traits<char>, std::allocator<char> > symbol, >> std::__cxx11::basic_string<char, std::char_traits<char>, >> std::allocator<char> > table_id='') >> >> >> When I tried to set LIBTBX_BUILD to /home/gergely/anaconda3 (this is >> sys.prefix on my system), I got other problems when importing. Can >> LIBTBX_BUILD be set in the conda package? >> >> >> >> >> --------------------------------------------------------------------------- >> FileNotFoundError Traceback (most recent call >> last) >> <ipython-input-1-7e2b144826cc> in <module> >> 26 from cctbx import sgtbx >> 27 #from cctbx import miller >> ---> 28 from iotbx import reflection_file_reader, mtz >> 29 sns.set_context("poster") >> 30 plt.rcParams.update({'figure.autolayout': True}) >> >> ~/anaconda3/lib/python3.6/site-packages/iotbx/reflection_file_reader.py >> in <module> >> 53 >> 54 from __future__ import absolute_import, division, print_function >> ---> 55 from iotbx import mtz >> 56 from iotbx.scalepack import merge as scalepack_merge >> 57 from iotbx.scalepack import no_merge_original_index as >> scalepack_no_merge >> >> ~/anaconda3/lib/python3.6/site-packages/iotbx/mtz/__init__.py in <module> >> 9 import iotbx_mtz_ext as ext >> 10 >> ---> 11 from iotbx.mtz import extract_from_symmetry_lib >> 12 from cctbx import xray >> 13 import cctbx.xray.observation_types >> >> >> ~/anaconda3/lib/python3.6/site-packages/iotbx/mtz/extract_from_symmetry_lib.py >> in <module> >> 1 from __future__ import absolute_import, division, print_function >> 2 from cctbx import sgtbx >> ----> 3 import libtbx.load_env >> 4 import os.path as op >> 5 from six.moves import range >> >> ~/anaconda3/lib/python3.6/site-packages/libtbx/load_env.py in <module> >> 3 import libtbx.env_config >> 4 import os >> ----> 5 libtbx.env = libtbx.env_config.unpickle() >> 6 libtbx.env.set_os_environ_all_dist() >> 7 libtbx.env.dispatcher_name = >> os.environ.get("LIBTBX_DISPATCHER_NAME") >> >> ~/anaconda3/lib/python3.6/site-packages/libtbx/env_config.py in unpickle() >> 2605 build_path = os.environ["LIBTBX_BUILD"] >> 2606 >> set_preferred_sys_prefix_and_sys_executable(build_path=build_path) >> -> 2607 libtbx_env = open(op.join(build_path, "libtbx_env"), "rb") >> 2608 env = pickle.load(libtbx_env) >> 2609 if (env.python_version_major_minor != sys.version_info[:2]): >> >> FileNotFoundError: [Errno 2] No such file or directory: >> '/home/gergely/anaconda3/libtbx_env' >> >> On Wed, Dec 18, 2019 at 9:10 AM Billy Poon <BKPoon(a)lbl.gov> wrote: >> > >> > Hi Gergely, >> > >> > I've uploaded linux packages to a new channel, cctbx-dev, and you can >> install it with >> > >> > conda install -c cctbx-dev cctbx >> > >> > in your current environment. You should set your ~/.condarc file to >> pull the other dependencies from the conda-forge channel first, so put >> conda-forge above cctbx. Mine looks like >> > >> > channels: >> > - conda-forge >> > - defaults >> > - cctbx >> > >> > Do you need dxtbx for your scripts? This package does not build that >> part. I think the plan is to build a separate conda package for dxtbx so >> that it can be updated more frequently. I can rebuild the packages to >> include it for testing, but the one being submitted to conda-forge will not >> have it. >> > >> > Also, your error message is probably due to version of HDF5 that the >> development build installs. The bootstrap.py script will install 1.10.4, >> but your other dependency is looking for 1.10.5. Installing this cctbx >> conda package should install 1.10.5, which should fix the issue. Also, I'm >> updating those environments and 1.10.5 will be the new default version. >> > >> > Lastly, the dispatchers will not work in these packages because the old >> paths during the build process are still in them and many of them expect >> some additional information that has not been updated in the packages yet. >> I'm in the process of doing that and will update the cctbx-dev channel when >> that's done. However, by starting python, you can import cctbx modules. So >> you can run commands like >> > >> > from scitbx.array_family import flex >> > a = flex.random_double(1000000) >> > b = flex.min_max_mean_double(a) >> > b.min >> > b.max >> > b.mean >> > >> > Thanks! >> > >> > -- >> > Billy K. Poon >> > Research Scientist, Molecular Biophysics and Integrated Bioimaging >> > Lawrence Berkeley National Laboratory >> > 1 Cyclotron Road, M/S 33R0345 >> > Berkeley, CA 94720 >> > Tel: (510) 486-5709 >> > Fax: (510) 486-5909 >> > Web: https://phenix-online.org >> > >> > >> > On Tue, Dec 17, 2019 at 5:39 AM Gergely Katona <gkatona(a)gmail.com> >> wrote: >> >> >> >> Dear Billy, >> >> >> >> Thank you for the detailed explanation, I look forward to do further >> >> testing! I aim to pool all modules under the same environment, if >> >> there are conflicts then I just try to reshuffle the order of imports. >> >> So far this did not cause problems for me even when I was using system >> >> python, but of course it is not the most prudent thing to do. With >> >> anaconda everything is much more standardized and isolated already and >> >> without being superuser I can have my familiar environment at any >> >> synchrotron based cluster. It is great that cctbx will be an integral >> >> part of this ecosystem and this was also the last thing holding me >> >> back from adopting python3. About hdf5, pymc3 requires it and >> >> importing causes a kernel restart with the following error messages, >> >> curiously if I import h5py first this can be avoided. >> >> >> >> Best wishes, >> >> >> >> Gergely >> >> >> >> import pymc3 as pm >> >> >> >> Warning! ***HDF5 library version mismatched error*** >> >> The HDF5 header files used to compile this application do not match >> >> the version used by the HDF5 library to which this application is >> linked. >> >> Data corruption or segmentation faults may occur if the application >> continues. >> >> This can happen when an application was compiled by one version of >> HDF5 but >> >> linked with a different version of static or shared HDF5 library. >> >> You should recompile the application or check your shared library >> related >> >> settings such as 'LD_LIBRARY_PATH'. >> >> You can, at your own risk, disable this warning by setting the >> environment >> >> variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'. >> >> Setting it to 2 or higher will suppress the warning messages totally. >> >> Headers are 1.10.4, library is 1.10.5 >> >> SUMMARY OF THE HDF5 CONFIGURATION >> >> ================================= >> >> >> >> General Information: >> >> ------------------- >> >> HDF5 Version: 1.10.5 >> >> Configured on: Tue Oct 22 12:02:13 UTC 2019 >> >> Configured by: conda@16247e67ecd5 >> >> Host system: x86_64-conda_cos6-linux-gnu >> >> Uname information: Linux 16247e67ecd5 4.15.0-1059-azure >> >> #64-Ubuntu SMP Fri Sep 13 17:02:44 UTC 2019 x86_64 x86_64 x86_64 >> >> GNU/Linux >> >> Byte sex: little-endian >> >> Installation point: /home/gergely/anaconda3 >> >> >> >> Compiling Options: >> >> ------------------ >> >> Build Mode: production >> >> Debugging Symbols: no >> >> Asserts: no >> >> Profiling: no >> >> Optimization Level: high >> >> >> >> Linking Options: >> >> ---------------- >> >> Libraries: static, shared >> >> Statically Linked Executables: >> >> LDFLAGS: -Wl,-O2 -Wl,--sort-common >> >> -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags >> >> -Wl,--gc-sections -Wl,-rpath,/home/gergely/anaconda3/lib >> >> -Wl,-rpath-link,/home/gergely/anaconda3/lib >> >> -L/home/gergely/anaconda3/lib >> >> H5_LDFLAGS: >> >> AM_LDFLAGS: -L/home/gergely/anaconda3/lib >> >> Extra libraries: -lrt -lpthread -lz -ldl -lm >> >> Archiver: >> >> >> /home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/_build_env/bin/x86_64-conda_cos6-linux-gnu-ar >> >> AR_FLAGS: cr >> >> Ranlib: >> >> >> /home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/_build_env/bin/x86_64-conda_cos6-linux-gnu-ranlib >> >> >> >> Languages: >> >> ---------- >> >> C: yes >> >> C Compiler: >> >> >> /home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc >> >> CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 >> >> -I/home/gergely/anaconda3/include >> >> H5_CPPFLAGS: -D_GNU_SOURCE >> >> -D_POSIX_C_SOURCE=200809L -DNDEBUG -UH5_DEBUG_API >> >> AM_CPPFLAGS: -I/home/gergely/anaconda3/include >> >> C Flags: -march=nocona -mtune=haswell >> >> -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 >> >> -ffunction-sections -pipe -I/home/gergely/anaconda3/include >> >> >> -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/work=/usr/local/src/conda/hdf5_split-1.10.5 >> >> -fdebug-prefix-map=/home/gergely/anaconda3=/usr/local/src/conda-prefix >> >> H5 C Flags: -std=c99 -pedantic -Wall -Wextra >> >> -Wbad-function-cast -Wc++-compat -Wcast-align -Wcast-qual -Wconversion >> >> -Wdeclaration-after-statement -Wdisabled-optimization -Wfloat-equal >> >> -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-declarations >> >> -Wmissing-include-dirs -Wmissing-prototypes -Wnested-externs >> >> -Wold-style-definition -Wpacked -Wpointer-arith -Wredundant-decls >> >> -Wshadow -Wstrict-prototypes -Wswitch-default -Wswitch-enum -Wundef >> >> -Wunused-macros -Wunsafe-loop-optimizations -Wwrite-strings >> >> -finline-functions -s -Wno-inline -Wno-aggregate-return >> >> -Wno-missing-format-attribute -Wno-missing-noreturn -O >> >> AM C Flags: >> >> Shared C Library: yes >> >> Static C Library: yes >> >> >> >> >> >> Fortran: yes >> >> Fortran Compiler: >> >> >> /home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/_build_env/bin/x86_64-conda_cos6-linux-gnu-gfortran >> >> Fortran Flags: >> >> H5 Fortran Flags: -pedantic -Wall -Wextra -Wunderflow >> >> -Wimplicit-interface -Wsurprising -Wno-c-binding-type -s -O2 >> >> AM Fortran Flags: >> >> Shared Fortran Library: yes >> >> Static Fortran Library: yes >> >> >> >> C++: yes >> >> C++ Compiler: >> >> >> /home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/_build_env/bin/x86_64-conda_cos6-linux-gnu-c++ >> >> C++ Flags: -fvisibility-inlines-hidden >> >> -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell >> >> -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 >> >> -ffunction-sections -pipe -I/home/gergely/anaconda3/include >> >> >> -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/work=/usr/local/src/conda/hdf5_split-1.10.5 >> >> -fdebug-prefix-map=/home/gergely/anaconda3=/usr/local/src/conda-prefix >> >> H5 C++ Flags: -pedantic -Wall -W -Wundef -Wshadow >> >> -Wpointer-arith -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion >> >> -Wredundant-decls -Winline -Wsign-promo -Woverloaded-virtual >> >> -Wold-style-cast -Weffc++ -Wreorder -Wnon-virtual-dtor >> >> -Wctor-dtor-privacy -Wabi -finline-functions -s -O >> >> AM C++ Flags: >> >> Shared C++ Library: yes >> >> Static C++ Library: yes >> >> >> >> Java: no >> >> >> >> >> >> Features: >> >> --------- >> >> Parallel HDF5: no >> >> Parallel Filtered Dataset Writes: no >> >> Large Parallel I/O: no >> >> High-level library: yes >> >> Threadsafety: yes >> >> Default API mapping: v110 >> >> With deprecated public symbols: yes >> >> I/O filters (external): deflate(zlib) >> >> MPE: no >> >> Direct VFD: no >> >> dmalloc: no >> >> Packages w/ extra debug output: none >> >> API tracing: no >> >> Using memory checker: yes >> >> Memory allocation sanity checks: no >> >> Function stack tracing: no >> >> Strict file format checks: no >> >> Optimization instrumentation: no >> >> >> >> On Tue, Dec 17, 2019 at 8:35 AM Billy Poon <BKPoon(a)lbl.gov> wrote: >> >> > >> >> > Hi Gergely, >> >> > >> >> > Let me build the test package tomorrow. All the gritty details for >> building with conda is being finalized and the official documentation will >> be updated to describe the steps. It would be too confusing to keep >> changing the documentation as the process evolves. You do have the general >> process, though, which is summarized as follows. >> >> > >> >> > 1) Installing dependencies. The cctbx_dependencies metapackage was >> an initial approach for managing the CCTBX dependencies, but after >> contacting the conda-forge folks, they recommended using the --only-deps >> flag. So when the CCTBX conda package is available, you'll be able to get a >> set of dependencies with, >> >> > >> >> > conda install -c conda-forge --only-deps cctbx >> >> > >> >> > By default, the bootstrap.py file will automatically install a set >> of dependencies in the "conda_base" directory (and a conda installation if >> one is not found). It just uses standard conda environment files located in >> libtbx/auto_build/conda_envs, so you do not need to install >> cctbx_dependencies as a separate step. The environment files avoid channel >> issues by explicitly defining the channel to pull the packages from and the >> cctbx channel just stores copies of packages from conda-forge. There were >> issues earlier where the conda-forge packages would sometimes be moved to a >> different label. The --use-conda flag also accepts a path to $CONDA_PREFIX >> if you want to use a specific environment for testing. >> >> > >> >> > 2) Building. The bootstrap.py file handles that with SCons. >> >> > >> >> > 3) Running. After building, there should be a setpaths.sh (and .csh) >> file that adds build/bin to your path. The build/bin directory has our >> dispatchers, which are just scripts that set up the environment variables >> for you. This prevents other programs from loading our libraries, whose >> versions may conflict. You should see that there is a "python" dispatcher, >> which is a convenience for developers. Otherwise, you can use >> libtbx.python, which will be able to import CCTBX modules. >> >> > >> >> > The running part is where the conda package for CCTBX will be >> different than this build. Since our Python files and extensions modules >> will be in the "site-packages" directory for Python, the PYTHONPATH >> variable will not be needed (and conda suggests that that variable not be >> set). The other CCTBX libraries will be in $CONDA_PREFIX/lib, so >> LD_LIBRARY_PATH is not needed. In an active environment, PATH will already >> be modified. And then our LIBTBX_BUILD directory can be set to sys.prefix. >> >> > >> >> > So with the conda package, you would only need to activate your >> conda environment and CCTBX should integrate with other conda packages. >> What is the conflict with hdf5? That's something that should be fixed. >> Thanks! >> >> > >> >> > -- >> >> > Billy K. Poon >> >> > Research Scientist, Molecular Biophysics and Integrated Bioimaging >> >> > Lawrence Berkeley National Laboratory >> >> > 1 Cyclotron Road, M/S 33R0345 >> >> > Berkeley, CA 94720 >> >> > Tel: (510) 486-5709 >> >> > Fax: (510) 486-5909 >> >> > Web: https://phenix-online.org >> >> > >> >> > >> >> > On Mon, Dec 16, 2019 at 2:53 AM Gergely Katona <gkatona(a)gmail.com> >> wrote: >> >> >> >> >> >> Dear Billy, >> >> >> >> >> >> Thank you for this update and for your efforts! I found a solution >> and >> >> >> indeed most things already work in anaconda3. The steps I took (even >> >> >> if these instructions will have short expiry date): >> >> >> >> >> >> Modified .condarc with: >> >> >> channels: >> >> >> - cctbx >> >> >> - conda-forge >> >> >> - defaults >> >> >> >> >> >> run >> >> >> conda conda install cctbx_dependencies python=3.6 >> >> >> >> >> >> I expect this will work without python=3.6 in the near future. >> >> >> >> >> >> Then compiling cctbx with anaconda3 python went without any problem >> >> >> when using these flags: >> >> >> python bootstrap.py --use-conda --python3 --nproc=12 >> >> >> >> >> >> Then I probably did the unorthodox thing and sourced these >> directories: >> >> >> >> >> >> setenv LIBTBX_BUILD /home/gergely/cctbx/build >> >> >> setenv PATH ${PATH}:/home/gergely/cctbx/build/bin >> >> >> setenv PYTHONPATH >> >> >> >> /home/gergely/cctbx/modules/cctbx_project:/home/gergely/cctbx/modules:/home/gergely/cctbx/modules/cctbx_project/boost_adaptbx:/home/gergely/cctbx/build/lib:/home/gergely/cctbx/conda_base/lib/python3.6/site-packages:$PYTHONPATH >> >> >> setenv LD_LIBRARY_PATH >> >> >> >> /home/gergely/cctbx/conda_base/lib:/home/gergely/cctbx/build/lib:$LD_LIBRARY_PATH >> >> >> >> >> >> There is probably a better way to put this into conda environment. >> >> >> With these steps I could run one of my scripts depending on cctbx. >> The >> >> >> only problem I found is that hdf5 library had conflict with another >> >> >> package in conda, but I does not find this as a showstopper. >> >> >> >> >> >> Best wishes, >> >> >> >> >> >> Gergely >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> On Fri, Dec 13, 2019 at 7:23 PM Billy Poon <BKPoon(a)lbl.gov> wrote: >> >> >> > >> >> >> > Hi Gergely, >> >> >> > >> >> >> > It's still a work in progress. I'm sorting out some Windows >> issues right now. I can probably build a test package on a separate channel >> for people that want to test it (let's say next week?). I'll provide >> instructions, but basically, the test conda package will be in its own >> separate channel and the dependencies will be pulled from the conda-forge >> channel. I want most things to be working correctly on Python 2.7, 3.6, >> 3.7, and 3.8 on all 3 platforms. >> >> >> > >> >> >> > Thanks! >> >> >> > >> >> >> > -- >> >> >> > Billy K. Poon >> >> >> > Research Scientist, Molecular Biophysics and Integrated Bioimaging >> >> >> > Lawrence Berkeley National Laboratory >> >> >> > 1 Cyclotron Road, M/S 33R0345 >> >> >> > Berkeley, CA 94720 >> >> >> > Tel: (510) 486-5709 >> >> >> > Fax: (510) 486-5909 >> >> >> > Web: https://phenix-online.org >> >> >> > >> >> >> > >> >> >> > On Fri, Dec 13, 2019 at 5:44 AM Gergely Katona <gkatona(a)gmail.com> >> wrote: >> >> >> >> >> >> >> >> Dear Billy, >> >> >> >> >> >> >> >> This sounds very promising and exciting. I am not sure if cctbx >> is >> >> >> >> already functional as a conda package in anaconda3 (Linux) or >> this is >> >> >> >> still work in progress. My technical expertise does not allow me >> to >> >> >> >> tell the difference. What I tried: >> >> >> >> >> >> >> >> Fresh install of anaconda3. Adding - cctbx and - conda-forge to >> >> >> >> .condarc . Installing pyside2 with conda. Running conda install >> >> >> >> conda_dependencies . I get a lot package version conflict, and I >> >> >> >> cannot import cctbx or iotbx to anaconda python. Am I following >> the >> >> >> >> right instructions? Or it is too early to expect that cctbx >> works when >> >> >> >> installed through conda? >> >> >> >> >> >> >> >> Best wishes, >> >> >> >> >> >> >> >> Gergely >> >> >> >> >> >> >> >> On Wed, Nov 27, 2019 at 3:56 PM Billy Poon <BKPoon(a)lbl.gov> >> wrote: >> >> >> >> > >> >> >> >> > Hi all, >> >> >> >> > >> >> >> >> > For a brief update, I have submitted a recipe for cctbxlite to >> conda-forge (https://github.com/conda-forge/staged-recipes/pull/10021) >> and support for Python 3.7 and 3.8 is being added ( >> https://github.com/cctbx/cctbx_project/pull/409). With some fixes for >> Windows (https://github.com/cctbx/cctbx_project/pull/416), all platforms >> (macOS, linux, and Windows) can build for Python 2.7, 3.6, 3.7, and 3.8. >> Some additional changes will be needed to get Windows to work with Python 3 >> and for tests to pass with Boost 1.70.0. That will enable the conda-forge >> recipe to build for all platforms and for all supported versions of Python. >> >> >> >> > >> >> >> >> > Currently, the conda-forge recipe will install into the conda >> python and cctbx imports can be done without sourcing the environment >> scripts. It looks like a lot of the environment variables being set in the >> dispatchers can be removed since the Python files and C++ extensions are in >> the right places. I'll update the libtbx_env file so that commands that >> load the environment can work correctly. >> >> >> >> > >> >> >> >> > -- >> >> >> >> > Billy K. Poon >> >> >> >> > Research Scientist, Molecular Biophysics and Integrated >> Bioimaging >> >> >> >> > Lawrence Berkeley National Laboratory >> >> >> >> > 1 Cyclotron Road, M/S 33R0345 >> >> >> >> > Berkeley, CA 94720 >> >> >> >> > Tel: (510) 486-5709 >> >> >> >> > Fax: (510) 486-5909 >> >> >> >> > Web: https://phenix-online.org >> >> >> >> > >> >> >> >> > >> >> >> >> > On Sun, Aug 25, 2019 at 2:33 PM Tristan Croll <tic20(a)cam.ac.uk> >> wrote: >> >> >> >> >> >> >> >> >> >> Hi Luc, >> >> >> >> >> >> >> >> >> >> That sounds promising. From there, I’d need to work out how >> to make a fully-packaged installer (basically a modified wheel file) for >> the ChimeraX ToolShed - the aim is for the end user to not have to worry >> about any of this. That adds a couple of complications - e.g. $LIBTBX_BUILD >> would need to be set dynamically before first import - but doesn’t seem >> insurmountable. >> >> >> >> >> >> >> >> >> >> Thanks, >> >> >> >> >> >> >> >> >> >> Tristan >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> Tristan Croll >> >> >> >> >> Research Fellow >> >> >> >> >> Cambridge Institute for Medical Research >> >> >> >> >> University of Cambridge CB2 0XY >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> > On 25 Aug 2019, at 18:31, Luc Bourhis < >> luc_j_bourhis(a)mac.com> wrote: >> >> >> >> >> > >> >> >> >> >> > Hi Tristan, >> >> >> >> >> > >> >> >> >> >> > cctbx could be built to use your ChimeraX python, now that >> cctbx is moving to Python 3. The option —with-python is there for that with >> the bootstrap script. The specific environment setup boil down to setting >> two environment variable LIBTBX_BUILD and either LD_LIBRARY_PATH on Linux, >> PATH on Win32, or DYLIB_LIBRARY_PATH on MacOS. If you work within a >> framework such as ChimeraX, that should not be difficult to ensure those >> two variables are set. >> >> >> >> >> > >> >> >> >> >> > Best wishes, >> >> >> >> >> > >> >> >> >> >> > Luc >> >> >> >> >> > >> >> >> >> >> > >> >> >> >> >> >> On 23 Aug 2019, at 19:02, Tristan Croll <tic20(a)cam.ac.uk> >> wrote: >> >> >> >> >> >> >> >> >> >> >> >> To add my two cents on this: probably the second-most >> common question I've had about ISOLDE's implementation is, "why didn't you >> use CCTBX?". The honest answer to that is, "I didn't know how." >> >> >> >> >> >> >> >> >> >> >> >> Still don't, really - although the current developments >> are rather promising. The problem I've faced is that CCTBX was designed as >> its own self-contained Python (2.7, until very recently) environment, with >> its own interpreter and a lot of very specific environment setup. Meanwhile >> I'm developing ISOLDE in ChimeraX, which is *also* its own self-contained >> Python (3.7) environment. To plug one into the other in that form... well, >> I don't think I'm a good enough programmer to really know where to start. >> >> >> >> >> >> >> >> >> >> >> >> The move to Conda and a more modular CCTBX architecture >> should make a lot more possible in that direction. Pip would be even better >> for me personally (ChimeraX can install directly from the PyPI, but doesn't >> interact with Conda) - but I understand pretty well the substantial >> challenge that would amount to (not least being that the PyPI imposes a >> limit - around 100MB from memory? - on the size of an individual package). >> >> >> >> >> >> >> >> >> >> >> >> Best regards, >> >> >> >> >> >> >> >> >> >> >> >> Tristan >> >> >> >> >> >> >> >> >> >> >> >>> On 2019-08-23 09:28, Luc Bourhis wrote: >> >> >> >> >> >>> Hi Graeme, >> >> >> >> >> >>> Yes, I know. But “black" is a program doing a very >> particular task >> >> >> >> >> >>> (code formatting from the top of my head). Requiring to >> use a wrapper >> >> >> >> >> >>> for python itself is another level. But ok, I think I am >> mellowing to >> >> >> >> >> >>> the idea after all! Talking with people around me, and >> extrapolating, >> >> >> >> >> >>> I would bet that, right now, a great majority of people >> interested by >> >> >> >> >> >>> cctbx in pip have already used the cctbx, so they know >> about the >> >> >> >> >> >>> Python wrapper, and they would not be too sanguine about >> that. My >> >> >> >> >> >>> concern is for the future, when pip will be the first >> time some people >> >> >> >> >> >>> use cctbx. Big fat warning notices on PyPI page and a >> better error >> >> >> >> >> >>> message when cctbx fails because LIBTBX_BUILD is not set >> would be >> >> >> >> >> >>> needed but that could be all right. >> >> >> >> >> >>> If we do a pip installer, we should aim at a minimal >> install: cctbx, >> >> >> >> >> >>> iotbx and their dependencies, and that’s it. >> >> >> >> >> >>> Best wishes, >> >> >> >> >> >>> Luc >> >> >> >> >> >>>> On 23 Aug 2019, at 07:17, Graeme.Winter(a)Diamond.ac.uk < >> Graeme.Winter(a)diamond.ac.uk> wrote: >> >> >> >> >> >>>> Without discussing the merits of this or whether we >> _choose_ to make the move to supporting PIP, I am certain it would be >> _possible_ - many other packages make dispatcher scripts when you pip >> install them e.g. >> >> >> >> >> >>>> Silver-Surfer rescale_f2 :) $ which black; cat $(which >> black) >> >> >> >> >> >>>> >> /Library/Frameworks/Python.framework/Versions/3.6/bin/black >> >> >> >> >> >>>> >> #!/Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6 >> >> >> >> >> >>>> # -*- coding: utf-8 -*- >> >> >> >> >> >>>> import re >> >> >> >> >> >>>> import sys >> >> >> >> >> >>>> from black import main >> >> >> >> >> >>>> if __name__ == '__main__': >> >> >> >> >> >>>> sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', >> sys.argv[0]) >> >> >> >> >> >>>> sys.exit(main()) >> >> >> >> >> >>>> So we _could_ work around the absence of LIBTBX_BUILD >> etc. in the system. Whether or not we elect to do the work is a different >> question, and it seems clear that here are very mixed opinions on this. >> >> >> >> >> >>>> Best wishes Graeme >> >> >> >> >> >>>> On 23 Aug 2019, at 01:21, Luc Bourhis < >> luc_j_bourhis(a)mac.com<mailto:[email protected]>> wrote: >> >> >> >> >> >>>> Hi, >> >> >> >> >> >>>> Even if we managed to ship our the boost dynamic >> libraries with pip, it would still not be pip-like, as we would still need >> our python wrappers to set LIBTBX_BUILD and LD_LIBRARY_PATH. Normal pip >> packages work with the standard python exe. LD_LIBRARY_PATH, we could get >> around that by changing the way we compile, using -Wl,-R, which is the >> runtime equivalent of build time -L. That’s a significant change that would >> need to be tested. But there is no way around setting LIBTBX_BUILD right >> now. Leaving that to the user is horrible. Perhaps there is a way to hack >> libtbx/env_config.py so that we can hardwire LIBTBX_BUILD in there when pip >> installs? >> >> >> >> >> >>>> Best wishes, >> >> >> >> >> >>>> Luc >> >> >> >> >> >>>> On 16 Aug 2019, at 22:47, Luc Bourhis < >> luc_j_bourhis(a)mac.com<mailto:[email protected]>> wrote: >> >> >> >> >> >>>> Hi, >> >> >> >> >> >>>> I did look into that many years ago, and even toyed with >> building a pip installer. What stopped me is the exact conclusion you >> reached too: the user would not have the pip experience he expects. You are >> right that it is a lot of effort but is it worth it? Considering that >> remark, I don’t think so. Now, Conda was created specifically to go beyond >> pip pure-python-only support. Since cctbx has garnered support for Conda, >> the best avenue imho is to go the extra length to have a package on >> Anaconda.org<http://anaconda.org/>, and then to advertise it hard to >> every potential user out there. >> >> >> >> >> >>>> Best wishes, >> >> >> >> >> >>>> Luc >> >> >> >> >> >>>> On 16 Aug 2019, at 21:45, Aaron Brewster < >> asbrewster(a)lbl.gov<mailto:[email protected]>> wrote: >> >> >> >> >> >>>> Hi, to avoid clouding Dorothee's documentation email >> thread, which I think is a highly useful enterprise, here's some thoughts >> about putting cctbx into pip. Pip doesn't install non-python dependencies >> well. I don't think boost is available as a package on pip (at least the >> package version we use). wxPython4 isn't portable through pip ( >> https://wiki.wxpython.org/How%20to%20install%20wxPython#Installing_wxPython…). >> MPI libraries are system dependent. If cctbx were a pure python package, >> pip would be fine, but cctbx is not. >> >> >> >> >> >>>> All that said, we could build a manylinux1 version of >> cctbx and upload it to PyPi (I'm just learning about this). For a pip >> package to be portable (which is a requirement for cctbx), it needs to >> conform to PEP513, the manylinux1 standard ( >> https://www.python.org/dev/peps/pep-0513/). For example, numpy is built >> according to this standard (see https://pypi.org/project/numpy/#files, >> where you'll see the manylinux1 wheel). Note, the manylinux1 standard is >> built with Centos 5.11 which we no longer support. >> >> >> >> >> >>>> There is also a manylinux2010 standard, which is based >> on Centos 6 (https://www.python.org/dev/peps/pep-0571/). This is likely >> a more attainable target (note though by default C++11 is not supported on >> Centos 6). >> >> >> >> >> >>>> If we built a manylinuxX version of cctbx and uploaded >> it to PyPi, the user would need all the non-python dependencies. There's >> no way to specify these in pip. For example, cctbx requires boost 1.63 or >> better. The user will need to have it in a place their python can find it, >> or we could package it ourselves and supply it, similar to how the pip h5py >> package now comes with an hd5f library, or how the pip numpy package >> includes an openblas library. We'd have to do the same for any packages we >> depend on that aren't on pip using the manylinux standards, such as >> wxPython4. >> >> >> >> >> >>>> Further, we need to think about how dials and other >> cctbx-based packages interact. If pip install cctbx is set up, how does >> pip install dials work, such that any dials shared libraries can find the >> cctbx libraries? Can shared libraries from one pip package link against >> libraries in another pip package? Would each package need to supply its >> own boost? Possibly this is well understood in the pip field, but not by >> me :) >> >> >> >> >> >>>> Finally, there's the option of providing a source pip >> package. This would require the full compiler toolchain for any given >> platform (macOS, linux, windows). These are likely available for >> developers, but not for general users. >> >> >> >> >> >>>> Anyway, these are some of the obstacles. Not saying it >> isn't possible, it's just a lot of effort. >> >> >> >> >> >>>> Thanks, >> >> >> >> >> >>>> -Aaron >> >> >> >> >> >>>> _______________________________________________ >> >> >> >> >> >>>> cctbxbb mailing list >> >> >> >> >> >>>> cctbxbb(a)phenix-online.org<mailto: >> cctbxbb(a)phenix-online.org> >> >> >> >> >> >>>> http://phenix-online.org/mailman/listinfo/cctbxbb >> >> >> >> >> >>>> _______________________________________________ >> >> >> >> >> >>>> cctbxbb mailing list >> >> >> >> >> >>>> cctbxbb(a)phenix-online.org<mailto: >> cctbxbb(a)phenix-online.org> >> >> >> >> >> >>>> http://phenix-online.org/mailman/listinfo/cctbxbb >> >> >> >> >> >>>> _______________________________________________ >> >> >> >> >> >>>> cctbxbb mailing list >> >> >> >> >> >>>> cctbxbb(a)phenix-online.org<mailto: >> cctbxbb(a)phenix-online.org> >> >> >> >> >> >>>> http://phenix-online.org/mailman/listinfo/cctbxbb >> >> >> >> >> >>>> -- >> >> >> >> >> >>>> This e-mail and any attachments may contain >> confidential, copyright and or privileged material, and are for the use of >> the intended addressee only. If you are not the intended addressee or an >> authorised recipient of the addressee please notify us of receipt by >> returning the e-mail and do not use, copy, retain, distribute or disclose >> the information in or attached to the e-mail. >> >> >> >> >> >>>> Any opinions expressed within this e-mail are those of >> the individual and not necessarily of Diamond Light Source Ltd. >> >> >> >> >> >>>> Diamond Light Source Ltd. cannot guarantee that this >> e-mail or any attachments are free from viruses and we cannot accept >> liability for any damage which you may sustain as a result of software >> viruses which may be transmitted in or with the message. >> >> >> >> >> >>>> Diamond Light Source Limited (company no. 4375679). >> Registered in England and Wales with its registered office at Diamond >> House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 >> 0DE, United Kingdom >> >> >> >> >> >>>> _______________________________________________ >> >> >> >> >> >>>> cctbxbb mailing list >> >> >> >> >> >>>> cctbxbb(a)phenix-online.org >> >> >> >> >> >>>> http://phenix-online.org/mailman/listinfo/cctbxbb >> >> >> >> >> >>> _______________________________________________ >> >> >> >> >> >>> cctbxbb mailing list >> >> >> >> >> >>> cctbxbb(a)phenix-online.org >> >> >> >> >> >>> http://phenix-online.org/mailman/listinfo/cctbxbb >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> >> >> >> >> >> cctbxbb mailing list >> >> >> >> >> >> cctbxbb(a)phenix-online.org >> >> >> >> >> >> http://phenix-online.org/mailman/listinfo/cctbxbb >> >> >> >> >> > >> >> >> >> >> > >> >> >> >> >> > _______________________________________________ >> >> >> >> >> > cctbxbb mailing list >> >> >> >> >> > cctbxbb(a)phenix-online.org >> >> >> >> >> > http://phenix-online.org/mailman/listinfo/cctbxbb >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> >> >> >> >> cctbxbb mailing list >> >> >> >> >> cctbxbb(a)phenix-online.org >> >> >> >> >> http://phenix-online.org/mailman/listinfo/cctbxbb >> >> >> >> > >> >> >> >> > _______________________________________________ >> >> >> >> > cctbxbb mailing list >> >> >> >> > cctbxbb(a)phenix-online.org >> >> >> >> > http://phenix-online.org/mailman/listinfo/cctbxbb >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> -- >> >> >> >> Gergely Katona, PhD >> >> >> >> Associate Professor >> >> >> >> Department of Chemistry and Molecular Biology, University of >> Gothenburg >> >> >> >> Box 462, 40530 Göteborg, Sweden >> >> >> >> Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910 >> >> >> >> Web: http://katonalab.eu, Email: gergely.katona(a)gu.se >> >> >> >> >> >> >> >> _______________________________________________ >> >> >> >> cctbxbb mailing list >> >> >> >> cctbxbb(a)phenix-online.org >> >> >> >> http://phenix-online.org/mailman/listinfo/cctbxbb >> >> >> > >> >> >> > _______________________________________________ >> >> >> > cctbxbb mailing list >> >> >> > cctbxbb(a)phenix-online.org >> >> >> > http://phenix-online.org/mailman/listinfo/cctbxbb >> >> >> >> >> >> >> >> >> >> >> >> -- >> >> >> Gergely Katona, PhD >> >> >> Associate Professor >> >> >> Department of Chemistry and Molecular Biology, University of >> Gothenburg >> >> >> Box 462, 40530 Göteborg, Sweden >> >> >> Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910 >> >> >> Web: http://katonalab.eu, Email: gergely.katona(a)gu.se >> >> >> >> >> >> _______________________________________________ >> >> >> cctbxbb mailing list >> >> >> cctbxbb(a)phenix-online.org >> >> >> http://phenix-online.org/mailman/listinfo/cctbxbb >> >> > >> >> > _______________________________________________ >> >> > cctbxbb mailing list >> >> > cctbxbb(a)phenix-online.org >> >> > http://phenix-online.org/mailman/listinfo/cctbxbb >> >> >> >> >> >> >> >> -- >> >> Gergely Katona, PhD >> >> Associate Professor >> >> Department of Chemistry and Molecular Biology, University of Gothenburg >> >> Box 462, 40530 Göteborg, Sweden >> >> Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910 >> >> Web: http://katonalab.eu, Email: gergely.katona(a)gu.se >> >> >> >> _______________________________________________ >> >> cctbxbb mailing list >> >> cctbxbb(a)phenix-online.org >> >> http://phenix-online.org/mailman/listinfo/cctbxbb >> > >> > _______________________________________________ >> > cctbxbb mailing list >> > cctbxbb(a)phenix-online.org >> > http://phenix-online.org/mailman/listinfo/cctbxbb >> >> >> >> -- >> Gergely Katona, PhD >> Associate Professor >> Department of Chemistry and Molecular Biology, University of Gothenburg >> Box 462, 40530 Göteborg, Sweden >> Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910 >> Web: http://katonalab.eu, Email: gergely.katona(a)gu.se >> >> _______________________________________________ >> cctbxbb mailing list >> cctbxbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/cctbxbb >> >

6 years, 1 month

Re: [cctbxbb] [EXTERNAL] cctbxbb Digest, Vol 129, Issue 6

by Mooers, Blaine H.M. (HSC)

By following Billy's directions and using new envs, I was able to install cctbx with conda on Mac OS 15.2 with Python 3.6, 3.7, and 3.8. I was able to run some simple scripts. I ran the test that Billy suggested and also got 30 errors. Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology College of Medicine University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center (BRC) Rm. 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 ________________________________________ From: cctbxbb-bounces(a)phenix-online.org [cctbxbb-bounces(a)phenix-online.org] on behalf of cctbxbb-request(a)phenix-online.org [cctbxbb-request(a)phenix-online.org] Sent: Friday, December 20, 2019 2:00 PM To: cctbxbb(a)phenix-online.org Subject: [EXTERNAL] cctbxbb Digest, Vol 129, Issue 6 Send cctbxbb mailing list submissions to cctbxbb(a)phenix-online.org To subscribe or unsubscribe via the World Wide Web, visit https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… or, via email, send a message with subject or body 'help' to cctbxbb-request(a)phenix-online.org You can reach the person managing the list at cctbxbb-owner(a)phenix-online.org When replying, please edit your Subject line so it is more specific than "Re: Contents of cctbxbb digest..." Today's Topics: 1. Re: some thoughts on cctbx and pip (Billy Poon) ---------------------------------------------------------------------- Message: 1 Date: Fri, 20 Dec 2019 11:15:35 -0800 From: Billy Poon <BKPoon(a)lbl.gov> To: cctbx mailing list <cctbxbb(a)phenix-online.org> Subject: Re: [cctbxbb] some thoughts on cctbx and pip Message-ID: <CAHmYUcYdeXspPwWW2fOOBg0p734p9XYKqS-LiXXqyU-ydBu4pw(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi everyone, I updated the conda packages on the cctbx-dev channel and there are also now packages for macOS. The old packages have been removed so you can create a new environment with conda create -n test -c cctbx-dev cctbx python=2.7 conda activate test where "test" is the environment name and 2.7 is the python version. For the python version, you can also pick 3.6, 3.7, or 3.8. I think the latest conda will install 3.8 as the default python if the python argument is not provided. Or install into an existing environment (with python already installed) with the same command as before, conda install -c cctbx-dev cctbx Again, your .condarc file should have conda-forge as the first channel so that dependencies can be pulled correctly. The dispatchers should work now and $LIBTBX_BUILD will be set on activation of an environment (and unset on environment deactivation) or after installing into an existing environment, so you can do more interesting things like iotbx.fetch_pdb --all --mtz 1kp8 However, this package does not install databases, so molprobity.molprobity 1kp8.pdb 1kp8.mtz will fail because the database is not available (also probe and reduce are not built). Some known issues in no particular order, 1) You can run "libtbx.run_tests_parallel module=cctbx nproc=Auto" to run tests, but not all the test files were copied, so I got 30 failures here. The final package will probably not have the test files. 2) The other python dispatchers, like "cctbx.python", were not updated, so those will fail. But you can just run "python" in the active environment. 3) Parts of mmtbx still need to be updated for Python 3. 4) The LIBTBX_BUILD variable should be set for sh and csh shells. Let me know if it's not working for your shell (i.e. "echo $LIBTBX_BUILD" should show the same thing as $CONDA_PREFIX). 5) One future step is to enable building other CCTBX-like modules with this conda package. This will require some bookkeeping updates so that modules in the conda environment and the modules being built are tracked properly. Also, making sure that all the necessary headers exist in $PREFIX/include. Gergely, let me know if your scripts are working. Happy holidays! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://urldefense.proofpoint.com/v2/url?u=https-3A__phenix-2Donline.org&d=… On Wed, Dec 18, 2019 at 11:25 AM Billy Poon <BKPoon(a)lbl.gov> wrote: > Hi Gergely, > > That's the other information that hasn't been updated yet in the conda > package. :) > > For LIBTBX_BUILD, I can set up environment variables sort of how the conda > gcc package sets up environment variables. I have to double check to see if > they're set after installation of the package and after activation of an > environment. The variable will just be a copy of $CONDA_PREFIX. > > The libtbx_env file is a file that exists in $LIBTBX_BUILD that basically > stores configuration information. I'll have to modify the contents to > update the locations of the different modules since the conda package will > not have a "modules" directory. > > -- > Billy K. Poon > Research Scientist, Molecular Biophysics and Integrated Bioimaging > Lawrence Berkeley National Laboratory > 1 Cyclotron Road, M/S 33R0345 > Berkeley, CA 94720 > Tel: (510) 486-5709 > Fax: (510) 486-5909 > Web: https://urldefense.proofpoint.com/v2/url?u=https-3A__phenix-2Donline.org&d=… > > > On Wed, Dec 18, 2019 at 2:08 AM Gergely Katona <gkatona(a)gmail.com> wrote: > >> Hi Billy, >> >> Conda install went fine with your instructions after rearranging the >> channels by putting cctbx last. I removed all environmental variables >> and previous build of cctbx. >> >> import sys >> print (sys.path, sys.prefix) >> >> ['/home/gergely/anaconda3/lib/https://urldefense.proofpoint.com/v2/url?u=http-3A__python36.zip&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=XYalX3Fy1IGs4p_M1YHMvPXXo6HJximT9mf_zMIckxU&s=ST4siK2y7PNpS4anr425eXK4FO6ig7oA-XNHoaHgCpY&e= ', >> '/home/gergely/anaconda3/lib/python3.6', >> '/home/gergely/anaconda3/lib/python3.6/lib-dynload', '', >> '/home/gergely/anaconda3/lib/python3.6/site-packages', >> '/home/gergely/anaconda3/lib/python3.6/site-packages/IPython/extensions', >> '/home/gergely/.ipython'] /home/gergely/anaconda3 >> >> Many imports went fine including pymc3, but I encountered problems >> with these three: >> >> from cctbx import miller >> import iotbx.pdb >> from iotbx import reflection_file_reader, mtz >> >> >> I also got type error when handling space groups. >> >> >> >> >> --------------------------------------------------------------------------- >> KeyError Traceback (most recent call >> last) >> <ipython-input-5-cedbd4f84f3d> in <module> >> 25 from cctbx import uctbx >> 26 from cctbx import sgtbx >> ---> 27 from cctbx import miller >> 28 #from iotbx import reflection_file_reader, mtz >> 29 sns.set_context("poster") >> >> ~/anaconda3/lib/python3.6/site-packages/cctbx/miller/https://urldefense.proofpoint.com/v2/url?u=http-3A__-5F-5Finit-5F-5F.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=XYalX3Fy1IGs4p_M1YHMvPXXo6HJximT9mf_zMIckxU&s=ou8J8HxatN0TDK1PJ-GUgX9YcOgS5Fayhbs61Wt2f7g&e= in >> <module> >> 11 >> 12 from cctbx import crystal >> ---> 13 from cctbx import maptbx >> 14 from cctbx import sgtbx >> 15 from cctbx.sgtbx import lattice_symmetry >> >> ~/anaconda3/lib/python3.6/site-packages/cctbx/maptbx/https://urldefense.proofpoint.com/v2/url?u=http-3A__-5F-5Finit-5F-5F.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=XYalX3Fy1IGs4p_M1YHMvPXXo6HJximT9mf_zMIckxU&s=ou8J8HxatN0TDK1PJ-GUgX9YcOgS5Fayhbs61Wt2f7g&e= in >> <module> >> 15 from libtbx import adopt_init_args >> 16 from libtbx.utils import Sorry >> ---> 17 import libtbx.load_env >> 18 import math >> 19 import sys, os >> >> ~/anaconda3/lib/python3.6/site-packages/libtbx/https://urldefense.proofpoint.com/v2/url?u=http-3A__load-5Fenv.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=XYalX3Fy1IGs4p_M1YHMvPXXo6HJximT9mf_zMIckxU&s=dUMVNgDtesLENoxBTvPr4XX4mczuZIsmZzdOmPlGbtI&e= in <module> >> 3 import libtbx.env_config >> 4 import os >> ----> 5 libtbx.env = libtbx.env_config.unpickle() >> 6 libtbx.env.set_os_environ_all_dist() >> 7 libtbx.env.dispatcher_name = >> os.environ.get("LIBTBX_DISPATCHER_NAME") >> >> ~/anaconda3/lib/python3.6/site-packages/libtbx/https://urldefense.proofpoint.com/v2/url?u=http-3A__env-5Fconfig.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=XYalX3Fy1IGs4p_M1YHMvPXXo6HJximT9mf_zMIckxU&s=2BeTV_6Dw8q_ulzvyRBt0YhebeaqhUvm-em6GAOEaI4&e= in unpickle() >> 2603 >> 2604 def unpickle(): >> -> 2605 build_path = os.environ["LIBTBX_BUILD"] >> 2606 >> set_preferred_sys_prefix_and_sys_executable(build_path=build_path) >> 2607 libtbx_env = open(op.join(build_path, "libtbx_env"), "rb") >> >> ~/anaconda3/lib/python3.6/https://urldefense.proofpoint.com/v2/url?u=http-3A__os.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=XYalX3Fy1IGs4p_M1YHMvPXXo6HJximT9mf_zMIckxU&s=y6dOvVLcNHYw8pJU1uwOEPGTH8lLyIp-mgtyv_X2bFQ&e= in __getitem__(self, key) >> 667 except KeyError: >> 668 # raise KeyError with the original key value >> --> 669 raise KeyError(key) from None >> 670 return self.decodevalue(value) >> 671 >> >> KeyError: 'LIBTBX_BUILD' >> >> >> >> >> --------------------------------------------------------------------------- >> ArgumentError Traceback (most recent call >> last) >> <ipython-input-7-2acd3a9ce26a> in <module> >> 26 return >> ms,msnam,mscent,msacent,msnamacent,msnamcent,msnamacent_dstar >> 27 >> ---> 28 >> ms,msnam,mscent,msacent,msnamacent,msnamcent,msnamacent_dstar=initializecrystal() >> >> <ipython-input-7-2acd3a9ce26a> in initializecrystal() >> 11 uc = uctbx.unit_cell(unit_cell) >> 12 wavelength = 1.54980 >> ---> 13 xtal_symm = crystal.symmetry(unit_cell=unit_cell, >> space_group_symbol="P 43 21 2") >> 14 >> 15 ms = >> miller.build_set(crystal_symmetry=xtal_symm,anomalous_flag=True, >> d_min=1.61) >> >> ~/anaconda3/lib/python3.6/site-packages/cctbx/crystal/https://urldefense.proofpoint.com/v2/url?u=http-3A__-5F-5Finit-5F-5F.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=XYalX3Fy1IGs4p_M1YHMvPXXo6HJximT9mf_zMIckxU&s=ou8J8HxatN0TDK1PJ-GUgX9YcOgS5Fayhbs61Wt2f7g&e= in >> __init__(self, unit_cell, space_group_symbol, space_group_info, >> space_group, correct_rhombohedral_setting_if_necessary, >> assert_is_compatible_unit_cell, raise_sorry_if_incompatible_unit_cell, >> force_compatible_unit_cell) >> 74 if (space_group_symbol is not None): >> 75 self._space_group_info = sgtbx.space_group_info( >> ---> 76 symbol=space_group_symbol) >> 77 elif (space_group is not None): >> 78 if (isinstance(space_group, sgtbx.space_group)): >> >> ~/anaconda3/lib/python3.6/site-packages/cctbx/sgtbx/https://urldefense.proofpoint.com/v2/url?u=http-3A__-5F-5Finit-5F-5F.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=XYalX3Fy1IGs4p_M1YHMvPXXo6HJximT9mf_zMIckxU&s=ou8J8HxatN0TDK1PJ-GUgX9YcOgS5Fayhbs61Wt2f7g&e= in >> __init__(self, symbol, table_id, group, number, space_group_t_den) >> 100 assert group is None >> 101 if (table_id is None): >> --> 102 symbols = space_group_symbols(symbol) >> 103 else: >> 104 if (isinstance(symbol, int)): symbol = str(symbol) >> >> ArgumentError: Python argument types in >> space_group_symbols.__init__(space_group_symbols, str) >> did not match C++ signature: >> __init__(_object*, int space_group_number) >> __init__(_object*, int space_group_number, >> std::__cxx11::basic_string<char, std::char_traits<char>, >> std::allocator<char> > extension='') >> __init__(_object*, int space_group_number, >> std::__cxx11::basic_string<char, std::char_traits<char>, >> std::allocator<char> > extension='', std::__cxx11::basic_string<char, >> std::char_traits<char>, std::allocator<char> > table_id='') >> __init__(_object*, std::__cxx11::basic_string<char, >> std::char_traits<char>, std::allocator<char> > symbol) >> __init__(_object*, std::__cxx11::basic_string<char, >> std::char_traits<char>, std::allocator<char> > symbol, >> std::__cxx11::basic_string<char, std::char_traits<char>, >> std::allocator<char> > table_id='') >> >> >> When I tried to set LIBTBX_BUILD to /home/gergely/anaconda3 (this is >> sys.prefix on my system), I got other problems when importing. Can >> LIBTBX_BUILD be set in the conda package? >> >> >> >> >> --------------------------------------------------------------------------- >> FileNotFoundError Traceback (most recent call >> last) >> <ipython-input-1-7e2b144826cc> in <module> >> 26 from cctbx import sgtbx >> 27 #from cctbx import miller >> ---> 28 from iotbx import reflection_file_reader, mtz >> 29 sns.set_context("poster") >> 30 plt.rcParams.update({'figure.autolayout': True}) >> >> ~/anaconda3/lib/python3.6/site-packages/iotbx/https://urldefense.proofpoint.com/v2/url?u=http-3A__reflection-5Ffile-5Freader.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=XYalX3Fy1IGs4p_M1YHMvPXXo6HJximT9mf_zMIckxU&s=yYMogebnDLYk0-5LYB00qDeyEYddmSEzic2HY01p1-4&e= >> in <module> >> 53 >> 54 from __future__ import absolute_import, division, print_function >> ---> 55 from iotbx import mtz >> 56 from iotbx.scalepack import merge as scalepack_merge >> 57 from iotbx.scalepack import no_merge_original_index as >> scalepack_no_merge >> >> ~/anaconda3/lib/python3.6/site-packages/iotbx/mtz/https://urldefense.proofpoint.com/v2/url?u=http-3A__-5F-5Finit-5F-5F.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=XYalX3Fy1IGs4p_M1YHMvPXXo6HJximT9mf_zMIckxU&s=ou8J8HxatN0TDK1PJ-GUgX9YcOgS5Fayhbs61Wt2f7g&e= in <module> >> 9 import iotbx_mtz_ext as ext >> 10 >> ---> 11 from iotbx.mtz import extract_from_symmetry_lib >> 12 from cctbx import xray >> 13 import cctbx.xray.observation_types >> >> >> ~/anaconda3/lib/python3.6/site-packages/iotbx/mtz/https://urldefense.proofpoint.com/v2/url?u=http-3A__extract-5Ffrom-5Fsymmetry-5Flib.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=XYalX3Fy1IGs4p_M1YHMvPXXo6HJximT9mf_zMIckxU&s=sdo4JC4HEfj-rC7w_ahWQIcYyaTeKakuavIvEeWWbf8&e= >> in <module> >> 1 from __future__ import absolute_import, division, print_function >> 2 from cctbx import sgtbx >> ----> 3 import libtbx.load_env >> 4 import os.path as op >> 5 from six.moves import range >> >> ~/anaconda3/lib/python3.6/site-packages/libtbx/https://urldefense.proofpoint.com/v2/url?u=http-3A__load-5Fenv.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=XYalX3Fy1IGs4p_M1YHMvPXXo6HJximT9mf_zMIckxU&s=dUMVNgDtesLENoxBTvPr4XX4mczuZIsmZzdOmPlGbtI&e= in <module> >> 3 import libtbx.env_config >> 4 import os >> ----> 5 libtbx.env = libtbx.env_config.unpickle() >> 6 libtbx.env.set_os_environ_all_dist() >> 7 libtbx.env.dispatcher_name = >> os.environ.get("LIBTBX_DISPATCHER_NAME") >> >> ~/anaconda3/lib/python3.6/site-packages/libtbx/https://urldefense.proofpoint.com/v2/url?u=http-3A__env-5Fconfig.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=XYalX3Fy1IGs4p_M1YHMvPXXo6HJximT9mf_zMIckxU&s=2BeTV_6Dw8q_ulzvyRBt0YhebeaqhUvm-em6GAOEaI4&e= in unpickle() >> 2605 build_path = os.environ["LIBTBX_BUILD"] >> 2606 >> set_preferred_sys_prefix_and_sys_executable(build_path=build_path) >> -> 2607 libtbx_env = open(op.join(build_path, "libtbx_env"), "rb") >> 2608 env = pickle.load(libtbx_env) >> 2609 if (env.python_version_major_minor != sys.version_info[:2]): >> >> FileNotFoundError: [Errno 2] No such file or directory: >> '/home/gergely/anaconda3/libtbx_env' >> >> On Wed, Dec 18, 2019 at 9:10 AM Billy Poon <BKPoon(a)lbl.gov> wrote: >> > >> > Hi Gergely, >> > >> > I've uploaded linux packages to a new channel, cctbx-dev, and you can >> install it with >> > >> > conda install -c cctbx-dev cctbx >> > >> > in your current environment. You should set your ~/.condarc file to >> pull the other dependencies from the conda-forge channel first, so put >> conda-forge above cctbx. Mine looks like >> > >> > channels: >> > - conda-forge >> > - defaults >> > - cctbx >> > >> > Do you need dxtbx for your scripts? This package does not build that >> part. I think the plan is to build a separate conda package for dxtbx so >> that it can be updated more frequently. I can rebuild the packages to >> include it for testing, but the one being submitted to conda-forge will not >> have it. >> > >> > Also, your error message is probably due to version of HDF5 that the >> development build installs. The https://urldefense.proofpoint.com/v2/url?u=http-3A__bootstrap.py&d=DwICAg&c… script will install 1.10.4, >> but your other dependency is looking for 1.10.5. Installing this cctbx >> conda package should install 1.10.5, which should fix the issue. Also, I'm >> updating those environments and 1.10.5 will be the new default version. >> > >> > Lastly, the dispatchers will not work in these packages because the old >> paths during the build process are still in them and many of them expect >> some additional information that has not been updated in the packages yet. >> I'm in the process of doing that and will update the cctbx-dev channel when >> that's done. However, by starting python, you can import cctbx modules. So >> you can run commands like >> > >> > from scitbx.array_family import flex >> > a = flex.random_double(1000000) >> > b = flex.min_max_mean_double(a) >> > b.min >> > b.max >> > b.mean >> > >> > Thanks! >> > >> > -- >> > Billy K. Poon >> > Research Scientist, Molecular Biophysics and Integrated Bioimaging >> > Lawrence Berkeley National Laboratory >> > 1 Cyclotron Road, M/S 33R0345 >> > Berkeley, CA 94720 >> > Tel: (510) 486-5709 >> > Fax: (510) 486-5909 >> > Web: https://urldefense.proofpoint.com/v2/url?u=https-3A__phenix-2Donline.org&d=… >> > >> > >> > On Tue, Dec 17, 2019 at 5:39 AM Gergely Katona <gkatona(a)gmail.com> >> wrote: >> >> >> >> Dear Billy, >> >> >> >> Thank you for the detailed explanation, I look forward to do further >> >> testing! I aim to pool all modules under the same environment, if >> >> there are conflicts then I just try to reshuffle the order of imports. >> >> So far this did not cause problems for me even when I was using system >> >> python, but of course it is not the most prudent thing to do. With >> >> anaconda everything is much more standardized and isolated already and >> >> without being superuser I can have my familiar environment at any >> >> synchrotron based cluster. It is great that cctbx will be an integral >> >> part of this ecosystem and this was also the last thing holding me >> >> back from adopting python3. About hdf5, pymc3 requires it and >> >> importing causes a kernel restart with the following error messages, >> >> curiously if I import h5py first this can be avoided. >> >> >> >> Best wishes, >> >> >> >> Gergely >> >> >> >> import pymc3 as pm >> >> >> >> Warning! ***HDF5 library version mismatched error*** >> >> The HDF5 header files used to compile this application do not match >> >> the version used by the HDF5 library to which this application is >> linked. >> >> Data corruption or segmentation faults may occur if the application >> continues. >> >> This can happen when an application was compiled by one version of >> HDF5 but >> >> linked with a different version of static or shared HDF5 library. >> >> You should recompile the application or check your shared library >> related >> >> settings such as 'LD_LIBRARY_PATH'. >> >> You can, at your own risk, disable this warning by setting the >> environment >> >> variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'. >> >> Setting it to 2 or higher will suppress the warning messages totally. >> >> Headers are 1.10.4, library is 1.10.5 >> >> SUMMARY OF THE HDF5 CONFIGURATION >> >> ================================= >> >> >> >> General Information: >> >> ------------------- >> >> HDF5 Version: 1.10.5 >> >> Configured on: Tue Oct 22 12:02:13 UTC 2019 >> >> Configured by: conda@16247e67ecd5 >> >> Host system: x86_64-conda_cos6-linux-gnu >> >> Uname information: Linux 16247e67ecd5 4.15.0-1059-azure >> >> #64-Ubuntu SMP Fri Sep 13 17:02:44 UTC 2019 x86_64 x86_64 x86_64 >> >> GNU/Linux >> >> Byte sex: little-endian >> >> Installation point: /home/gergely/anaconda3 >> >> >> >> Compiling Options: >> >> ------------------ >> >> Build Mode: production >> >> Debugging Symbols: no >> >> Asserts: no >> >> Profiling: no >> >> Optimization Level: high >> >> >> >> Linking Options: >> >> ---------------- >> >> Libraries: static, shared >> >> Statically Linked Executables: >> >> LDFLAGS: -Wl,-O2 -Wl,--sort-common >> >> -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags >> >> -Wl,--gc-sections -Wl,-rpath,/home/gergely/anaconda3/lib >> >> -Wl,-rpath-link,/home/gergely/anaconda3/lib >> >> -L/home/gergely/anaconda3/lib >> >> H5_LDFLAGS: >> >> AM_LDFLAGS: -L/home/gergely/anaconda3/lib >> >> Extra libraries: -lrt -lpthread -lz -ldl -lm >> >> Archiver: >> >> >> /home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/_build_env/bin/x86_64-conda_cos6-linux-gnu-ar >> >> AR_FLAGS: cr >> >> Ranlib: >> >> >> /home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/_build_env/bin/x86_64-conda_cos6-linux-gnu-ranlib >> >> >> >> Languages: >> >> ---------- >> >> C: yes >> >> C Compiler: >> >> >> /home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc >> >> CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 >> >> -I/home/gergely/anaconda3/include >> >> H5_CPPFLAGS: -D_GNU_SOURCE >> >> -D_POSIX_C_SOURCE=200809L -DNDEBUG -UH5_DEBUG_API >> >> AM_CPPFLAGS: -I/home/gergely/anaconda3/include >> >> C Flags: -march=nocona -mtune=haswell >> >> -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 >> >> -ffunction-sections -pipe -I/home/gergely/anaconda3/include >> >> >> -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/work=/usr/local/src/conda/hdf5_split-1.10.5 >> >> -fdebug-prefix-map=/home/gergely/anaconda3=/usr/local/src/conda-prefix >> >> H5 C Flags: -std=c99 -pedantic -Wall -Wextra >> >> -Wbad-function-cast -Wc++-compat -Wcast-align -Wcast-qual -Wconversion >> >> -Wdeclaration-after-statement -Wdisabled-optimization -Wfloat-equal >> >> -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-declarations >> >> -Wmissing-include-dirs -Wmissing-prototypes -Wnested-externs >> >> -Wold-style-definition -Wpacked -Wpointer-arith -Wredundant-decls >> >> -Wshadow -Wstrict-prototypes -Wswitch-default -Wswitch-enum -Wundef >> >> -Wunused-macros -Wunsafe-loop-optimizations -Wwrite-strings >> >> -finline-functions -s -Wno-inline -Wno-aggregate-return >> >> -Wno-missing-format-attribute -Wno-missing-noreturn -O >> >> AM C Flags: >> >> Shared C Library: yes >> >> Static C Library: yes >> >> >> >> >> >> Fortran: yes >> >> Fortran Compiler: >> >> >> /home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/_build_env/bin/x86_64-conda_cos6-linux-gnu-gfortran >> >> Fortran Flags: >> >> H5 Fortran Flags: -pedantic -Wall -Wextra -Wunderflow >> >> -Wimplicit-interface -Wsurprising -Wno-c-binding-type -s -O2 >> >> AM Fortran Flags: >> >> Shared Fortran Library: yes >> >> Static Fortran Library: yes >> >> >> >> C++: yes >> >> C++ Compiler: >> >> >> /home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/_build_env/bin/x86_64-conda_cos6-linux-gnu-c++ >> >> C++ Flags: -fvisibility-inlines-hidden >> >> -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell >> >> -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 >> >> -ffunction-sections -pipe -I/home/gergely/anaconda3/include >> >> >> -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/work=/usr/local/src/conda/hdf5_split-1.10.5 >> >> -fdebug-prefix-map=/home/gergely/anaconda3=/usr/local/src/conda-prefix >> >> H5 C++ Flags: -pedantic -Wall -W -Wundef -Wshadow >> >> -Wpointer-arith -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion >> >> -Wredundant-decls -Winline -Wsign-promo -Woverloaded-virtual >> >> -Wold-style-cast -Weffc++ -Wreorder -Wnon-virtual-dtor >> >> -Wctor-dtor-privacy -Wabi -finline-functions -s -O >> >> AM C++ Flags: >> >> Shared C++ Library: yes >> >> Static C++ Library: yes >> >> >> >> Java: no >> >> >> >> >> >> Features: >> >> --------- >> >> Parallel HDF5: no >> >> Parallel Filtered Dataset Writes: no >> >> Large Parallel I/O: no >> >> High-level library: yes >> >> Threadsafety: yes >> >> Default API mapping: v110 >> >> With deprecated public symbols: yes >> >> I/O filters (external): deflate(zlib) >> >> MPE: no >> >> Direct VFD: no >> >> dmalloc: no >> >> Packages w/ extra debug output: none >> >> API tracing: no >> >> Using memory checker: yes >> >> Memory allocation sanity checks: no >> >> Function stack tracing: no >> >> Strict file format checks: no >> >> Optimization instrumentation: no >> >> >> >> On Tue, Dec 17, 2019 at 8:35 AM Billy Poon <BKPoon(a)lbl.gov> wrote: >> >> > >> >> > Hi Gergely, >> >> > >> >> > Let me build the test package tomorrow. All the gritty details for >> building with conda is being finalized and the official documentation will >> be updated to describe the steps. It would be too confusing to keep >> changing the documentation as the process evolves. You do have the general >> process, though, which is summarized as follows. >> >> > >> >> > 1) Installing dependencies. The cctbx_dependencies metapackage was >> an initial approach for managing the CCTBX dependencies, but after >> contacting the conda-forge folks, they recommended using the --only-deps >> flag. So when the CCTBX conda package is available, you'll be able to get a >> set of dependencies with, >> >> > >> >> > conda install -c conda-forge --only-deps cctbx >> >> > >> >> > By default, the https://urldefense.proofpoint.com/v2/url?u=http-3A__bootstrap.py&d=DwICAg&c… file will automatically install a set >> of dependencies in the "conda_base" directory (and a conda installation if >> one is not found). It just uses standard conda environment files located in >> libtbx/auto_build/conda_envs, so you do not need to install >> cctbx_dependencies as a separate step. The environment files avoid channel >> issues by explicitly defining the channel to pull the packages from and the >> cctbx channel just stores copies of packages from conda-forge. There were >> issues earlier where the conda-forge packages would sometimes be moved to a >> different label. The --use-conda flag also accepts a path to $CONDA_PREFIX >> if you want to use a specific environment for testing. >> >> > >> >> > 2) Building. The https://urldefense.proofpoint.com/v2/url?u=http-3A__bootstrap.py&d=DwICAg&c… file handles that with SCons. >> >> > >> >> > 3) Running. After building, there should be a https://urldefense.proofpoint.com/v2/url?u=http-3A__setpaths.sh&d=DwICAg&c=… (and .csh) >> file that adds build/bin to your path. The build/bin directory has our >> dispatchers, which are just scripts that set up the environment variables >> for you. This prevents other programs from loading our libraries, whose >> versions may conflict. You should see that there is a "python" dispatcher, >> which is a convenience for developers. Otherwise, you can use >> libtbx.python, which will be able to import CCTBX modules. >> >> > >> >> > The running part is where the conda package for CCTBX will be >> different than this build. Since our Python files and extensions modules >> will be in the "site-packages" directory for Python, the PYTHONPATH >> variable will not be needed (and conda suggests that that variable not be >> set). The other CCTBX libraries will be in $CONDA_PREFIX/lib, so >> LD_LIBRARY_PATH is not needed. In an active environment, PATH will already >> be modified. And then our LIBTBX_BUILD directory can be set to sys.prefix. >> >> > >> >> > So with the conda package, you would only need to activate your >> conda environment and CCTBX should integrate with other conda packages. >> What is the conflict with hdf5? That's something that should be fixed. >> Thanks! >> >> > >> >> > -- >> >> > Billy K. Poon >> >> > Research Scientist, Molecular Biophysics and Integrated Bioimaging >> >> > Lawrence Berkeley National Laboratory >> >> > 1 Cyclotron Road, M/S 33R0345 >> >> > Berkeley, CA 94720 >> >> > Tel: (510) 486-5709 >> >> > Fax: (510) 486-5909 >> >> > Web: https://urldefense.proofpoint.com/v2/url?u=https-3A__phenix-2Donline.org&d=… >> >> > >> >> > >> >> > On Mon, Dec 16, 2019 at 2:53 AM Gergely Katona <gkatona(a)gmail.com> >> wrote: >> >> >> >> >> >> Dear Billy, >> >> >> >> >> >> Thank you for this update and for your efforts! I found a solution >> and >> >> >> indeed most things already work in anaconda3. The steps I took (even >> >> >> if these instructions will have short expiry date): >> >> >> >> >> >> Modified .condarc with: >> >> >> channels: >> >> >> - cctbx >> >> >> - conda-forge >> >> >> - defaults >> >> >> >> >> >> run >> >> >> conda conda install cctbx_dependencies python=3.6 >> >> >> >> >> >> I expect this will work without python=3.6 in the near future. >> >> >> >> >> >> Then compiling cctbx with anaconda3 python went without any problem >> >> >> when using these flags: >> >> >> python https://urldefense.proofpoint.com/v2/url?u=http-3A__bootstrap.py&d=DwICAg&c… --use-conda --python3 --nproc=12 >> >> >> >> >> >> Then I probably did the unorthodox thing and sourced these >> directories: >> >> >> >> >> >> setenv LIBTBX_BUILD /home/gergely/cctbx/build >> >> >> setenv PATH ${PATH}:/home/gergely/cctbx/build/bin >> >> >> setenv PYTHONPATH >> >> >> >> /home/gergely/cctbx/modules/cctbx_project:/home/gergely/cctbx/modules:/home/gergely/cctbx/modules/cctbx_project/boost_adaptbx:/home/gergely/cctbx/build/lib:/home/gergely/cctbx/conda_base/lib/python3.6/site-packages:$PYTHONPATH >> >> >> setenv LD_LIBRARY_PATH >> >> >> >> /home/gergely/cctbx/conda_base/lib:/home/gergely/cctbx/build/lib:$LD_LIBRARY_PATH >> >> >> >> >> >> There is probably a better way to put this into conda environment. >> >> >> With these steps I could run one of my scripts depending on cctbx. >> The >> >> >> only problem I found is that hdf5 library had conflict with another >> >> >> package in conda, but I does not find this as a showstopper. >> >> >> >> >> >> Best wishes, >> >> >> >> >> >> Gergely >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> On Fri, Dec 13, 2019 at 7:23 PM Billy Poon <BKPoon(a)lbl.gov> wrote: >> >> >> > >> >> >> > Hi Gergely, >> >> >> > >> >> >> > It's still a work in progress. I'm sorting out some Windows >> issues right now. I can probably build a test package on a separate channel >> for people that want to test it (let's say next week?). I'll provide >> instructions, but basically, the test conda package will be in its own >> separate channel and the dependencies will be pulled from the conda-forge >> channel. I want most things to be working correctly on Python 2.7, 3.6, >> 3.7, and 3.8 on all 3 platforms. >> >> >> > >> >> >> > Thanks! >> >> >> > >> >> >> > -- >> >> >> > Billy K. Poon >> >> >> > Research Scientist, Molecular Biophysics and Integrated Bioimaging >> >> >> > Lawrence Berkeley National Laboratory >> >> >> > 1 Cyclotron Road, M/S 33R0345 >> >> >> > Berkeley, CA 94720 >> >> >> > Tel: (510) 486-5709 >> >> >> > Fax: (510) 486-5909 >> >> >> > Web: https://urldefense.proofpoint.com/v2/url?u=https-3A__phenix-2Donline.org&d=… >> >> >> > >> >> >> > >> >> >> > On Fri, Dec 13, 2019 at 5:44 AM Gergely Katona <gkatona(a)gmail.com> >> wrote: >> >> >> >> >> >> >> >> Dear Billy, >> >> >> >> >> >> >> >> This sounds very promising and exciting. I am not sure if cctbx >> is >> >> >> >> already functional as a conda package in anaconda3 (Linux) or >> this is >> >> >> >> still work in progress. My technical expertise does not allow me >> to >> >> >> >> tell the difference. What I tried: >> >> >> >> >> >> >> >> Fresh install of anaconda3. Adding - cctbx and - conda-forge to >> >> >> >> .condarc . Installing pyside2 with conda. Running conda install >> >> >> >> conda_dependencies . I get a lot package version conflict, and I >> >> >> >> cannot import cctbx or iotbx to anaconda python. Am I following >> the >> >> >> >> right instructions? Or it is too early to expect that cctbx >> works when >> >> >> >> installed through conda? >> >> >> >> >> >> >> >> Best wishes, >> >> >> >> >> >> >> >> Gergely >> >> >> >> >> >> >> >> On Wed, Nov 27, 2019 at 3:56 PM Billy Poon <BKPoon(a)lbl.gov> >> wrote: >> >> >> >> > >> >> >> >> > Hi all, >> >> >> >> > >> >> >> >> > For a brief update, I have submitted a recipe for cctbxlite to >> conda-forge (https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_conda-2Dfor… ) >> and support for Python 3.7 and 3.8 is being added ( >> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_cctbx_cctbx… ). With some fixes for >> Windows (https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_cctbx_cctbx… ), all platforms >> (macOS, linux, and Windows) can build for Python 2.7, 3.6, 3.7, and 3.8. >> Some additional changes will be needed to get Windows to work with Python 3 >> and for tests to pass with Boost 1.70.0. That will enable the conda-forge >> recipe to build for all platforms and for all supported versions of Python. >> >> >> >> > >> >> >> >> > Currently, the conda-forge recipe will install into the conda >> python and cctbx imports can be done without sourcing the environment >> scripts. It looks like a lot of the environment variables being set in the >> dispatchers can be removed since the Python files and C++ extensions are in >> the right places. I'll update the libtbx_env file so that commands that >> load the environment can work correctly. >> >> >> >> > >> >> >> >> > -- >> >> >> >> > Billy K. Poon >> >> >> >> > Research Scientist, Molecular Biophysics and Integrated >> Bioimaging >> >> >> >> > Lawrence Berkeley National Laboratory >> >> >> >> > 1 Cyclotron Road, M/S 33R0345 >> >> >> >> > Berkeley, CA 94720 >> >> >> >> > Tel: (510) 486-5709 >> >> >> >> > Fax: (510) 486-5909 >> >> >> >> > Web: https://urldefense.proofpoint.com/v2/url?u=https-3A__phenix-2Donline.org&d=… >> >> >> >> > >> >> >> >> > >> >> >> >> > On Sun, Aug 25, 2019 at 2:33 PM Tristan Croll <tic20(a)cam.ac.uk> >> wrote: >> >> >> >> >> >> >> >> >> >> Hi Luc, >> >> >> >> >> >> >> >> >> >> That sounds promising. From there, I?d need to work out how >> to make a fully-packaged installer (basically a modified wheel file) for >> the ChimeraX ToolShed - the aim is for the end user to not have to worry >> about any of this. That adds a couple of complications - e.g. $LIBTBX_BUILD >> would need to be set dynamically before first import - but doesn?t seem >> insurmountable. >> >> >> >> >> >> >> >> >> >> Thanks, >> >> >> >> >> >> >> >> >> >> Tristan >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> Tristan Croll >> >> >> >> >> Research Fellow >> >> >> >> >> Cambridge Institute for Medical Research >> >> >> >> >> University of Cambridge CB2 0XY >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> > On 25 Aug 2019, at 18:31, Luc Bourhis < >> luc_j_bourhis(a)mac.com> wrote: >> >> >> >> >> > >> >> >> >> >> > Hi Tristan, >> >> >> >> >> > >> >> >> >> >> > cctbx could be built to use your ChimeraX python, now that >> cctbx is moving to Python 3. The option ?with-python is there for that with >> the bootstrap script. The specific environment setup boil down to setting >> two environment variable LIBTBX_BUILD and either LD_LIBRARY_PATH on Linux, >> PATH on Win32, or DYLIB_LIBRARY_PATH on MacOS. If you work within a >> framework such as ChimeraX, that should not be difficult to ensure those >> two variables are set. >> >> >> >> >> > >> >> >> >> >> > Best wishes, >> >> >> >> >> > >> >> >> >> >> > Luc >> >> >> >> >> > >> >> >> >> >> > >> >> >> >> >> >> On 23 Aug 2019, at 19:02, Tristan Croll <tic20(a)cam.ac.uk> >> wrote: >> >> >> >> >> >> >> >> >> >> >> >> To add my two cents on this: probably the second-most >> common question I've had about ISOLDE's implementation is, "why didn't you >> use CCTBX?". The honest answer to that is, "I didn't know how." >> >> >> >> >> >> >> >> >> >> >> >> Still don't, really - although the current developments >> are rather promising. The problem I've faced is that CCTBX was designed as >> its own self-contained Python (2.7, until very recently) environment, with >> its own interpreter and a lot of very specific environment setup. Meanwhile >> I'm developing ISOLDE in ChimeraX, which is *also* its own self-contained >> Python (3.7) environment. To plug one into the other in that form... well, >> I don't think I'm a good enough programmer to really know where to start. >> >> >> >> >> >> >> >> >> >> >> >> The move to Conda and a more modular CCTBX architecture >> should make a lot more possible in that direction. Pip would be even better >> for me personally (ChimeraX can install directly from the PyPI, but doesn't >> interact with Conda) - but I understand pretty well the substantial >> challenge that would amount to (not least being that the PyPI imposes a >> limit - around 100MB from memory? - on the size of an individual package). >> >> >> >> >> >> >> >> >> >> >> >> Best regards, >> >> >> >> >> >> >> >> >> >> >> >> Tristan >> >> >> >> >> >> >> >> >> >> >> >>> On 2019-08-23 09:28, Luc Bourhis wrote: >> >> >> >> >> >>> Hi Graeme, >> >> >> >> >> >>> Yes, I know. But ?black" is a program doing a very >> particular task >> >> >> >> >> >>> (code formatting from the top of my head). Requiring to >> use a wrapper >> >> >> >> >> >>> for python itself is another level. But ok, I think I am >> mellowing to >> >> >> >> >> >>> the idea after all! Talking with people around me, and >> extrapolating, >> >> >> >> >> >>> I would bet that, right now, a great majority of people >> interested by >> >> >> >> >> >>> cctbx in pip have already used the cctbx, so they know >> about the >> >> >> >> >> >>> Python wrapper, and they would not be too sanguine about >> that. My >> >> >> >> >> >>> concern is for the future, when pip will be the first >> time some people >> >> >> >> >> >>> use cctbx. Big fat warning notices on PyPI page and a >> better error >> >> >> >> >> >>> message when cctbx fails because LIBTBX_BUILD is not set >> would be >> >> >> >> >> >>> needed but that could be all right. >> >> >> >> >> >>> If we do a pip installer, we should aim at a minimal >> install: cctbx, >> >> >> >> >> >>> iotbx and their dependencies, and that?s it. >> >> >> >> >> >>> Best wishes, >> >> >> >> >> >>> Luc >> >> >> >> >> >>>> On 23 Aug 2019, at 07:17, Graeme.Winter(a)Diamond.ac.uk < >> Graeme.Winter(a)diamond.ac.uk> wrote: >> >> >> >> >> >>>> Without discussing the merits of this or whether we >> _choose_ to make the move to supporting PIP, I am certain it would be >> _possible_ - many other packages make dispatcher scripts when you pip >> install them e.g. >> >> >> >> >> >>>> Silver-Surfer rescale_f2 :) $ which black; cat $(which >> black) >> >> >> >> >> >>>> >> /Library/Frameworks/Python.framework/Versions/3.6/bin/black >> >> >> >> >> >>>> >> #!/Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6 >> >> >> >> >> >>>> # -*- coding: utf-8 -*- >> >> >> >> >> >>>> import re >> >> >> >> >> >>>> import sys >> >> >> >> >> >>>> from black import main >> >> >> >> >> >>>> if __name__ == '__main__': >> >> >> >> >> >>>> sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', >> sys.argv[0]) >> >> >> >> >> >>>> sys.exit(main()) >> >> >> >> >> >>>> So we _could_ work around the absence of LIBTBX_BUILD >> etc. in the system. Whether or not we elect to do the work is a different >> question, and it seems clear that here are very mixed opinions on this. >> >> >> >> >> >>>> Best wishes Graeme >> >> >> >> >> >>>> On 23 Aug 2019, at 01:21, Luc Bourhis < >> luc_j_bourhis(a)mac.com<mailto:[email protected]>> wrote: >> >> >> >> >> >>>> Hi, >> >> >> >> >> >>>> Even if we managed to ship our the boost dynamic >> libraries with pip, it would still not be pip-like, as we would still need >> our python wrappers to set LIBTBX_BUILD and LD_LIBRARY_PATH. Normal pip >> packages work with the standard python exe. LD_LIBRARY_PATH, we could get >> around that by changing the way we compile, using -Wl,-R, which is the >> runtime equivalent of build time -L. That?s a significant change that would >> need to be tested. But there is no way around setting LIBTBX_BUILD right >> now. Leaving that to the user is horrible. Perhaps there is a way to hack >> libtbx/https://urldefense.proofpoint.com/v2/url?u=http-3A__env-5Fconfig.py&… so that we can hardwire LIBTBX_BUILD in there when pip >> installs? >> >> >> >> >> >>>> Best wishes, >> >> >> >> >> >>>> Luc >> >> >> >> >> >>>> On 16 Aug 2019, at 22:47, Luc Bourhis < >> luc_j_bourhis(a)mac.com<mailto:[email protected]>> wrote: >> >> >> >> >> >>>> Hi, >> >> >> >> >> >>>> I did look into that many years ago, and even toyed with >> building a pip installer. What stopped me is the exact conclusion you >> reached too: the user would not have the pip experience he expects. You are >> right that it is a lot of effort but is it worth it? Considering that >> remark, I don?t think so. Now, Conda was created specifically to go beyond >> pip pure-python-only support. Since cctbx has garnered support for Conda, >> the best avenue imho is to go the extra length to have a package on >> https://urldefense.proofpoint.com/v2/url?u=http-3A__Anaconda.org&d=DwICAg&c… <https://urldefense.proofpoint.com/v2/url?u=http-3A__anaconda.org_&d=DwICAg&… >, and then to advertise it hard to >> every potential user out there. >> >> >> >> >> >>>> Best wishes, >> >> >> >> >> >>>> Luc >> >> >> >> >> >>>> On 16 Aug 2019, at 21:45, Aaron Brewster < >> asbrewster(a)lbl.gov<mailto:[email protected]>> wrote: >> >> >> >> >> >>>> Hi, to avoid clouding Dorothee's documentation email >> thread, which I think is a highly useful enterprise, here's some thoughts >> about putting cctbx into pip. Pip doesn't install non-python dependencies >> well. I don't think boost is available as a package on pip (at least the >> package version we use). wxPython4 isn't portable through pip ( >> https://urldefense.proofpoint.com/v2/url?u=https-3A__wiki.wxpython.org_How-… ). >> MPI libraries are system dependent. If cctbx were a pure python package, >> pip would be fine, but cctbx is not. >> >> >> >> >> >>>> All that said, we could build a manylinux1 version of >> cctbx and upload it to PyPi (I'm just learning about this). For a pip >> package to be portable (which is a requirement for cctbx), it needs to >> conform to PEP513, the manylinux1 standard ( >> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.python.org_dev_pep… ). For example, numpy is built >> according to this standard (see https://urldefense.proofpoint.com/v2/url?u=https-3A__pypi.org_project_numpy… , >> where you'll see the manylinux1 wheel). Note, the manylinux1 standard is >> built with Centos 5.11 which we no longer support. >> >> >> >> >> >>>> There is also a manylinux2010 standard, which is based >> on Centos 6 (https://urldefense.proofpoint.com/v2/url?u=https-3A__www.python.org_dev_pep… ). This is likely >> a more attainable target (note though by default C++11 is not supported on >> Centos 6). >> >> >> >> >> >>>> If we built a manylinuxX version of cctbx and uploaded >> it to PyPi, the user would need all the non-python dependencies. There's >> no way to specify these in pip. For example, cctbx requires boost 1.63 or >> better. The user will need to have it in a place their python can find it, >> or we could package it ourselves and supply it, similar to how the pip h5py >> package now comes with an hd5f library, or how the pip numpy package >> includes an openblas library. We'd have to do the same for any packages we >> depend on that aren't on pip using the manylinux standards, such as >> wxPython4. >> >> >> >> >> >>>> Further, we need to think about how dials and other >> cctbx-based packages interact. If pip install cctbx is set up, how does >> pip install dials work, such that any dials shared libraries can find the >> cctbx libraries? Can shared libraries from one pip package link against >> libraries in another pip package? Would each package need to supply its >> own boost? Possibly this is well understood in the pip field, but not by >> me :) >> >> >> >> >> >>>> Finally, there's the option of providing a source pip >> package. This would require the full compiler toolchain for any given >> platform (macOS, linux, windows). These are likely available for >> developers, but not for general users. >> >> >> >> >> >>>> Anyway, these are some of the obstacles. Not saying it >> isn't possible, it's just a lot of effort. >> >> >> >> >> >>>> Thanks, >> >> >> >> >> >>>> -Aaron >> >> >> >> >> >>>> _______________________________________________ >> >> >> >> >> >>>> cctbxbb mailing list >> >> >> >> >> >>>> cctbxbb(a)phenix-online.org<mailto: >> cctbxbb(a)phenix-online.org> >> >> >> >> >> >>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… >> >> >> >> >> >>>> _______________________________________________ >> >> >> >> >> >>>> cctbxbb mailing list >> >> >> >> >> >>>> cctbxbb(a)phenix-online.org<mailto: >> cctbxbb(a)phenix-online.org> >> >> >> >> >> >>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… >> >> >> >> >> >>>> _______________________________________________ >> >> >> >> >> >>>> cctbxbb mailing list >> >> >> >> >> >>>> cctbxbb(a)phenix-online.org<mailto: >> cctbxbb(a)phenix-online.org> >> >> >> >> >> >>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… >> >> >> >> >> >>>> -- >> >> >> >> >> >>>> This e-mail and any attachments may contain >> confidential, copyright and or privileged material, and are for the use of >> the intended addressee only. If you are not the intended addressee or an >> authorised recipient of the addressee please notify us of receipt by >> returning the e-mail and do not use, copy, retain, distribute or disclose >> the information in or attached to the e-mail. >> >> >> >> >> >>>> Any opinions expressed within this e-mail are those of >> the individual and not necessarily of Diamond Light Source Ltd. >> >> >> >> >> >>>> Diamond Light Source Ltd. cannot guarantee that this >> e-mail or any attachments are free from viruses and we cannot accept >> liability for any damage which you may sustain as a result of software >> viruses which may be transmitted in or with the message. >> >> >> >> >> >>>> Diamond Light Source Limited (company no. 4375679). >> Registered in England and Wales with its registered office at Diamond >> House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 >> 0DE, United Kingdom >> >> >> >> >> >>>> _______________________________________________ >> >> >> >> >> >>>> cctbxbb mailing list >> >> >> >> >> >>>> cctbxbb(a)phenix-online.org >> >> >> >> >> >>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… >> >> >> >> >> >>> _______________________________________________ >> >> >> >> >> >>> cctbxbb mailing list >> >> >> >> >> >>> cctbxbb(a)phenix-online.org >> >> >> >> >> >>> https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> >> >> >> >> >> cctbxbb mailing list >> >> >> >> >> >> cctbxbb(a)phenix-online.org >> >> >> >> >> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… >> >> >> >> >> > >> >> >> >> >> > >> >> >> >> >> > _______________________________________________ >> >> >> >> >> > cctbxbb mailing list >> >> >> >> >> > cctbxbb(a)phenix-online.org >> >> >> >> >> > https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> >> >> >> >> cctbxbb mailing list >> >> >> >> >> cctbxbb(a)phenix-online.org >> >> >> >> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… >> >> >> >> > >> >> >> >> > _______________________________________________ >> >> >> >> > cctbxbb mailing list >> >> >> >> > cctbxbb(a)phenix-online.org >> >> >> >> > https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> -- >> >> >> >> Gergely Katona, PhD >> >> >> >> Associate Professor >> >> >> >> Department of Chemistry and Molecular Biology, University of >> Gothenburg >> >> >> >> Box 462, 40530 G?teborg, Sweden >> >> >> >> Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910 >> >> >> >> Web: https://urldefense.proofpoint.com/v2/url?u=http-3A__katonalab.eu&d=DwICAg&c… , Email: gergely.katona(a)gu.se >> >> >> >> >> >> >> >> _______________________________________________ >> >> >> >> cctbxbb mailing list >> >> >> >> cctbxbb(a)phenix-online.org >> >> >> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… >> >> >> > >> >> >> > _______________________________________________ >> >> >> > cctbxbb mailing list >> >> >> > cctbxbb(a)phenix-online.org >> >> >> > https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… >> >> >> >> >> >> >> >> >> >> >> >> -- >> >> >> Gergely Katona, PhD >> >> >> Associate Professor >> >> >> Department of Chemistry and Molecular Biology, University of >> Gothenburg >> >> >> Box 462, 40530 G?teborg, Sweden >> >> >> Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910 >> >> >> Web: https://urldefense.proofpoint.com/v2/url?u=http-3A__katonalab.eu&d=DwICAg&c… , Email: gergely.katona(a)gu.se >> >> >> >> >> >> _______________________________________________ >> >> >> cctbxbb mailing list >> >> >> cctbxbb(a)phenix-online.org >> >> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… >> >> > >> >> > _______________________________________________ >> >> > cctbxbb mailing list >> >> > cctbxbb(a)phenix-online.org >> >> > https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… >> >> >> >> >> >> >> >> -- >> >> Gergely Katona, PhD >> >> Associate Professor >> >> Department of Chemistry and Molecular Biology, University of Gothenburg >> >> Box 462, 40530 G?teborg, Sweden >> >> Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910 >> >> Web: https://urldefense.proofpoint.com/v2/url?u=http-3A__katonalab.eu&d=DwICAg&c… , Email: gergely.katona(a)gu.se >> >> >> >> _______________________________________________ >> >> cctbxbb mailing list >> >> cctbxbb(a)phenix-online.org >> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… >> > >> > _______________________________________________ >> > cctbxbb mailing list >> > cctbxbb(a)phenix-online.org >> > https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… >> >> >> >> -- >> Gergely Katona, PhD >> Associate Professor >> Department of Chemistry and Molecular Biology, University of Gothenburg >> Box 462, 40530 G?teborg, Sweden >> Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910 >> Web: https://urldefense.proofpoint.com/v2/url?u=http-3A__katonalab.eu&d=DwICAg&c… , Email: gergely.katona(a)gu.se >> >> _______________________________________________ >> cctbxbb mailing list >> cctbxbb(a)phenix-online.org >> https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… >> >

6 years, 1 month

Re: [phenixbb] phenix.map_to_model input mtz file failure --caution on using map_to_model with X-ray data

by Dale Tronrud

First we have to agree on exactly what we are talking about. I presumed we were talking about real space refinement against an experimental map such as one gets in cryo-EM. In that case there are no Fobs. Reciprocal space is a fiction and should be avoided. If you are working, instead, with a 2Fo-Fc map then just do reciprocal space refinement. I don't know of any reason to do whole-molecule real space refinement when you are working with crystal diffraction data. Reciprocal space is where the experiment lives and the analysis should be done there. In cases of model building it is computationally quicker to do a local real space refinement to touch up a model just so you can see if it looks reasonable before going back into reciprocal space. This real space refinement is quick-and-dirty and any flaws will be erased by the proper reciprocal space refinement that follows. As for "neighborhood correlation" I was thinking of cryo-EM maps. Since the individual measurements (pictures) are real space in nature, I can't imagine an experimental error in the voltage of one voxel wouldn't tend to show up similarly in its neighbors. The whole group of voxels will be illuminated by electrons who all had very similar histories passing through the microscope. We have similar situations with diffraction data. A reflection whose neighbor is in a shadow has a much higher chance of being shadowed itself. Our spots, however, are much further apart on the detector than the voxels of an EM image. There is another type of correlation that is probably more important. Our diffraction spots are separated enough that you cannot predict the intensity of a reflection based on its neighbors. You can make a very good prediction of the darkness of a voxel based on its neighbors. If you leave out one voxel, as a test set member, you could easily deduce its hidden value without even building a molecular model - just interpolate. You can't do that with diffraction data. This means if you want to leave out a chunk of map data for a test set you have to pull out a big enough piece (many contiguous voxels) that you can't deduce anything about their opaqueness from the remaining image. To do this you have to know something about how the microscope works. Dale Tronrud On 6/13/2017 4:08 PM, Edward A. Berry wrote: >> To unbias you would have to calculate a >> new map with current Fcalc's for every iteration of the model, but this >> method would not take into account the neighborhood correlation present >> in experimental maps.) > > Thanks, Dale, > Could you explain this "neighborhood correlation"? > > My very simple (maybe too simple) understanding of how real space would > bias reflections is as follows: > > You make a map using phases (and Fc?) from the current model and Fobs. > But you omit the free set. > > Now if you take the fourier transform of that unmodified map, you would > get back > exactly the coefficients you put in: 2Fo-Fc (?) for the working > reflections, > and zero for the free set. > > Then you make modifications to the model to make its density match as > nearly > as possible the density of the map. If you were able to make the density of > the model exactly match that of the map, then the Fc for the model would > be that of the map. > > Of course you can never make the density of the model exactly match that of > the map - modelization is the severest form of density modification. > But, to the extent that you make the model's density more nearly like that > of the map, the Fourier transform of the new model will be more > like that of the map. > > That means for the working reflections, Fc will get closer to 2Fo-Fc > which brings them closer to Fo; and the R-work improves. > (If there is error in the Fobs, that will be reflected in the map, > and the Fcalc of the model will tend toward these eromeous Fobs > (fitting the error) and Rwork will get better than it should (bias).) > Free reflections will move closer to zero, and most likely Rfree > will get worse. > > I think that's all consistent with what you wrote, but then > I had the impression that the bias could be prevented by making the > map with Fc for the test set (proposed in an old paper by Ivan > Rayment. That way the free reflections get are following the > process by their coupling to neighboring reflections in reciprocal > space (neighborhood correlation?), the same way they do in reciprocal > space refinement, rather than the Fobs being used. The information > in these free Fcalc is coming from the neighboring working reflections > due to redundancy of information in a finely sampled molecular transform. > > Ed > > > > On 06/13/2017 05:40 PM, Dale Tronrud wrote: >> >> >> On 6/13/2017 12:30 PM, Edward A. Berry wrote: >>> Thanks, Pavel, >>> I really appreciate your taking the time to generate the example. >>> >>> While I agree with Tim and Ian that refinement to convergence should >>> remove the bias making it perhaps not a serious problem, my question was >>> in fact whether there is any bias immediately after the refinement. >>> >>> I will need to study this example a bit, but one thing I notice is >>> that you are doing exactly what I was guessing, comparing Rfree >>> after real-space refinement with and without using the free set. >>> Then, I still think, we >>>>>> have to think about how much of that difference results from >>>>>> bias towards the observed values (when the reflections are included) >>>>>> and >>>>>> how much is from bias towards zero (when the free set is excluded). >>> >> Of course the model is refined as though the test set Fourier >> components were equal to zero. In reciprocal space refinement when you >> leave a reflection out of the "sum over all reflections" when >> calculating the difference map you are saying that you have no opinion >> about the amplitude of that reflection. When you calculate a real space >> map from Fourier coefficients you can't not have an opinion, i.e. you >> can't leave a term out of the sum you can only set that term to zero. >> If your model produces a prediction for that term which is not equal to >> zero it will be penalized. (If you set that term to Fcalc you tie your >> model to its starting point. To unbias you would have to calculate a >> new map with current Fcalc's for every iteration of the model, but this >> method would not take into account the neighborhood correlation present >> in experimental maps.) >> >> What this means is that Rfree is not a meaningful stat for assessing >> overfitting of real space refinement. This is hardly a surprise. A >> test of a refinement protocol has to be based on the mathematics of that >> protocol, not the protocol you happened to have used yesterday. If you >> want an unbiased estimate of the quality of a real space refinement you >> have to leave out a region of the map and then see how well the model >> fits that region. This is harder to do in an automated fashion and >> there will be a lot of caveats about your results (e.g. you know about >> the ability to fit one region but does that generalize to other areas?). >> If you recall there are a lot of caveats about Rfree too - we have just >> stopped worrying about them. (e.g. low resolution vrs high resolution >> reflections, choosing based on shells or randomly, what to do about >> ncs...) >> >> I think you should consider yourself on the wrong track if you come >> up with a statistical test, but haven't given any thought to the actual >> experiment that produced your map. >> >> Dale Tronrud >> >>> Things I need to look at- >>> What are R and R-free for the original refined model >>> What are R and R-free after shaking (did RSR lower R but not Rfree, or >>> did it raise Rfree? >>> What if RSR is done using a map made with fill-in strategy? >>> >>> Ed >>> >>> On 06/13/2017 02:15 PM, Pavel Afonine wrote: >>>> Hi Ed, >>>> >>>> Including free-r reflections into map calculation and then using such >>>> map in real-space refinement of entire model will affect Rfree. Here >>>> is a simple example that illustrates my statement, step-by-step: >>>> >>>> 1) Get data and model from PDB: >>>> >>>> phenix.fetch_pdb 1f8t --mtz >>>> >>>> 2) Compute two 2mFo-DFc maps: one includes all reflections the other >>>> one has no free-r terms: >>>> >>>> phenix.python run.py 1f8t.{pdb,mtz} >>>> >>>> This will create an MTZ file (map_coeffs.mtz) that contains Fourier >>>> map coefficients for both maps. >>>> >>>> 3) Shake model a bit: >>>> >>>> phenix.dynamics 1f8t.pdb number_of_steps=500 >>>> >>>> 4) Run real-space refinement using two maps: >>>> >>>> phenix.real_space_refine map_coeffs.mtz 1f8t_shaken.pdb >>>> label="work,PHIwork" ncs_constraints=false output.file_name_prefix=work >>>> >>>> phenix.real_space_refine map_coeffs.mtz 1f8t_shaken.pdb >>>> label="all,PHIall" ncs_constraints=false output.file_name_prefix=all >>>> >>>> 5) Compute R-factors using data and real-space refined models: >>>> >>>> phenix.model_vs_data 1f8t.mtz all_real_space_refined.pdb >>>> r_work(re-computed) : 0.2419 >>>> r_free(re-computed) : 0.2441 >>>> >>>> phenix.model_vs_data 1f8t.mtz work_real_space_refined.pdb >>>> r_work(re-computed) : 0.2444 >>>> r_free(re-computed) : 0.2756 >>>> >>>> The result is self-explicable and is inline with Tom's reply to Wei. >>>> >>>> All files necessary to reproduce calculations above are here: >>>> http://cci.lbl.gov/~afonine/tmp/ >>>> >>>> All the best, >>>> Pavel >>>> >>>> >>>> On 6/8/17 10:05, Tim Gruene wrote: >>>>> Hi Ed, >>>>> >>>>> including the 'free' reflections in the map for modelling does not >>>>> taint the >>>>> value of Rfree. That is a misconception that i s very persistent (as >>>>> prejudice >>>>> usually are). I believe it was Ian Tickle who formulated that when >>>>> you simply >>>>> refine long enough towards convergence, all reflections excluded from >>>>> refinement >>>>> will become independent, i.e. you can assign a new set for Rfree >>>>> every time >>>>> you refine, if you wish so. >>>>> >>>>> This concept is the reason why Rcomplete (the "better" equivalent to >>>>> Rfree for >>>>> small data sets with < 10,000 unique reflections), introduced by Axel >>>>> Brunger, >>>>> works, as we could demonstrate in doi: 10.1073/pnas.1502136112 >>>>> >>>>> So nothing to worry about when including all reflections in map >>>>> calculations. >>>>> >>>>> Cheers, >>>>> Tim >>>>> >>>>> On Thursday, June 8, 2017 12:42:53 PM CEST Edward A. Berry wrote: >>>>>> Hi, Tom, >>>>>> Please forgive what may be a silly question from an outsider who >>>>>> hasn't >>>>>> really kept up with the crystallography literature or even all the >>>>>> Phenix >>>>>> newsletters- What is the evidence that including the free set in >>>>>> real space >>>>>> refinement biases R-free of the resulting model? Is this Rfree also >>>>>> biased >>>>>> when map coefficients use "fill-in" for the excluded free >>>>>> reflections (and >>>>>> is that what phenix.remove_free_from_map does?). >>>>>> >>>>>> My point is that literally excluding the free reflections, as >>>>>> opposed to >>>>>> substituting their values with Fc, will bias the free set toward >>>>>> grossly >>>>>> incorrect values (namely zero) and therefore greatly worsen R-free. >>>>>> Thus if >>>>>> the evidence for bias is that you get worse R-free when you >>>>>> exclude the >>>>>> free set, you have to think about how much of that difference >>>>>> results from >>>>>> bias towards the observed values (when the reflections are included) >>>>>> and >>>>>> how much is from bias towards zero (when the free set is excluded). >>>>>> (Again, I realize this may be all very well understood by the >>>>>> crystallography community and properly taken care of in phenix; I'm >>>>>> just >>>>>> asking for my own information) eab >>>>>> >>>>>> On 06/08/2017 07:28 AM, Terwilliger, Thomas Charles wrote: >>>>>>> Hi Wei, >>>>>>> >>>>>>> >>>>>>> I want to give a word of caution about how to use >>>>>>> phenix.map_to_model on >>>>>>> crystallographic data...The bottom line is you should remove the >>>>>>> test set >>>>>>> from your map coefficients before running phenix.map_to model on >>>>>>> X-ray >>>>>>> data. Here is why: >>>>>>> >>>>>>> >>>>>>> phenix.map_to_model uses real-space refinement, which is refinement >>>>>>> against the map. If you supply map coefficients that include your >>>>>>> test >>>>>>> reflections, then you will be refining against data that is in your >>>>>>> test >>>>>>> set. This will make your Rfree invalid when you go back and >>>>>>> refine your >>>>>>> model against the original crystallographic data. >>>>>>> >>>>>>> >>>>>>> To remove the test set from your map coefficients you can use: >>>>>>> >>>>>>> >>>>>>> phenix.remove_free_from_map map_coeffs=my_map_coeffs.mtz >>>>>>> free_in=my_data_file_with_freeR_flags.mtz >>>>>>> mtz_out=my_map_coeffs_no_free.mtz >>>>>>> >>>>>>> >>>>>>> Also note that phenix.map_to_model uses a fixed map (it does not do >>>>>>> density modification). Consequently for most crystallographic >>>>>>> data at >>>>>>> moderate resolution or higher phenix.autobuild is going to do much >>>>>>> better >>>>>>> than phenix.map_to_model. >>>>>>> >>>>>>> >>>>>>> All the best, >>>>>>> >>>>>>> Tom T >>>>>>> >>>>>>> >>>>>>> -------------------------------------------------------------------------- >>>>>>> >>>>>>> >>>>>>> -------------------------------------------------------------------------- >>>>>>> >>>>>>> >>>>>>> -------------------------------------------------------------------------- >>>>>>> >>>>>>> >>>>>>> -------------------------------------------------------------------------- >>>>>>> >>>>>>> >>>>>>> -------------------------------------------------------------------------- >>>>>>> >>>>>>> >>>>>>> -------------------------------------------------------------------------- >>>>>>> >>>>>>> >>>>>>> -------------------------------------------------------------------------- >>>>>>> >>>>>>> >>>>>>> -------------------------------------------------------------------------- >>>>>>> >>>>>>> >>>>>>> -------------------------------------------------------------------------- >>>>>>> >>>>>>> >>>>>>> -------------------------------------------------------------------------- >>>>>>> >>>>>>> >>>>>>> -------------------------------------------------------------------------- >>>>>>> >>>>>>> >>>>>>> -------------------------------------------------------------------------- >>>>>>> >>>>>>> >>>>>>> -------------------------------------------------------------------------- >>>>>>> >>>>>>> >>>>>>> ---------------------------- *From:*[email protected] >>>>>>> <dingding830106(a)163.com> on behalf ofdancingdream(a)163.com >>>>>>> <dancingdream(a)163.com> *Sent:* Tuesday, June 6, 2017 9:16 PM >>>>>>> *To:* Terwilliger, Thomas Charles >>>>>>> *Cc:*[email protected] >>>>>>> *Subject:* Re:Re: [phenixbb] phenix.map_to_model input mtz file >>>>>>> failure >>>>>>> Dear Thomas, >>>>>>> I use CAD to convert the labels from FDM->FWT, PHIDM->PHFWT, then >>>>>>> submit >>>>>>> this job again (without map_coeffs_labels=... ), and everything >>>>>>> seems ok. >>>>>>> Thank you very much for you help. >>>>>>> Best! >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Wei Ding >>>>>>> P.O.Box 603 >>>>>>> The Institute of Physics,Chinese Academy of Sciences >>>>>>> Beijing,China >>>>>>> 100190 >>>>>>> Tel: +86-10-82649083 >>>>>>> >>>>>>> E-mail:[email protected] <mailto:[email protected]> >>>>>>> >>>>>>> At 2017-06-07 10:32:14, "Terwilliger, Thomas Charles" >>>>> <terwilliger(a)lanl.gov> wrote: >>>>>>> Hi Wei, >>>>>>> >>>>>>> >>>>>>> I'm sorry for the trouble! >>>>>>> >>>>>>> >>>>>>> If you supply an MTZ file that has FWT,PHFWT or similar >>>>>>> labels, then >>>>>>> you can skip the "labels=...." statement and it should run. >>>>>>> >>>>>>> >>>>>>> Let me know if that does not work! >>>>>>> All the best, >>>>>>> >>>>>>> Tom T >>>>>>> >>>>>>> >>>>>>> >>>>>>> ---------------------------------------------------------------------- >>>>>>> >>>>>>> >>>>>>> ---------------------------------------------------------------------- >>>>>>> >>>>>>> >>>>>>> ---------------------------------------------------------------------- >>>>>>> >>>>>>> >>>>>>> ---------------------------------------------------------------------- >>>>>>> >>>>>>> >>>>>>> ---------------------------------------------------------------------- >>>>>>> >>>>>>> >>>>>>> ---------------------------------------------------------------------- >>>>>>> >>>>>>> >>>>>>> ---------------------------------------------------------------------- >>>>>>> >>>>>>> >>>>>>> ---------------------------------------------------------------------- >>>>>>> >>>>>>> >>>>>>> ---------------------------------------------------------------------- >>>>>>> >>>>>>> >>>>>>> ---------------------------------------------------------------------- >>>>>>> >>>>>>> >>>>>>> ---------------------------------------------------------------------- >>>>>>> >>>>>>> >>>>>>> ---------------------------------------------------------------------- >>>>>>> >>>>>>> >>>>>>> ---------------------------------------------------------------------- >>>>>>> >>>>>>> >>>>>>> ---------------------------------------------------------------------- >>>>>>> >>>>>>> ---------- *From:*[email protected] >>>>>>> <mailto:[email protected]> >>>>>>> <phenixbb-bounces(a)phenix-online.org >>>>>>> <mailto:[email protected]>> on behalf of >>>>>>> dancingdream(a)163.com <mailto:[email protected]> >>>>>>> <dancingdream(a)163.com <mailto:[email protected]>> *Sent:* >>>>>>> Tuesday, >>>>>>> June 6, 2017 8:19 PM >>>>>>> *To:*[email protected] >>>>>>> <mailto:[email protected]> >>>>>>> *Subject:* [phenixbb] phenix.map_to_model input mtz file >>>>>>> failure >>>>>>> Dear Phenix bb, >>>>>>> I intend to build a initial model by phenix.map_to_model. >>>>>>> And the >>>>>>> command line is as follows: phenix.map_to_model_1.12rc0-2787 >>>>>>> map_coeffs_file=../rep_dm.mtz map_coeffs_labels="'FP,SIGFP' >>>>>>> 'PHIDM' >>>>>>> 'FOMDM'" seq_file=../resolve.seq is_crystal=True >>>>>>> use_sg_symmetry=True density_select=False >>>>>>> truncate_at_d_min=True >>>>>>> and the feedback like this: >>>>>>> Sorry: No initial assignment made for map_coeffs. Labels used: >>>>>>> FP,SIGFP PHIDM FOMDM. Available labels: ['PHIB', 'FOM', >>>>>>> 'HLA,HLB,HLC,HLD', 'FP,SIGFP', 'PHIDM', 'FOMDM', 'FDM', >>>>>>> 'HLADM,HLBDM,HLCDM,HLDDM'] NOTE: grouped labels like >>>>>>> 'FP,SIGFP' must >>>>>>> stay together, >>>>>>> have commas, and have no spaces. If they come from an MTZ >>>>>>> file, >>>>>>> they must be in adjacent columns as well. >>>>>>> Suggested labels to use: PHIDM FOMDM >>>>>>> I try many other input format of map_coeffs_labels, such as >>>>>>> map_coeffs_labels="FP,SIGFP PHIDM FOMDM" >>>>>>> map_coeffs_labels=["FP,SIGFP PHIDM FOMDM"] >>>>>>> ... ... >>>>>>> but the result is the same. Dose anyone can tell me how to fix >>>>>>> this >>>>>>> problem? Thank a lot. >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Wei Ding >>>>>>> P.O.Box 603 >>>>>>> The Institute of Physics,Chinese Academy of Sciences >>>>>>> Beijing,China >>>>>>> 100190 >>>>>>> Tel: +86-10-82649083 >>>>>>> E-mail:[email protected] <mailto:[email protected]> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> phenixbb mailing list >>>>>>> phenixbb(a)phenix-online.org >>>>>>> http://phenix-online.org/mailman/listinfo/phenixbb >>>>>>> Unsubscribe:[email protected] >>>>>> _______________________________________________ >>>>>> phenixbb mailing list >>>>>> phenixbb(a)phenix-online.org >>>>>> http://phenix-online.org/mailman/listinfo/phenixbb >>>>>> Unsubscribe:[email protected] >>>>> >>>>> >>>>> _______________________________________________ >>>>> phenixbb mailing list >>>>> phenixbb(a)phenix-online.org >>>>> http://phenix-online.org/mailman/listinfo/phenixbb >>>>> Unsubscribe:[email protected] >>>> >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://phenix-online.org/mailman/listinfo/phenixbb >>> Unsubscribe: phenixbb-leave(a)phenix-online.org >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org >> >

8 years, 7 months

Re: [cctbxbb] some thoughts on cctbx and pip

by Gergely Katona

I found some other errors when using the test environment. --------------------------------------------------------------------------- RuntimeError Traceback (most recent call last) <ipython-input-1-fe308b345b3f> in <module> 10 import scipy as sp 11 from scipy import linalg ---> 12 import iotbx.pdb 13 import cctbx 14 import pandas as pd ~/anaconda3/envs/test/lib/python3.8/site-packages/iotbx/pdb/__init__.py in <module> 8 9 import iotbx.pdb.records ---> 10 import iotbx.pdb.hierarchy 11 from scitbx import matrix 12 ~/anaconda3/envs/test/lib/python3.8/site-packages/iotbx/pdb/hierarchy.py in <module> 14 from six.moves import cStringIO as StringIO 15 from iotbx.pdb import hy36encode, hy36decode ---> 16 import iotbx.cif.model 17 from cctbx import crystal 18 from libtbx import group_args ~/anaconda3/envs/test/lib/python3.8/site-packages/iotbx/cif/__init__.py in <module> 19 20 from cctbx.array_family import flex ---> 21 from cctbx import miller 22 from iotbx.cif import model, builders, geometry 23 from libtbx.containers import OrderedDict ~/anaconda3/envs/test/lib/python3.8/site-packages/cctbx/miller/__init__.py in <module> 11 12 from cctbx import crystal ---> 13 from cctbx import maptbx 14 from cctbx import sgtbx 15 from cctbx.sgtbx import lattice_symmetry ~/anaconda3/envs/test/lib/python3.8/site-packages/cctbx/maptbx/__init__.py in <module> 15 from libtbx import adopt_init_args 16 from libtbx.utils import Sorry ---> 17 import libtbx.load_env 18 import math 19 import sys, os ~/anaconda3/envs/test/lib/python3.8/site-packages/libtbx/load_env.py in <module> 3 import libtbx.env_config 4 import os ----> 5 libtbx.env = libtbx.env_config.unpickle() 6 libtbx.env.set_os_environ_all_dist() 7 libtbx.env.dispatcher_name = os.environ.get("LIBTBX_DISPATCHER_NAME") ~/anaconda3/envs/test/lib/python3.8/site-packages/libtbx/env_config.py in unpickle() 2736 env = pickle.load(libtbx_env) 2737 if (env.python_version_major_minor != sys.version_info[:2]): -> 2738 env.raise_python_version_incompatible() 2739 if (op.realpath(build_path) != op.realpath(abs(env.build_path))): 2740 env.build_path.reset(build_path) ~/anaconda3/envs/test/lib/python3.8/site-packages/libtbx/env_config.py in raise_python_version_incompatible(self, prev_pvmm) 469 if (prev_pvmm is None): 470 prev_pvmm = "%d.%d" % self.python_version_major_minor --> 471 raise RuntimeError("Python version incompatible with this build:\n" 472 + " Build directory: %s\n" % show_string(abs(self.build_path)) 473 + " Python version used initially: %s\n" % prev_pvmm RuntimeError: Python version incompatible with this build: Build directory: "/home/gergely/anaconda3" Python version used initially: 3.6 Python version in use now: 3.8 Interestingly in the base environment all import worked, but I got an error at: ArgumentError Traceback (most recent call last) <ipython-input-4-5bc71c36e121> in <module> 33 atm_odd.set_b(0) 34 ---> 35 odd.write_pdb_file("bdiff_in_even_000.pdb") #skriver ny pdb med dessa inkluderade 36 dfWBvals=pd.DataFrame(rows_list) ~/anaconda3/lib/python3.6/site-packages/iotbx/pdb/__init__.py in write_pdb_file(self, file_name, open_append, crystal_symmetry, cryst1_z, write_scale_records, append_end, atom_hetatm, sigatm, anisou, siguij) 930 siguij=True): 931 if (crystal_symmetry is Auto): --> 932 crystal_symmetry = self.crystal_symmetry() 933 if (cryst1_z is Auto): 934 cryst1_z = self.extract_cryst1_z_columns() ~/anaconda3/lib/python3.6/site-packages/iotbx/pdb/__init__.py in crystal_symmetry(self, crystal_symmetry, weak_symmetry) 1218 crystal_symmetry=None, 1219 weak_symmetry=False): -> 1220 self_symmetry = self.crystal_symmetry_from_cryst1() 1221 if (self_symmetry is None): 1222 self_symmetry = self._crystal_symmetry_from_cns_remark_sg() ~/anaconda3/lib/python3.6/site-packages/iotbx/pdb/__init__.py in crystal_symmetry_from_cryst1(self) 1195 for line in self.crystallographic_section(): 1196 if (line.startswith("CRYST1")): -> 1197 return cryst1_interpretation.crystal_symmetry(cryst1_record=line) 1198 return None 1199 ~/anaconda3/lib/python3.6/site-packages/iotbx/pdb/cryst1_interpretation.py in crystal_symmetry(cryst1_record) 136 space_group_info=None) 137 space_group_info = categorize(cryst1_record.sgroup).space_group_info( --> 138 unit_cell=u) 139 return crystal.symmetry(unit_cell=u, space_group_info=space_group_info) ~/anaconda3/lib/python3.6/site-packages/iotbx/pdb/cryst1_interpretation.py in space_group_info(self, unit_cell) 85 if (self.symbol is None): return None 86 if (self.category is None): ---> 87 try: return sgtbx.space_group_info(self.symbol) 88 except RuntimeError: return None 89 if (isinstance(unit_cell, uctbx.ext.unit_cell)): ~/anaconda3/lib/python3.6/site-packages/cctbx/sgtbx/__init__.py in __init__(self, symbol, table_id, group, number, space_group_t_den) 100 assert group is None 101 if (table_id is None): --> 102 symbols = space_group_symbols(symbol) 103 else: 104 if (isinstance(symbol, int)): symbol = str(symbol) ArgumentError: Python argument types in space_group_symbols.__init__(space_group_symbols, str) did not match C++ signature: __init__(_object*, int space_group_number) __init__(_object*, int space_group_number, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > extension='') __init__(_object*, int space_group_number, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > extension='', std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > table_id='') __init__(_object*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > symbol) __init__(_object*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > symbol, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > table_id='') Gergely On Fri, Jan 3, 2020 at 1:44 PM Gergely Katona <gkatona(a)gmail.com> wrote: > > Dear Billy, > > I did some tests installing in my base conda was not troublefree in > python 3.8. Running iotbx.fetch_pdb --all --mtz 1kp8 resulted in boost > related error when converting to mtz. Installing into a test > environment went fine with iotbx.fetch_pdb --all --mtz 1kp8 running > successfully. I could add pymc3, jupyter and seaborn and iotbx still > did not break. My LIBTBX_BUILD is not set however in the test > environment, which breaks miller when I was trying to import it. > Manually setting the LIBTBX_BUILD to CONDA_PREFIX (setenv LIBTBX_BUILD > $CONDA_PREFIX) fixes this and one of my script works fine! I will come > back if I find some problems with my other scripts, but so far this > looks promising! > > > Happy new year! > > Gergely > > > > > > On Fri, Dec 20, 2019 at 8:16 PM Billy Poon <BKPoon(a)lbl.gov> wrote: > > > > Hi everyone, > > > > I updated the conda packages on the cctbx-dev channel and there are also now packages for macOS. The old packages have been removed so you can create a new environment with > > > > conda create -n test -c cctbx-dev cctbx python=2.7 > > conda activate test > > > > where "test" is the environment name and 2.7 is the python version. For the python version, you can also pick 3.6, 3.7, or 3.8. I think the latest conda will install 3.8 as the default python if the python argument is not provided. Or install into an existing environment (with python already installed) with the same command as before, > > > > conda install -c cctbx-dev cctbx > > > > Again, your .condarc file should have conda-forge as the first channel so that dependencies can be pulled correctly. > > > > The dispatchers should work now and $LIBTBX_BUILD will be set on activation of an environment (and unset on environment deactivation) or after installing into an existing environment, so you can do more interesting things like > > > > iotbx.fetch_pdb --all --mtz 1kp8 > > > > However, this package does not install databases, so > > > > molprobity.molprobity 1kp8.pdb 1kp8.mtz > > > > will fail because the database is not available (also probe and reduce are not built). > > > > Some known issues in no particular order, > > > > 1) You can run "libtbx.run_tests_parallel module=cctbx nproc=Auto" to run tests, but not all the test files were copied, so I got 30 failures here. The final package will probably not have the test files. > > 2) The other python dispatchers, like "cctbx.python", were not updated, so those will fail. But you can just run "python" in the active environment. > > 3) Parts of mmtbx still need to be updated for Python 3. > > 4) The LIBTBX_BUILD variable should be set for sh and csh shells. Let me know if it's not working for your shell (i.e. "echo $LIBTBX_BUILD" should show the same thing as $CONDA_PREFIX). > > 5) One future step is to enable building other CCTBX-like modules with this conda package. This will require some bookkeeping updates so that modules in the conda environment and the modules being built are tracked properly. Also, making sure that all the necessary headers exist in $PREFIX/include. > > > > Gergely, let me know if your scripts are working. > > > > Happy holidays! > > > > -- > > Billy K. Poon > > Research Scientist, Molecular Biophysics and Integrated Bioimaging > > Lawrence Berkeley National Laboratory > > 1 Cyclotron Road, M/S 33R0345 > > Berkeley, CA 94720 > > Tel: (510) 486-5709 > > Fax: (510) 486-5909 > > Web: https://phenix-online.org > > > > > > On Wed, Dec 18, 2019 at 11:25 AM Billy Poon <BKPoon(a)lbl.gov> wrote: > >> > >> Hi Gergely, > >> > >> That's the other information that hasn't been updated yet in the conda package. :) > >> > >> For LIBTBX_BUILD, I can set up environment variables sort of how the conda gcc package sets up environment variables. I have to double check to see if they're set after installation of the package and after activation of an environment. The variable will just be a copy of $CONDA_PREFIX. > >> > >> The libtbx_env file is a file that exists in $LIBTBX_BUILD that basically stores configuration information. I'll have to modify the contents to update the locations of the different modules since the conda package will not have a "modules" directory. > >> > >> -- > >> Billy K. Poon > >> Research Scientist, Molecular Biophysics and Integrated Bioimaging > >> Lawrence Berkeley National Laboratory > >> 1 Cyclotron Road, M/S 33R0345 > >> Berkeley, CA 94720 > >> Tel: (510) 486-5709 > >> Fax: (510) 486-5909 > >> Web: https://phenix-online.org > >> > >> > >> On Wed, Dec 18, 2019 at 2:08 AM Gergely Katona <gkatona(a)gmail.com> wrote: > >>> > >>> Hi Billy, > >>> > >>> Conda install went fine with your instructions after rearranging the > >>> channels by putting cctbx last. I removed all environmental variables > >>> and previous build of cctbx. > >>> > >>> import sys > >>> print (sys.path, sys.prefix) > >>> > >>> ['/home/gergely/anaconda3/lib/python36.zip', > >>> '/home/gergely/anaconda3/lib/python3.6', > >>> '/home/gergely/anaconda3/lib/python3.6/lib-dynload', '', > >>> '/home/gergely/anaconda3/lib/python3.6/site-packages', > >>> '/home/gergely/anaconda3/lib/python3.6/site-packages/IPython/extensions', > >>> '/home/gergely/.ipython'] /home/gergely/anaconda3 > >>> > >>> Many imports went fine including pymc3, but I encountered problems > >>> with these three: > >>> > >>> from cctbx import miller > >>> import iotbx.pdb > >>> from iotbx import reflection_file_reader, mtz > >>> > >>> > >>> I also got type error when handling space groups. > >>> > >>> > >>> > >>> --------------------------------------------------------------------------- > >>> KeyError Traceback (most recent call last) > >>> <ipython-input-5-cedbd4f84f3d> in <module> > >>> 25 from cctbx import uctbx > >>> 26 from cctbx import sgtbx > >>> ---> 27 from cctbx import miller > >>> 28 #from iotbx import reflection_file_reader, mtz > >>> 29 sns.set_context("poster") > >>> > >>> ~/anaconda3/lib/python3.6/site-packages/cctbx/miller/__init__.py in <module> > >>> 11 > >>> 12 from cctbx import crystal > >>> ---> 13 from cctbx import maptbx > >>> 14 from cctbx import sgtbx > >>> 15 from cctbx.sgtbx import lattice_symmetry > >>> > >>> ~/anaconda3/lib/python3.6/site-packages/cctbx/maptbx/__init__.py in <module> > >>> 15 from libtbx import adopt_init_args > >>> 16 from libtbx.utils import Sorry > >>> ---> 17 import libtbx.load_env > >>> 18 import math > >>> 19 import sys, os > >>> > >>> ~/anaconda3/lib/python3.6/site-packages/libtbx/load_env.py in <module> > >>> 3 import libtbx.env_config > >>> 4 import os > >>> ----> 5 libtbx.env = libtbx.env_config.unpickle() > >>> 6 libtbx.env.set_os_environ_all_dist() > >>> 7 libtbx.env.dispatcher_name = os.environ.get("LIBTBX_DISPATCHER_NAME") > >>> > >>> ~/anaconda3/lib/python3.6/site-packages/libtbx/env_config.py in unpickle() > >>> 2603 > >>> 2604 def unpickle(): > >>> -> 2605 build_path = os.environ["LIBTBX_BUILD"] > >>> 2606 set_preferred_sys_prefix_and_sys_executable(build_path=build_path) > >>> 2607 libtbx_env = open(op.join(build_path, "libtbx_env"), "rb") > >>> > >>> ~/anaconda3/lib/python3.6/os.py in __getitem__(self, key) > >>> 667 except KeyError: > >>> 668 # raise KeyError with the original key value > >>> --> 669 raise KeyError(key) from None > >>> 670 return self.decodevalue(value) > >>> 671 > >>> > >>> KeyError: 'LIBTBX_BUILD' > >>> > >>> > >>> > >>> --------------------------------------------------------------------------- > >>> ArgumentError Traceback (most recent call last) > >>> <ipython-input-7-2acd3a9ce26a> in <module> > >>> 26 return ms,msnam,mscent,msacent,msnamacent,msnamcent,msnamacent_dstar > >>> 27 > >>> ---> 28 ms,msnam,mscent,msacent,msnamacent,msnamcent,msnamacent_dstar=initializecrystal() > >>> > >>> <ipython-input-7-2acd3a9ce26a> in initializecrystal() > >>> 11 uc = uctbx.unit_cell(unit_cell) > >>> 12 wavelength = 1.54980 > >>> ---> 13 xtal_symm = crystal.symmetry(unit_cell=unit_cell, > >>> space_group_symbol="P 43 21 2") > >>> 14 > >>> 15 ms = > >>> miller.build_set(crystal_symmetry=xtal_symm,anomalous_flag=True, > >>> d_min=1.61) > >>> > >>> ~/anaconda3/lib/python3.6/site-packages/cctbx/crystal/__init__.py in > >>> __init__(self, unit_cell, space_group_symbol, space_group_info, > >>> space_group, correct_rhombohedral_setting_if_necessary, > >>> assert_is_compatible_unit_cell, raise_sorry_if_incompatible_unit_cell, > >>> force_compatible_unit_cell) > >>> 74 if (space_group_symbol is not None): > >>> 75 self._space_group_info = sgtbx.space_group_info( > >>> ---> 76 symbol=space_group_symbol) > >>> 77 elif (space_group is not None): > >>> 78 if (isinstance(space_group, sgtbx.space_group)): > >>> > >>> ~/anaconda3/lib/python3.6/site-packages/cctbx/sgtbx/__init__.py in > >>> __init__(self, symbol, table_id, group, number, space_group_t_den) > >>> 100 assert group is None > >>> 101 if (table_id is None): > >>> --> 102 symbols = space_group_symbols(symbol) > >>> 103 else: > >>> 104 if (isinstance(symbol, int)): symbol = str(symbol) > >>> > >>> ArgumentError: Python argument types in > >>> space_group_symbols.__init__(space_group_symbols, str) > >>> did not match C++ signature: > >>> __init__(_object*, int space_group_number) > >>> __init__(_object*, int space_group_number, > >>> std::__cxx11::basic_string<char, std::char_traits<char>, > >>> std::allocator<char> > extension='') > >>> __init__(_object*, int space_group_number, > >>> std::__cxx11::basic_string<char, std::char_traits<char>, > >>> std::allocator<char> > extension='', std::__cxx11::basic_string<char, > >>> std::char_traits<char>, std::allocator<char> > table_id='') > >>> __init__(_object*, std::__cxx11::basic_string<char, > >>> std::char_traits<char>, std::allocator<char> > symbol) > >>> __init__(_object*, std::__cxx11::basic_string<char, > >>> std::char_traits<char>, std::allocator<char> > symbol, > >>> std::__cxx11::basic_string<char, std::char_traits<char>, > >>> std::allocator<char> > table_id='') > >>> > >>> > >>> When I tried to set LIBTBX_BUILD to /home/gergely/anaconda3 (this is > >>> sys.prefix on my system), I got other problems when importing. Can > >>> LIBTBX_BUILD be set in the conda package? > >>> > >>> > >>> > >>> --------------------------------------------------------------------------- > >>> FileNotFoundError Traceback (most recent call last) > >>> <ipython-input-1-7e2b144826cc> in <module> > >>> 26 from cctbx import sgtbx > >>> 27 #from cctbx import miller > >>> ---> 28 from iotbx import reflection_file_reader, mtz > >>> 29 sns.set_context("poster") > >>> 30 plt.rcParams.update({'figure.autolayout': True}) > >>> > >>> ~/anaconda3/lib/python3.6/site-packages/iotbx/reflection_file_reader.py > >>> in <module> > >>> 53 > >>> 54 from __future__ import absolute_import, division, print_function > >>> ---> 55 from iotbx import mtz > >>> 56 from iotbx.scalepack import merge as scalepack_merge > >>> 57 from iotbx.scalepack import no_merge_original_index as > >>> scalepack_no_merge > >>> > >>> ~/anaconda3/lib/python3.6/site-packages/iotbx/mtz/__init__.py in <module> > >>> 9 import iotbx_mtz_ext as ext > >>> 10 > >>> ---> 11 from iotbx.mtz import extract_from_symmetry_lib > >>> 12 from cctbx import xray > >>> 13 import cctbx.xray.observation_types > >>> > >>> ~/anaconda3/lib/python3.6/site-packages/iotbx/mtz/extract_from_symmetry_lib.py > >>> in <module> > >>> 1 from __future__ import absolute_import, division, print_function > >>> 2 from cctbx import sgtbx > >>> ----> 3 import libtbx.load_env > >>> 4 import os.path as op > >>> 5 from six.moves import range > >>> > >>> ~/anaconda3/lib/python3.6/site-packages/libtbx/load_env.py in <module> > >>> 3 import libtbx.env_config > >>> 4 import os > >>> ----> 5 libtbx.env = libtbx.env_config.unpickle() > >>> 6 libtbx.env.set_os_environ_all_dist() > >>> 7 libtbx.env.dispatcher_name = os.environ.get("LIBTBX_DISPATCHER_NAME") > >>> > >>> ~/anaconda3/lib/python3.6/site-packages/libtbx/env_config.py in unpickle() > >>> 2605 build_path = os.environ["LIBTBX_BUILD"] > >>> 2606 set_preferred_sys_prefix_and_sys_executable(build_path=build_path) > >>> -> 2607 libtbx_env = open(op.join(build_path, "libtbx_env"), "rb") > >>> 2608 env = pickle.load(libtbx_env) > >>> 2609 if (env.python_version_major_minor != sys.version_info[:2]): > >>> > >>> FileNotFoundError: [Errno 2] No such file or directory: > >>> '/home/gergely/anaconda3/libtbx_env' > >>> > >>> On Wed, Dec 18, 2019 at 9:10 AM Billy Poon <BKPoon(a)lbl.gov> wrote: > >>> > > >>> > Hi Gergely, > >>> > > >>> > I've uploaded linux packages to a new channel, cctbx-dev, and you can install it with > >>> > > >>> > conda install -c cctbx-dev cctbx > >>> > > >>> > in your current environment. You should set your ~/.condarc file to pull the other dependencies from the conda-forge channel first, so put conda-forge above cctbx. Mine looks like > >>> > > >>> > channels: > >>> > - conda-forge > >>> > - defaults > >>> > - cctbx > >>> > > >>> > Do you need dxtbx for your scripts? This package does not build that part. I think the plan is to build a separate conda package for dxtbx so that it can be updated more frequently. I can rebuild the packages to include it for testing, but the one being submitted to conda-forge will not have it. > >>> > > >>> > Also, your error message is probably due to version of HDF5 that the development build installs. The bootstrap.py script will install 1.10.4, but your other dependency is looking for 1.10.5. Installing this cctbx conda package should install 1.10.5, which should fix the issue. Also, I'm updating those environments and 1.10.5 will be the new default version. > >>> > > >>> > Lastly, the dispatchers will not work in these packages because the old paths during the build process are still in them and many of them expect some additional information that has not been updated in the packages yet. I'm in the process of doing that and will update the cctbx-dev channel when that's done. However, by starting python, you can import cctbx modules. So you can run commands like > >>> > > >>> > from scitbx.array_family import flex > >>> > a = flex.random_double(1000000) > >>> > b = flex.min_max_mean_double(a) > >>> > b.min > >>> > b.max > >>> > b.mean > >>> > > >>> > Thanks! > >>> > > >>> > -- > >>> > Billy K. Poon > >>> > Research Scientist, Molecular Biophysics and Integrated Bioimaging > >>> > Lawrence Berkeley National Laboratory > >>> > 1 Cyclotron Road, M/S 33R0345 > >>> > Berkeley, CA 94720 > >>> > Tel: (510) 486-5709 > >>> > Fax: (510) 486-5909 > >>> > Web: https://phenix-online.org > >>> > > >>> > > >>> > On Tue, Dec 17, 2019 at 5:39 AM Gergely Katona <gkatona(a)gmail.com> wrote: > >>> >> > >>> >> Dear Billy, > >>> >> > >>> >> Thank you for the detailed explanation, I look forward to do further > >>> >> testing! I aim to pool all modules under the same environment, if > >>> >> there are conflicts then I just try to reshuffle the order of imports. > >>> >> So far this did not cause problems for me even when I was using system > >>> >> python, but of course it is not the most prudent thing to do. With > >>> >> anaconda everything is much more standardized and isolated already and > >>> >> without being superuser I can have my familiar environment at any > >>> >> synchrotron based cluster. It is great that cctbx will be an integral > >>> >> part of this ecosystem and this was also the last thing holding me > >>> >> back from adopting python3. About hdf5, pymc3 requires it and > >>> >> importing causes a kernel restart with the following error messages, > >>> >> curiously if I import h5py first this can be avoided. > >>> >> > >>> >> Best wishes, > >>> >> > >>> >> Gergely > >>> >> > >>> >> import pymc3 as pm > >>> >> > >>> >> Warning! ***HDF5 library version mismatched error*** > >>> >> The HDF5 header files used to compile this application do not match > >>> >> the version used by the HDF5 library to which this application is linked. > >>> >> Data corruption or segmentation faults may occur if the application continues. > >>> >> This can happen when an application was compiled by one version of HDF5 but > >>> >> linked with a different version of static or shared HDF5 library. > >>> >> You should recompile the application or check your shared library related > >>> >> settings such as 'LD_LIBRARY_PATH'. > >>> >> You can, at your own risk, disable this warning by setting the environment > >>> >> variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'. > >>> >> Setting it to 2 or higher will suppress the warning messages totally. > >>> >> Headers are 1.10.4, library is 1.10.5 > >>> >> SUMMARY OF THE HDF5 CONFIGURATION > >>> >> ================================= > >>> >> > >>> >> General Information: > >>> >> ------------------- > >>> >> HDF5 Version: 1.10.5 > >>> >> Configured on: Tue Oct 22 12:02:13 UTC 2019 > >>> >> Configured by: conda@16247e67ecd5 > >>> >> Host system: x86_64-conda_cos6-linux-gnu > >>> >> Uname information: Linux 16247e67ecd5 4.15.0-1059-azure > >>> >> #64-Ubuntu SMP Fri Sep 13 17:02:44 UTC 2019 x86_64 x86_64 x86_64 > >>> >> GNU/Linux > >>> >> Byte sex: little-endian > >>> >> Installation point: /home/gergely/anaconda3 > >>> >> > >>> >> Compiling Options: > >>> >> ------------------ > >>> >> Build Mode: production > >>> >> Debugging Symbols: no > >>> >> Asserts: no > >>> >> Profiling: no > >>> >> Optimization Level: high > >>> >> > >>> >> Linking Options: > >>> >> ---------------- > >>> >> Libraries: static, shared > >>> >> Statically Linked Executables: > >>> >> LDFLAGS: -Wl,-O2 -Wl,--sort-common > >>> >> -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags > >>> >> -Wl,--gc-sections -Wl,-rpath,/home/gergely/anaconda3/lib > >>> >> -Wl,-rpath-link,/home/gergely/anaconda3/lib > >>> >> -L/home/gergely/anaconda3/lib > >>> >> H5_LDFLAGS: > >>> >> AM_LDFLAGS: -L/home/gergely/anaconda3/lib > >>> >> Extra libraries: -lrt -lpthread -lz -ldl -lm > >>> >> Archiver: > >>> >> /home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/_build_env/bin/x86_64-conda_cos6-linux-gnu-ar > >>> >> AR_FLAGS: cr > >>> >> Ranlib: > >>> >> /home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/_build_env/bin/x86_64-conda_cos6-linux-gnu-ranlib > >>> >> > >>> >> Languages: > >>> >> ---------- > >>> >> C: yes > >>> >> C Compiler: > >>> >> /home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc > >>> >> CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 > >>> >> -I/home/gergely/anaconda3/include > >>> >> H5_CPPFLAGS: -D_GNU_SOURCE > >>> >> -D_POSIX_C_SOURCE=200809L -DNDEBUG -UH5_DEBUG_API > >>> >> AM_CPPFLAGS: -I/home/gergely/anaconda3/include > >>> >> C Flags: -march=nocona -mtune=haswell > >>> >> -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 > >>> >> -ffunction-sections -pipe -I/home/gergely/anaconda3/include > >>> >> -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/work=/usr/local/src/conda/hdf5_split-1.10.5 > >>> >> -fdebug-prefix-map=/home/gergely/anaconda3=/usr/local/src/conda-prefix > >>> >> H5 C Flags: -std=c99 -pedantic -Wall -Wextra > >>> >> -Wbad-function-cast -Wc++-compat -Wcast-align -Wcast-qual -Wconversion > >>> >> -Wdeclaration-after-statement -Wdisabled-optimization -Wfloat-equal > >>> >> -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-declarations > >>> >> -Wmissing-include-dirs -Wmissing-prototypes -Wnested-externs > >>> >> -Wold-style-definition -Wpacked -Wpointer-arith -Wredundant-decls > >>> >> -Wshadow -Wstrict-prototypes -Wswitch-default -Wswitch-enum -Wundef > >>> >> -Wunused-macros -Wunsafe-loop-optimizations -Wwrite-strings > >>> >> -finline-functions -s -Wno-inline -Wno-aggregate-return > >>> >> -Wno-missing-format-attribute -Wno-missing-noreturn -O > >>> >> AM C Flags: > >>> >> Shared C Library: yes > >>> >> Static C Library: yes > >>> >> > >>> >> > >>> >> Fortran: yes > >>> >> Fortran Compiler: > >>> >> /home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/_build_env/bin/x86_64-conda_cos6-linux-gnu-gfortran > >>> >> Fortran Flags: > >>> >> H5 Fortran Flags: -pedantic -Wall -Wextra -Wunderflow > >>> >> -Wimplicit-interface -Wsurprising -Wno-c-binding-type -s -O2 > >>> >> AM Fortran Flags: > >>> >> Shared Fortran Library: yes > >>> >> Static Fortran Library: yes > >>> >> > >>> >> C++: yes > >>> >> C++ Compiler: > >>> >> /home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/_build_env/bin/x86_64-conda_cos6-linux-gnu-c++ > >>> >> C++ Flags: -fvisibility-inlines-hidden > >>> >> -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell > >>> >> -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 > >>> >> -ffunction-sections -pipe -I/home/gergely/anaconda3/include > >>> >> -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/work=/usr/local/src/conda/hdf5_split-1.10.5 > >>> >> -fdebug-prefix-map=/home/gergely/anaconda3=/usr/local/src/conda-prefix > >>> >> H5 C++ Flags: -pedantic -Wall -W -Wundef -Wshadow > >>> >> -Wpointer-arith -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion > >>> >> -Wredundant-decls -Winline -Wsign-promo -Woverloaded-virtual > >>> >> -Wold-style-cast -Weffc++ -Wreorder -Wnon-virtual-dtor > >>> >> -Wctor-dtor-privacy -Wabi -finline-functions -s -O > >>> >> AM C++ Flags: > >>> >> Shared C++ Library: yes > >>> >> Static C++ Library: yes > >>> >> > >>> >> Java: no > >>> >> > >>> >> > >>> >> Features: > >>> >> --------- > >>> >> Parallel HDF5: no > >>> >> Parallel Filtered Dataset Writes: no > >>> >> Large Parallel I/O: no > >>> >> High-level library: yes > >>> >> Threadsafety: yes > >>> >> Default API mapping: v110 > >>> >> With deprecated public symbols: yes > >>> >> I/O filters (external): deflate(zlib) > >>> >> MPE: no > >>> >> Direct VFD: no > >>> >> dmalloc: no > >>> >> Packages w/ extra debug output: none > >>> >> API tracing: no > >>> >> Using memory checker: yes > >>> >> Memory allocation sanity checks: no > >>> >> Function stack tracing: no > >>> >> Strict file format checks: no > >>> >> Optimization instrumentation: no > >>> >> > >>> >> On Tue, Dec 17, 2019 at 8:35 AM Billy Poon <BKPoon(a)lbl.gov> wrote: > >>> >> > > >>> >> > Hi Gergely, > >>> >> > > >>> >> > Let me build the test package tomorrow. All the gritty details for building with conda is being finalized and the official documentation will be updated to describe the steps. It would be too confusing to keep changing the documentation as the process evolves. You do have the general process, though, which is summarized as follows. > >>> >> > > >>> >> > 1) Installing dependencies. The cctbx_dependencies metapackage was an initial approach for managing the CCTBX dependencies, but after contacting the conda-forge folks, they recommended using the --only-deps flag. So when the CCTBX conda package is available, you'll be able to get a set of dependencies with, > >>> >> > > >>> >> > conda install -c conda-forge --only-deps cctbx > >>> >> > > >>> >> > By default, the bootstrap.py file will automatically install a set of dependencies in the "conda_base" directory (and a conda installation if one is not found). It just uses standard conda environment files located in libtbx/auto_build/conda_envs, so you do not need to install cctbx_dependencies as a separate step. The environment files avoid channel issues by explicitly defining the channel to pull the packages from and the cctbx channel just stores copies of packages from conda-forge. There were issues earlier where the conda-forge packages would sometimes be moved to a different label. The --use-conda flag also accepts a path to $CONDA_PREFIX if you want to use a specific environment for testing. > >>> >> > > >>> >> > 2) Building. The bootstrap.py file handles that with SCons. > >>> >> > > >>> >> > 3) Running. After building, there should be a setpaths.sh (and .csh) file that adds build/bin to your path. The build/bin directory has our dispatchers, which are just scripts that set up the environment variables for you. This prevents other programs from loading our libraries, whose versions may conflict. You should see that there is a "python" dispatcher, which is a convenience for developers. Otherwise, you can use libtbx.python, which will be able to import CCTBX modules. > >>> >> > > >>> >> > The running part is where the conda package for CCTBX will be different than this build. Since our Python files and extensions modules will be in the "site-packages" directory for Python, the PYTHONPATH variable will not be needed (and conda suggests that that variable not be set). The other CCTBX libraries will be in $CONDA_PREFIX/lib, so LD_LIBRARY_PATH is not needed. In an active environment, PATH will already be modified. And then our LIBTBX_BUILD directory can be set to sys.prefix. > >>> >> > > >>> >> > So with the conda package, you would only need to activate your conda environment and CCTBX should integrate with other conda packages. What is the conflict with hdf5? That's something that should be fixed. Thanks! > >>> >> > > >>> >> > -- > >>> >> > Billy K. Poon > >>> >> > Research Scientist, Molecular Biophysics and Integrated Bioimaging > >>> >> > Lawrence Berkeley National Laboratory > >>> >> > 1 Cyclotron Road, M/S 33R0345 > >>> >> > Berkeley, CA 94720 > >>> >> > Tel: (510) 486-5709 > >>> >> > Fax: (510) 486-5909 > >>> >> > Web: https://phenix-online.org > >>> >> > > >>> >> > > >>> >> > On Mon, Dec 16, 2019 at 2:53 AM Gergely Katona <gkatona(a)gmail.com> wrote: > >>> >> >> > >>> >> >> Dear Billy, > >>> >> >> > >>> >> >> Thank you for this update and for your efforts! I found a solution and > >>> >> >> indeed most things already work in anaconda3. The steps I took (even > >>> >> >> if these instructions will have short expiry date): > >>> >> >> > >>> >> >> Modified .condarc with: > >>> >> >> channels: > >>> >> >> - cctbx > >>> >> >> - conda-forge > >>> >> >> - defaults > >>> >> >> > >>> >> >> run > >>> >> >> conda conda install cctbx_dependencies python=3.6 > >>> >> >> > >>> >> >> I expect this will work without python=3.6 in the near future. > >>> >> >> > >>> >> >> Then compiling cctbx with anaconda3 python went without any problem > >>> >> >> when using these flags: > >>> >> >> python bootstrap.py --use-conda --python3 --nproc=12 > >>> >> >> > >>> >> >> Then I probably did the unorthodox thing and sourced these directories: > >>> >> >> > >>> >> >> setenv LIBTBX_BUILD /home/gergely/cctbx/build > >>> >> >> setenv PATH ${PATH}:/home/gergely/cctbx/build/bin > >>> >> >> setenv PYTHONPATH > >>> >> >> /home/gergely/cctbx/modules/cctbx_project:/home/gergely/cctbx/modules:/home/gergely/cctbx/modules/cctbx_project/boost_adaptbx:/home/gergely/cctbx/build/lib:/home/gergely/cctbx/conda_base/lib/python3.6/site-packages:$PYTHONPATH > >>> >> >> setenv LD_LIBRARY_PATH > >>> >> >> /home/gergely/cctbx/conda_base/lib:/home/gergely/cctbx/build/lib:$LD_LIBRARY_PATH > >>> >> >> > >>> >> >> There is probably a better way to put this into conda environment. > >>> >> >> With these steps I could run one of my scripts depending on cctbx. The > >>> >> >> only problem I found is that hdf5 library had conflict with another > >>> >> >> package in conda, but I does not find this as a showstopper. > >>> >> >> > >>> >> >> Best wishes, > >>> >> >> > >>> >> >> Gergely > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> On Fri, Dec 13, 2019 at 7:23 PM Billy Poon <BKPoon(a)lbl.gov> wrote: > >>> >> >> > > >>> >> >> > Hi Gergely, > >>> >> >> > > >>> >> >> > It's still a work in progress. I'm sorting out some Windows issues right now. I can probably build a test package on a separate channel for people that want to test it (let's say next week?). I'll provide instructions, but basically, the test conda package will be in its own separate channel and the dependencies will be pulled from the conda-forge channel. I want most things to be working correctly on Python 2.7, 3.6, 3.7, and 3.8 on all 3 platforms. > >>> >> >> > > >>> >> >> > Thanks! > >>> >> >> > > >>> >> >> > -- > >>> >> >> > Billy K. Poon > >>> >> >> > Research Scientist, Molecular Biophysics and Integrated Bioimaging > >>> >> >> > Lawrence Berkeley National Laboratory > >>> >> >> > 1 Cyclotron Road, M/S 33R0345 > >>> >> >> > Berkeley, CA 94720 > >>> >> >> > Tel: (510) 486-5709 > >>> >> >> > Fax: (510) 486-5909 > >>> >> >> > Web: https://phenix-online.org > >>> >> >> > > >>> >> >> > > >>> >> >> > On Fri, Dec 13, 2019 at 5:44 AM Gergely Katona <gkatona(a)gmail.com> wrote: > >>> >> >> >> > >>> >> >> >> Dear Billy, > >>> >> >> >> > >>> >> >> >> This sounds very promising and exciting. I am not sure if cctbx is > >>> >> >> >> already functional as a conda package in anaconda3 (Linux) or this is > >>> >> >> >> still work in progress. My technical expertise does not allow me to > >>> >> >> >> tell the difference. What I tried: > >>> >> >> >> > >>> >> >> >> Fresh install of anaconda3. Adding - cctbx and - conda-forge to > >>> >> >> >> .condarc . Installing pyside2 with conda. Running conda install > >>> >> >> >> conda_dependencies . I get a lot package version conflict, and I > >>> >> >> >> cannot import cctbx or iotbx to anaconda python. Am I following the > >>> >> >> >> right instructions? Or it is too early to expect that cctbx works when > >>> >> >> >> installed through conda? > >>> >> >> >> > >>> >> >> >> Best wishes, > >>> >> >> >> > >>> >> >> >> Gergely > >>> >> >> >> > >>> >> >> >> On Wed, Nov 27, 2019 at 3:56 PM Billy Poon <BKPoon(a)lbl.gov> wrote: > >>> >> >> >> > > >>> >> >> >> > Hi all, > >>> >> >> >> > > >>> >> >> >> > For a brief update, I have submitted a recipe for cctbxlite to conda-forge (https://github.com/conda-forge/staged-recipes/pull/10021) and support for Python 3.7 and 3.8 is being added (https://github.com/cctbx/cctbx_project/pull/409). With some fixes for Windows (https://github.com/cctbx/cctbx_project/pull/416), all platforms (macOS, linux, and Windows) can build for Python 2.7, 3.6, 3.7, and 3.8. Some additional changes will be needed to get Windows to work with Python 3 and for tests to pass with Boost 1.70.0. That will enable the conda-forge recipe to build for all platforms and for all supported versions of Python. > >>> >> >> >> > > >>> >> >> >> > Currently, the conda-forge recipe will install into the conda python and cctbx imports can be done without sourcing the environment scripts. It looks like a lot of the environment variables being set in the dispatchers can be removed since the Python files and C++ extensions are in the right places. I'll update the libtbx_env file so that commands that load the environment can work correctly. > >>> >> >> >> > > >>> >> >> >> > -- > >>> >> >> >> > Billy K. Poon > >>> >> >> >> > Research Scientist, Molecular Biophysics and Integrated Bioimaging > >>> >> >> >> > Lawrence Berkeley National Laboratory > >>> >> >> >> > 1 Cyclotron Road, M/S 33R0345 > >>> >> >> >> > Berkeley, CA 94720 > >>> >> >> >> > Tel: (510) 486-5709 > >>> >> >> >> > Fax: (510) 486-5909 > >>> >> >> >> > Web: https://phenix-online.org > >>> >> >> >> > > >>> >> >> >> > > >>> >> >> >> > On Sun, Aug 25, 2019 at 2:33 PM Tristan Croll <tic20(a)cam.ac.uk> wrote: > >>> >> >> >> >> > >>> >> >> >> >> Hi Luc, > >>> >> >> >> >> > >>> >> >> >> >> That sounds promising. From there, I’d need to work out how to make a fully-packaged installer (basically a modified wheel file) for the ChimeraX ToolShed - the aim is for the end user to not have to worry about any of this. That adds a couple of complications - e.g. $LIBTBX_BUILD would need to be set dynamically before first import - but doesn’t seem insurmountable. > >>> >> >> >> >> > >>> >> >> >> >> Thanks, > >>> >> >> >> >> > >>> >> >> >> >> Tristan > >>> >> >> >> >> > >>> >> >> >> >> > >>> >> >> >> >> > >>> >> >> >> >> Tristan Croll > >>> >> >> >> >> Research Fellow > >>> >> >> >> >> Cambridge Institute for Medical Research > >>> >> >> >> >> University of Cambridge CB2 0XY > >>> >> >> >> >> > >>> >> >> >> >> > >>> >> >> >> >> > >>> >> >> >> >> > >>> >> >> >> >> > On 25 Aug 2019, at 18:31, Luc Bourhis <luc_j_bourhis(a)mac.com> wrote: > >>> >> >> >> >> > > >>> >> >> >> >> > Hi Tristan, > >>> >> >> >> >> > > >>> >> >> >> >> > cctbx could be built to use your ChimeraX python, now that cctbx is moving to Python 3. The option —with-python is there for that with the bootstrap script. The specific environment setup boil down to setting two environment variable LIBTBX_BUILD and either LD_LIBRARY_PATH on Linux, PATH on Win32, or DYLIB_LIBRARY_PATH on MacOS. If you work within a framework such as ChimeraX, that should not be difficult to ensure those two variables are set. > >>> >> >> >> >> > > >>> >> >> >> >> > Best wishes, > >>> >> >> >> >> > > >>> >> >> >> >> > Luc > >>> >> >> >> >> > > >>> >> >> >> >> > > >>> >> >> >> >> >> On 23 Aug 2019, at 19:02, Tristan Croll <tic20(a)cam.ac.uk> wrote: > >>> >> >> >> >> >> > >>> >> >> >> >> >> To add my two cents on this: probably the second-most common question I've had about ISOLDE's implementation is, "why didn't you use CCTBX?". The honest answer to that is, "I didn't know how." > >>> >> >> >> >> >> > >>> >> >> >> >> >> Still don't, really - although the current developments are rather promising. The problem I've faced is that CCTBX was designed as its own self-contained Python (2.7, until very recently) environment, with its own interpreter and a lot of very specific environment setup. Meanwhile I'm developing ISOLDE in ChimeraX, which is *also* its own self-contained Python (3.7) environment. To plug one into the other in that form... well, I don't think I'm a good enough programmer to really know where to start. > >>> >> >> >> >> >> > >>> >> >> >> >> >> The move to Conda and a more modular CCTBX architecture should make a lot more possible in that direction. Pip would be even better for me personally (ChimeraX can install directly from the PyPI, but doesn't interact with Conda) - but I understand pretty well the substantial challenge that would amount to (not least being that the PyPI imposes a limit - around 100MB from memory? - on the size of an individual package). > >>> >> >> >> >> >> > >>> >> >> >> >> >> Best regards, > >>> >> >> >> >> >> > >>> >> >> >> >> >> Tristan > >>> >> >> >> >> >> > >>> >> >> >> >> >>> On 2019-08-23 09:28, Luc Bourhis wrote: > >>> >> >> >> >> >>> Hi Graeme, > >>> >> >> >> >> >>> Yes, I know. But “black" is a program doing a very particular task > >>> >> >> >> >> >>> (code formatting from the top of my head). Requiring to use a wrapper > >>> >> >> >> >> >>> for python itself is another level. But ok, I think I am mellowing to > >>> >> >> >> >> >>> the idea after all! Talking with people around me, and extrapolating, > >>> >> >> >> >> >>> I would bet that, right now, a great majority of people interested by > >>> >> >> >> >> >>> cctbx in pip have already used the cctbx, so they know about the > >>> >> >> >> >> >>> Python wrapper, and they would not be too sanguine about that. My > >>> >> >> >> >> >>> concern is for the future, when pip will be the first time some people > >>> >> >> >> >> >>> use cctbx. Big fat warning notices on PyPI page and a better error > >>> >> >> >> >> >>> message when cctbx fails because LIBTBX_BUILD is not set would be > >>> >> >> >> >> >>> needed but that could be all right. > >>> >> >> >> >> >>> If we do a pip installer, we should aim at a minimal install: cctbx, > >>> >> >> >> >> >>> iotbx and their dependencies, and that’s it. > >>> >> >> >> >> >>> Best wishes, > >>> >> >> >> >> >>> Luc > >>> >> >> >> >> >>>> On 23 Aug 2019, at 07:17, Graeme.Winter(a)Diamond.ac.uk <Graeme.Winter(a)diamond.ac.uk> wrote: > >>> >> >> >> >> >>>> Without discussing the merits of this or whether we _choose_ to make the move to supporting PIP, I am certain it would be _possible_ - many other packages make dispatcher scripts when you pip install them e.g. > >>> >> >> >> >> >>>> Silver-Surfer rescale_f2 :) $ which black; cat $(which black) > >>> >> >> >> >> >>>> /Library/Frameworks/Python.framework/Versions/3.6/bin/black > >>> >> >> >> >> >>>> #!/Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6 > >>> >> >> >> >> >>>> # -*- coding: utf-8 -*- > >>> >> >> >> >> >>>> import re > >>> >> >> >> >> >>>> import sys > >>> >> >> >> >> >>>> from black import main > >>> >> >> >> >> >>>> if __name__ == '__main__': > >>> >> >> >> >> >>>> sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0]) > >>> >> >> >> >> >>>> sys.exit(main()) > >>> >> >> >> >> >>>> So we _could_ work around the absence of LIBTBX_BUILD etc. in the system. Whether or not we elect to do the work is a different question, and it seems clear that here are very mixed opinions on this. > >>> >> >> >> >> >>>> Best wishes Graeme > >>> >> >> >> >> >>>> On 23 Aug 2019, at 01:21, Luc Bourhis <luc_j_bourhis(a)mac.com<mailto:[email protected]>> wrote: > >>> >> >> >> >> >>>> Hi, > >>> >> >> >> >> >>>> Even if we managed to ship our the boost dynamic libraries with pip, it would still not be pip-like, as we would still need our python wrappers to set LIBTBX_BUILD and LD_LIBRARY_PATH. Normal pip packages work with the standard python exe. LD_LIBRARY_PATH, we could get around that by changing the way we compile, using -Wl,-R, which is the runtime equivalent of build time -L. That’s a significant change that would need to be tested. But there is no way around setting LIBTBX_BUILD right now. Leaving that to the user is horrible. Perhaps there is a way to hack libtbx/env_config.py so that we can hardwire LIBTBX_BUILD in there when pip installs? > >>> >> >> >> >> >>>> Best wishes, > >>> >> >> >> >> >>>> Luc > >>> >> >> >> >> >>>> On 16 Aug 2019, at 22:47, Luc Bourhis <luc_j_bourhis(a)mac.com<mailto:[email protected]>> wrote: > >>> >> >> >> >> >>>> Hi, > >>> >> >> >> >> >>>> I did look into that many years ago, and even toyed with building a pip installer. What stopped me is the exact conclusion you reached too: the user would not have the pip experience he expects. You are right that it is a lot of effort but is it worth it? Considering that remark, I don’t think so. Now, Conda was created specifically to go beyond pip pure-python-only support. Since cctbx has garnered support for Conda, the best avenue imho is to go the extra length to have a package on Anaconda.org<http://anaconda.org/>, and then to advertise it hard to every potential user out there. > >>> >> >> >> >> >>>> Best wishes, > >>> >> >> >> >> >>>> Luc > >>> >> >> >> >> >>>> On 16 Aug 2019, at 21:45, Aaron Brewster <asbrewster(a)lbl.gov<mailto:[email protected]>> wrote: > >>> >> >> >> >> >>>> Hi, to avoid clouding Dorothee's documentation email thread, which I think is a highly useful enterprise, here's some thoughts about putting cctbx into pip. Pip doesn't install non-python dependencies well. I don't think boost is available as a package on pip (at least the package version we use). wxPython4 isn't portable through pip (https://wiki.wxpython.org/How%20to%20install%20wxPython#Installing_wxPython…). MPI libraries are system dependent. If cctbx were a pure python package, pip would be fine, but cctbx is not. > >>> >> >> >> >> >>>> All that said, we could build a manylinux1 version of cctbx and upload it to PyPi (I'm just learning about this). For a pip package to be portable (which is a requirement for cctbx), it needs to conform to PEP513, the manylinux1 standard (https://www.python.org/dev/peps/pep-0513/). For example, numpy is built according to this standard (see https://pypi.org/project/numpy/#files, where you'll see the manylinux1 wheel). Note, the manylinux1 standard is built with Centos 5.11 which we no longer support. > >>> >> >> >> >> >>>> There is also a manylinux2010 standard, which is based on Centos 6 (https://www.python.org/dev/peps/pep-0571/). This is likely a more attainable target (note though by default C++11 is not supported on Centos 6). > >>> >> >> >> >> >>>> If we built a manylinuxX version of cctbx and uploaded it to PyPi, the user would need all the non-python dependencies. There's no way to specify these in pip. For example, cctbx requires boost 1.63 or better. The user will need to have it in a place their python can find it, or we could package it ourselves and supply it, similar to how the pip h5py package now comes with an hd5f library, or how the pip numpy package includes an openblas library. We'd have to do the same for any packages we depend on that aren't on pip using the manylinux standards, such as wxPython4. > >>> >> >> >> >> >>>> Further, we need to think about how dials and other cctbx-based packages interact. If pip install cctbx is set up, how does pip install dials work, such that any dials shared libraries can find the cctbx libraries? Can shared libraries from one pip package link against libraries in another pip package? Would each package need to supply its own boost? Possibly this is well understood in the pip field, but not by me :) > >>> >> >> >> >> >>>> Finally, there's the option of providing a source pip package. This would require the full compiler toolchain for any given platform (macOS, linux, windows). These are likely available for developers, but not for general users. > >>> >> >> >> >> >>>> Anyway, these are some of the obstacles. Not saying it isn't possible, it's just a lot of effort. > >>> >> >> >> >> >>>> Thanks, > >>> >> >> >> >> >>>> -Aaron > >>> >> >> >> >> >>>> _______________________________________________ > >>> >> >> >> >> >>>> cctbxbb mailing list > >>> >> >> >> >> >>>> cctbxbb(a)phenix-online.org<mailto:[email protected]> > >>> >> >> >> >> >>>> http://phenix-online.org/mailman/listinfo/cctbxbb > >>> >> >> >> >> >>>> _______________________________________________ > >>> >> >> >> >> >>>> cctbxbb mailing list > >>> >> >> >> >> >>>> cctbxbb(a)phenix-online.org<mailto:[email protected]> > >>> >> >> >> >> >>>> http://phenix-online.org/mailman/listinfo/cctbxbb > >>> >> >> >> >> >>>> _______________________________________________ > >>> >> >> >> >> >>>> cctbxbb mailing list > >>> >> >> >> >> >>>> cctbxbb(a)phenix-online.org<mailto:[email protected]> > >>> >> >> >> >> >>>> http://phenix-online.org/mailman/listinfo/cctbxbb > >>> >> >> >> >> >>>> -- > >>> >> >> >> >> >>>> This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. > >>> >> >> >> >> >>>> Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. > >>> >> >> >> >> >>>> Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. > >>> >> >> >> >> >>>> Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom > >>> >> >> >> >> >>>> _______________________________________________ > >>> >> >> >> >> >>>> cctbxbb mailing list > >>> >> >> >> >> >>>> cctbxbb(a)phenix-online.org > >>> >> >> >> >> >>>> http://phenix-online.org/mailman/listinfo/cctbxbb > >>> >> >> >> >> >>> _______________________________________________ > >>> >> >> >> >> >>> cctbxbb mailing list > >>> >> >> >> >> >>> cctbxbb(a)phenix-online.org > >>> >> >> >> >> >>> http://phenix-online.org/mailman/listinfo/cctbxbb > >>> >> >> >> >> >> > >>> >> >> >> >> >> > >>> >> >> >> >> >> _______________________________________________ > >>> >> >> >> >> >> cctbxbb mailing list > >>> >> >> >> >> >> cctbxbb(a)phenix-online.org > >>> >> >> >> >> >> http://phenix-online.org/mailman/listinfo/cctbxbb > >>> >> >> >> >> > > >>> >> >> >> >> > > >>> >> >> >> >> > _______________________________________________ > >>> >> >> >> >> > cctbxbb mailing list > >>> >> >> >> >> > cctbxbb(a)phenix-online.org > >>> >> >> >> >> > http://phenix-online.org/mailman/listinfo/cctbxbb > >>> >> >> >> >> > >>> >> >> >> >> > >>> >> >> >> >> _______________________________________________ > >>> >> >> >> >> cctbxbb mailing list > >>> >> >> >> >> cctbxbb(a)phenix-online.org > >>> >> >> >> >> http://phenix-online.org/mailman/listinfo/cctbxbb > >>> >> >> >> > > >>> >> >> >> > _______________________________________________ > >>> >> >> >> > cctbxbb mailing list > >>> >> >> >> > cctbxbb(a)phenix-online.org > >>> >> >> >> > http://phenix-online.org/mailman/listinfo/cctbxbb > >>> >> >> >> > >>> >> >> >> > >>> >> >> >> > >>> >> >> >> -- > >>> >> >> >> Gergely Katona, PhD > >>> >> >> >> Associate Professor > >>> >> >> >> Department of Chemistry and Molecular Biology, University of Gothenburg > >>> >> >> >> Box 462, 40530 Göteborg, Sweden > >>> >> >> >> Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910 > >>> >> >> >> Web: http://katonalab.eu, Email: gergely.katona(a)gu.se > >>> >> >> >> > >>> >> >> >> _______________________________________________ > >>> >> >> >> cctbxbb mailing list > >>> >> >> >> cctbxbb(a)phenix-online.org > >>> >> >> >> http://phenix-online.org/mailman/listinfo/cctbxbb > >>> >> >> > > >>> >> >> > _______________________________________________ > >>> >> >> > cctbxbb mailing list > >>> >> >> > cctbxbb(a)phenix-online.org > >>> >> >> > http://phenix-online.org/mailman/listinfo/cctbxbb > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> -- > >>> >> >> Gergely Katona, PhD > >>> >> >> Associate Professor > >>> >> >> Department of Chemistry and Molecular Biology, University of Gothenburg > >>> >> >> Box 462, 40530 Göteborg, Sweden > >>> >> >> Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910 > >>> >> >> Web: http://katonalab.eu, Email: gergely.katona(a)gu.se > >>> >> >> > >>> >> >> _______________________________________________ > >>> >> >> cctbxbb mailing list > >>> >> >> cctbxbb(a)phenix-online.org > >>> >> >> http://phenix-online.org/mailman/listinfo/cctbxbb > >>> >> > > >>> >> > _______________________________________________ > >>> >> > cctbxbb mailing list > >>> >> > cctbxbb(a)phenix-online.org > >>> >> > http://phenix-online.org/mailman/listinfo/cctbxbb > >>> >> > >>> >> > >>> >> > >>> >> -- > >>> >> Gergely Katona, PhD > >>> >> Associate Professor > >>> >> Department of Chemistry and Molecular Biology, University of Gothenburg > >>> >> Box 462, 40530 Göteborg, Sweden > >>> >> Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910 > >>> >> Web: http://katonalab.eu, Email: gergely.katona(a)gu.se > >>> >> > >>> >> _______________________________________________ > >>> >> cctbxbb mailing list > >>> >> cctbxbb(a)phenix-online.org > >>> >> http://phenix-online.org/mailman/listinfo/cctbxbb > >>> > > >>> > _______________________________________________ > >>> > cctbxbb mailing list > >>> > cctbxbb(a)phenix-online.org > >>> > http://phenix-online.org/mailman/listinfo/cctbxbb > >>> > >>> > >>> > >>> -- > >>> Gergely Katona, PhD > >>> Associate Professor > >>> Department of Chemistry and Molecular Biology, University of Gothenburg > >>> Box 462, 40530 Göteborg, Sweden > >>> Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910 > >>> Web: http://katonalab.eu, Email: gergely.katona(a)gu.se > >>> > >>> _______________________________________________ > >>> cctbxbb mailing list > >>> cctbxbb(a)phenix-online.org > >>> http://phenix-online.org/mailman/listinfo/cctbxbb > > > > _______________________________________________ > > cctbxbb mailing list > > cctbxbb(a)phenix-online.org > > http://phenix-online.org/mailman/listinfo/cctbxbb > > > > -- > Gergely Katona, Professor > Department of Chemistry and Molecular Biology, University of Gothenburg > Box 462, 40530 Göteborg, Sweden > Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910 > Web: http://katonalab.eu, Email: gergely.katona(a)gu.se -- Gergely Katona, Professor Department of Chemistry and Molecular Biology, University of Gothenburg Box 462, 40530 Göteborg, Sweden Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910 Web: http://katonalab.eu, Email: gergely.katona(a)gu.se

6 years, 1 month

Re: [cctbxbb] some thoughts on cctbx and pip

by Billy Poon

Hi Gergely, Happy New Year! Can you provide the output to "conda list" for each environment? I suspect that the old version of cctbx might still be around. Is there a file named PYTHON_VERSION_MAJOR_MINOR in "/home/gergely/anaconda3/lib"? If so, delete that file. To make sure you are downloading a new copy of the package, clear the cache where conda keeps copies of all the packages. To do that, you can run "conda clean -y --all". You can remove the "-y" flag if you want to see what will be deleted. The hash for the new linux package should be h8b68381_0. The last error looks like an incompatible version of boost or gcc library was installed. The output from "conda list" should show the boost and boost-cpp packages coming from conda-forge. I would avoid installing into the root or base environment because that usually pulls from the default channels. All the dependencies should be pulled from the conda-forge channel. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org On Fri, Jan 3, 2020 at 2:20 PM Gergely Katona <gkatona(a)gmail.com> wrote: > I found some other errors when using the test environment. > > > --------------------------------------------------------------------------- > RuntimeError Traceback (most recent call last) > <ipython-input-1-fe308b345b3f> in <module> > 10 import scipy as sp > 11 from scipy import linalg > ---> 12 import iotbx.pdb > 13 import cctbx > 14 import pandas as pd > > ~/anaconda3/envs/test/lib/python3.8/site-packages/iotbx/pdb/__init__.py > in <module> > 8 > 9 import iotbx.pdb.records > ---> 10 import iotbx.pdb.hierarchy > 11 from scitbx import matrix > 12 > > ~/anaconda3/envs/test/lib/python3.8/site-packages/iotbx/pdb/hierarchy.py > in <module> > 14 from six.moves import cStringIO as StringIO > 15 from iotbx.pdb import hy36encode, hy36decode > ---> 16 import iotbx.cif.model > 17 from cctbx import crystal > 18 from libtbx import group_args > > ~/anaconda3/envs/test/lib/python3.8/site-packages/iotbx/cif/__init__.py > in <module> > 19 > 20 from cctbx.array_family import flex > ---> 21 from cctbx import miller > 22 from iotbx.cif import model, builders, geometry > 23 from libtbx.containers import OrderedDict > > ~/anaconda3/envs/test/lib/python3.8/site-packages/cctbx/miller/__init__.py > in <module> > 11 > 12 from cctbx import crystal > ---> 13 from cctbx import maptbx > 14 from cctbx import sgtbx > 15 from cctbx.sgtbx import lattice_symmetry > > ~/anaconda3/envs/test/lib/python3.8/site-packages/cctbx/maptbx/__init__.py > in <module> > 15 from libtbx import adopt_init_args > 16 from libtbx.utils import Sorry > ---> 17 import libtbx.load_env > 18 import math > 19 import sys, os > > ~/anaconda3/envs/test/lib/python3.8/site-packages/libtbx/load_env.py in > <module> > 3 import libtbx.env_config > 4 import os > ----> 5 libtbx.env = libtbx.env_config.unpickle() > 6 libtbx.env.set_os_environ_all_dist() > 7 libtbx.env.dispatcher_name = > os.environ.get("LIBTBX_DISPATCHER_NAME") > > ~/anaconda3/envs/test/lib/python3.8/site-packages/libtbx/env_config.py > in unpickle() > 2736 env = pickle.load(libtbx_env) > 2737 if (env.python_version_major_minor != sys.version_info[:2]): > -> 2738 env.raise_python_version_incompatible() > 2739 if (op.realpath(build_path) != op.realpath(abs(env.build_path))): > 2740 env.build_path.reset(build_path) > > ~/anaconda3/envs/test/lib/python3.8/site-packages/libtbx/env_config.py > in raise_python_version_incompatible(self, prev_pvmm) > 469 if (prev_pvmm is None): > 470 prev_pvmm = "%d.%d" % self.python_version_major_minor > --> 471 raise RuntimeError("Python version incompatible with this > build:\n" > 472 + " Build directory: %s\n" % > show_string(abs(self.build_path)) > 473 + " Python version used initially: %s\n" % prev_pvmm > > RuntimeError: Python version incompatible with this build: > Build directory: "/home/gergely/anaconda3" > Python version used initially: 3.6 > Python version in use now: 3.8 > > > Interestingly in the base environment all import worked, but I got an > error at: > > > ArgumentError Traceback (most recent call last) > <ipython-input-4-5bc71c36e121> in <module> > 33 atm_odd.set_b(0) > 34 > ---> 35 odd.write_pdb_file("bdiff_in_even_000.pdb") #skriver ny pdb > med dessa inkluderade > 36 dfWBvals=pd.DataFrame(rows_list) > > ~/anaconda3/lib/python3.6/site-packages/iotbx/pdb/__init__.py in > write_pdb_file(self, file_name, open_append, crystal_symmetry, > cryst1_z, write_scale_records, append_end, atom_hetatm, sigatm, > anisou, siguij) > 930 siguij=True): > 931 if (crystal_symmetry is Auto): > --> 932 crystal_symmetry = self.crystal_symmetry() > 933 if (cryst1_z is Auto): > 934 cryst1_z = self.extract_cryst1_z_columns() > > ~/anaconda3/lib/python3.6/site-packages/iotbx/pdb/__init__.py in > crystal_symmetry(self, crystal_symmetry, weak_symmetry) > 1218 crystal_symmetry=None, > 1219 weak_symmetry=False): > -> 1220 self_symmetry = self.crystal_symmetry_from_cryst1() > 1221 if (self_symmetry is None): > 1222 self_symmetry = self._crystal_symmetry_from_cns_remark_sg() > > ~/anaconda3/lib/python3.6/site-packages/iotbx/pdb/__init__.py in > crystal_symmetry_from_cryst1(self) > 1195 for line in self.crystallographic_section(): > 1196 if (line.startswith("CRYST1")): > -> 1197 return > cryst1_interpretation.crystal_symmetry(cryst1_record=line) > 1198 return None > 1199 > > ~/anaconda3/lib/python3.6/site-packages/iotbx/pdb/cryst1_interpretation.py > in crystal_symmetry(cryst1_record) > 136 space_group_info=None) > 137 space_group_info = > categorize(cryst1_record.sgroup).space_group_info( > --> 138 unit_cell=u) > 139 return crystal.symmetry(unit_cell=u, > space_group_info=space_group_info) > > ~/anaconda3/lib/python3.6/site-packages/iotbx/pdb/cryst1_interpretation.py > in space_group_info(self, unit_cell) > 85 if (self.symbol is None): return None > 86 if (self.category is None): > ---> 87 try: return sgtbx.space_group_info(self.symbol) > 88 except RuntimeError: return None > 89 if (isinstance(unit_cell, uctbx.ext.unit_cell)): > > ~/anaconda3/lib/python3.6/site-packages/cctbx/sgtbx/__init__.py in > __init__(self, symbol, table_id, group, number, space_group_t_den) > 100 assert group is None > 101 if (table_id is None): > --> 102 symbols = space_group_symbols(symbol) > 103 else: > 104 if (isinstance(symbol, int)): symbol = str(symbol) > > ArgumentError: Python argument types in > space_group_symbols.__init__(space_group_symbols, str) > did not match C++ signature: > __init__(_object*, int space_group_number) > __init__(_object*, int space_group_number, > std::__cxx11::basic_string<char, std::char_traits<char>, > std::allocator<char> > extension='') > __init__(_object*, int space_group_number, > std::__cxx11::basic_string<char, std::char_traits<char>, > std::allocator<char> > extension='', std::__cxx11::basic_string<char, > std::char_traits<char>, std::allocator<char> > table_id='') > __init__(_object*, std::__cxx11::basic_string<char, > std::char_traits<char>, std::allocator<char> > symbol) > __init__(_object*, std::__cxx11::basic_string<char, > std::char_traits<char>, std::allocator<char> > symbol, > std::__cxx11::basic_string<char, std::char_traits<char>, > std::allocator<char> > table_id='') > > > Gergely > > > > On Fri, Jan 3, 2020 at 1:44 PM Gergely Katona <gkatona(a)gmail.com> wrote: > > > > Dear Billy, > > > > I did some tests installing in my base conda was not troublefree in > > python 3.8. Running iotbx.fetch_pdb --all --mtz 1kp8 resulted in boost > > related error when converting to mtz. Installing into a test > > environment went fine with iotbx.fetch_pdb --all --mtz 1kp8 running > > successfully. I could add pymc3, jupyter and seaborn and iotbx still > > did not break. My LIBTBX_BUILD is not set however in the test > > environment, which breaks miller when I was trying to import it. > > Manually setting the LIBTBX_BUILD to CONDA_PREFIX (setenv LIBTBX_BUILD > > $CONDA_PREFIX) fixes this and one of my script works fine! I will come > > back if I find some problems with my other scripts, but so far this > > looks promising! > > > > > > Happy new year! > > > > Gergely > > > > > > > > > > > > On Fri, Dec 20, 2019 at 8:16 PM Billy Poon <BKPoon(a)lbl.gov> wrote: > > > > > > Hi everyone, > > > > > > I updated the conda packages on the cctbx-dev channel and there are > also now packages for macOS. The old packages have been removed so you can > create a new environment with > > > > > > conda create -n test -c cctbx-dev cctbx python=2.7 > > > conda activate test > > > > > > where "test" is the environment name and 2.7 is the python version. > For the python version, you can also pick 3.6, 3.7, or 3.8. I think the > latest conda will install 3.8 as the default python if the python argument > is not provided. Or install into an existing environment (with python > already installed) with the same command as before, > > > > > > conda install -c cctbx-dev cctbx > > > > > > Again, your .condarc file should have conda-forge as the first channel > so that dependencies can be pulled correctly. > > > > > > The dispatchers should work now and $LIBTBX_BUILD will be set on > activation of an environment (and unset on environment deactivation) or > after installing into an existing environment, so you can do more > interesting things like > > > > > > iotbx.fetch_pdb --all --mtz 1kp8 > > > > > > However, this package does not install databases, so > > > > > > molprobity.molprobity 1kp8.pdb 1kp8.mtz > > > > > > will fail because the database is not available (also probe and reduce > are not built). > > > > > > Some known issues in no particular order, > > > > > > 1) You can run "libtbx.run_tests_parallel module=cctbx nproc=Auto" to > run tests, but not all the test files were copied, so I got 30 failures > here. The final package will probably not have the test files. > > > 2) The other python dispatchers, like "cctbx.python", were not > updated, so those will fail. But you can just run "python" in the active > environment. > > > 3) Parts of mmtbx still need to be updated for Python 3. > > > 4) The LIBTBX_BUILD variable should be set for sh and csh shells. Let > me know if it's not working for your shell (i.e. "echo $LIBTBX_BUILD" > should show the same thing as $CONDA_PREFIX). > > > 5) One future step is to enable building other CCTBX-like modules with > this conda package. This will require some bookkeeping updates so that > modules in the conda environment and the modules being built are tracked > properly. Also, making sure that all the necessary headers exist in > $PREFIX/include. > > > > > > Gergely, let me know if your scripts are working. > > > > > > Happy holidays! > > > > > > -- > > > Billy K. Poon > > > Research Scientist, Molecular Biophysics and Integrated Bioimaging > > > Lawrence Berkeley National Laboratory > > > 1 Cyclotron Road, M/S 33R0345 > > > Berkeley, CA 94720 > > > Tel: (510) 486-5709 > > > Fax: (510) 486-5909 > > > Web: https://phenix-online.org > > > > > > > > > On Wed, Dec 18, 2019 at 11:25 AM Billy Poon <BKPoon(a)lbl.gov> wrote: > > >> > > >> Hi Gergely, > > >> > > >> That's the other information that hasn't been updated yet in the > conda package. :) > > >> > > >> For LIBTBX_BUILD, I can set up environment variables sort of how the > conda gcc package sets up environment variables. I have to double check to > see if they're set after installation of the package and after activation > of an environment. The variable will just be a copy of $CONDA_PREFIX. > > >> > > >> The libtbx_env file is a file that exists in $LIBTBX_BUILD that > basically stores configuration information. I'll have to modify the > contents to update the locations of the different modules since the conda > package will not have a "modules" directory. > > >> > > >> -- > > >> Billy K. Poon > > >> Research Scientist, Molecular Biophysics and Integrated Bioimaging > > >> Lawrence Berkeley National Laboratory > > >> 1 Cyclotron Road, M/S 33R0345 > > >> Berkeley, CA 94720 > > >> Tel: (510) 486-5709 > > >> Fax: (510) 486-5909 > > >> Web: https://phenix-online.org > > >> > > >> > > >> On Wed, Dec 18, 2019 at 2:08 AM Gergely Katona <gkatona(a)gmail.com> > wrote: > > >>> > > >>> Hi Billy, > > >>> > > >>> Conda install went fine with your instructions after rearranging the > > >>> channels by putting cctbx last. I removed all environmental variables > > >>> and previous build of cctbx. > > >>> > > >>> import sys > > >>> print (sys.path, sys.prefix) > > >>> > > >>> ['/home/gergely/anaconda3/lib/python36.zip', > > >>> '/home/gergely/anaconda3/lib/python3.6', > > >>> '/home/gergely/anaconda3/lib/python3.6/lib-dynload', '', > > >>> '/home/gergely/anaconda3/lib/python3.6/site-packages', > > >>> > '/home/gergely/anaconda3/lib/python3.6/site-packages/IPython/extensions', > > >>> '/home/gergely/.ipython'] /home/gergely/anaconda3 > > >>> > > >>> Many imports went fine including pymc3, but I encountered problems > > >>> with these three: > > >>> > > >>> from cctbx import miller > > >>> import iotbx.pdb > > >>> from iotbx import reflection_file_reader, mtz > > >>> > > >>> > > >>> I also got type error when handling space groups. > > >>> > > >>> > > >>> > > >>> > --------------------------------------------------------------------------- > > >>> KeyError Traceback (most recent > call last) > > >>> <ipython-input-5-cedbd4f84f3d> in <module> > > >>> 25 from cctbx import uctbx > > >>> 26 from cctbx import sgtbx > > >>> ---> 27 from cctbx import miller > > >>> 28 #from iotbx import reflection_file_reader, mtz > > >>> 29 sns.set_context("poster") > > >>> > > >>> ~/anaconda3/lib/python3.6/site-packages/cctbx/miller/__init__.py in > <module> > > >>> 11 > > >>> 12 from cctbx import crystal > > >>> ---> 13 from cctbx import maptbx > > >>> 14 from cctbx import sgtbx > > >>> 15 from cctbx.sgtbx import lattice_symmetry > > >>> > > >>> ~/anaconda3/lib/python3.6/site-packages/cctbx/maptbx/__init__.py in > <module> > > >>> 15 from libtbx import adopt_init_args > > >>> 16 from libtbx.utils import Sorry > > >>> ---> 17 import libtbx.load_env > > >>> 18 import math > > >>> 19 import sys, os > > >>> > > >>> ~/anaconda3/lib/python3.6/site-packages/libtbx/load_env.py in > <module> > > >>> 3 import libtbx.env_config > > >>> 4 import os > > >>> ----> 5 libtbx.env = libtbx.env_config.unpickle() > > >>> 6 libtbx.env.set_os_environ_all_dist() > > >>> 7 libtbx.env.dispatcher_name = > os.environ.get("LIBTBX_DISPATCHER_NAME") > > >>> > > >>> ~/anaconda3/lib/python3.6/site-packages/libtbx/env_config.py in > unpickle() > > >>> 2603 > > >>> 2604 def unpickle(): > > >>> -> 2605 build_path = os.environ["LIBTBX_BUILD"] > > >>> 2606 > set_preferred_sys_prefix_and_sys_executable(build_path=build_path) > > >>> 2607 libtbx_env = open(op.join(build_path, "libtbx_env"), "rb") > > >>> > > >>> ~/anaconda3/lib/python3.6/os.py in __getitem__(self, key) > > >>> 667 except KeyError: > > >>> 668 # raise KeyError with the original key value > > >>> --> 669 raise KeyError(key) from None > > >>> 670 return self.decodevalue(value) > > >>> 671 > > >>> > > >>> KeyError: 'LIBTBX_BUILD' > > >>> > > >>> > > >>> > > >>> > --------------------------------------------------------------------------- > > >>> ArgumentError Traceback (most recent > call last) > > >>> <ipython-input-7-2acd3a9ce26a> in <module> > > >>> 26 return > ms,msnam,mscent,msacent,msnamacent,msnamcent,msnamacent_dstar > > >>> 27 > > >>> ---> 28 > ms,msnam,mscent,msacent,msnamacent,msnamcent,msnamacent_dstar=initializecrystal() > > >>> > > >>> <ipython-input-7-2acd3a9ce26a> in initializecrystal() > > >>> 11 uc = uctbx.unit_cell(unit_cell) > > >>> 12 wavelength = 1.54980 > > >>> ---> 13 xtal_symm = crystal.symmetry(unit_cell=unit_cell, > > >>> space_group_symbol="P 43 21 2") > > >>> 14 > > >>> 15 ms = > > >>> miller.build_set(crystal_symmetry=xtal_symm,anomalous_flag=True, > > >>> d_min=1.61) > > >>> > > >>> ~/anaconda3/lib/python3.6/site-packages/cctbx/crystal/__init__.py in > > >>> __init__(self, unit_cell, space_group_symbol, space_group_info, > > >>> space_group, correct_rhombohedral_setting_if_necessary, > > >>> assert_is_compatible_unit_cell, > raise_sorry_if_incompatible_unit_cell, > > >>> force_compatible_unit_cell) > > >>> 74 if (space_group_symbol is not None): > > >>> 75 self._space_group_info = sgtbx.space_group_info( > > >>> ---> 76 symbol=space_group_symbol) > > >>> 77 elif (space_group is not None): > > >>> 78 if (isinstance(space_group, sgtbx.space_group)): > > >>> > > >>> ~/anaconda3/lib/python3.6/site-packages/cctbx/sgtbx/__init__.py in > > >>> __init__(self, symbol, table_id, group, number, space_group_t_den) > > >>> 100 assert group is None > > >>> 101 if (table_id is None): > > >>> --> 102 symbols = space_group_symbols(symbol) > > >>> 103 else: > > >>> 104 if (isinstance(symbol, int)): symbol = str(symbol) > > >>> > > >>> ArgumentError: Python argument types in > > >>> space_group_symbols.__init__(space_group_symbols, str) > > >>> did not match C++ signature: > > >>> __init__(_object*, int space_group_number) > > >>> __init__(_object*, int space_group_number, > > >>> std::__cxx11::basic_string<char, std::char_traits<char>, > > >>> std::allocator<char> > extension='') > > >>> __init__(_object*, int space_group_number, > > >>> std::__cxx11::basic_string<char, std::char_traits<char>, > > >>> std::allocator<char> > extension='', std::__cxx11::basic_string<char, > > >>> std::char_traits<char>, std::allocator<char> > table_id='') > > >>> __init__(_object*, std::__cxx11::basic_string<char, > > >>> std::char_traits<char>, std::allocator<char> > symbol) > > >>> __init__(_object*, std::__cxx11::basic_string<char, > > >>> std::char_traits<char>, std::allocator<char> > symbol, > > >>> std::__cxx11::basic_string<char, std::char_traits<char>, > > >>> std::allocator<char> > table_id='') > > >>> > > >>> > > >>> When I tried to set LIBTBX_BUILD to /home/gergely/anaconda3 (this is > > >>> sys.prefix on my system), I got other problems when importing. Can > > >>> LIBTBX_BUILD be set in the conda package? > > >>> > > >>> > > >>> > > >>> > --------------------------------------------------------------------------- > > >>> FileNotFoundError Traceback (most recent > call last) > > >>> <ipython-input-1-7e2b144826cc> in <module> > > >>> 26 from cctbx import sgtbx > > >>> 27 #from cctbx import miller > > >>> ---> 28 from iotbx import reflection_file_reader, mtz > > >>> 29 sns.set_context("poster") > > >>> 30 plt.rcParams.update({'figure.autolayout': True}) > > >>> > > >>> > ~/anaconda3/lib/python3.6/site-packages/iotbx/reflection_file_reader.py > > >>> in <module> > > >>> 53 > > >>> 54 from __future__ import absolute_import, division, > print_function > > >>> ---> 55 from iotbx import mtz > > >>> 56 from iotbx.scalepack import merge as scalepack_merge > > >>> 57 from iotbx.scalepack import no_merge_original_index as > > >>> scalepack_no_merge > > >>> > > >>> ~/anaconda3/lib/python3.6/site-packages/iotbx/mtz/__init__.py in > <module> > > >>> 9 import iotbx_mtz_ext as ext > > >>> 10 > > >>> ---> 11 from iotbx.mtz import extract_from_symmetry_lib > > >>> 12 from cctbx import xray > > >>> 13 import cctbx.xray.observation_types > > >>> > > >>> > ~/anaconda3/lib/python3.6/site-packages/iotbx/mtz/extract_from_symmetry_lib.py > > >>> in <module> > > >>> 1 from __future__ import absolute_import, division, > print_function > > >>> 2 from cctbx import sgtbx > > >>> ----> 3 import libtbx.load_env > > >>> 4 import os.path as op > > >>> 5 from six.moves import range > > >>> > > >>> ~/anaconda3/lib/python3.6/site-packages/libtbx/load_env.py in > <module> > > >>> 3 import libtbx.env_config > > >>> 4 import os > > >>> ----> 5 libtbx.env = libtbx.env_config.unpickle() > > >>> 6 libtbx.env.set_os_environ_all_dist() > > >>> 7 libtbx.env.dispatcher_name = > os.environ.get("LIBTBX_DISPATCHER_NAME") > > >>> > > >>> ~/anaconda3/lib/python3.6/site-packages/libtbx/env_config.py in > unpickle() > > >>> 2605 build_path = os.environ["LIBTBX_BUILD"] > > >>> 2606 > set_preferred_sys_prefix_and_sys_executable(build_path=build_path) > > >>> -> 2607 libtbx_env = open(op.join(build_path, "libtbx_env"), "rb") > > >>> 2608 env = pickle.load(libtbx_env) > > >>> 2609 if (env.python_version_major_minor != > sys.version_info[:2]): > > >>> > > >>> FileNotFoundError: [Errno 2] No such file or directory: > > >>> '/home/gergely/anaconda3/libtbx_env' > > >>> > > >>> On Wed, Dec 18, 2019 at 9:10 AM Billy Poon <BKPoon(a)lbl.gov> wrote: > > >>> > > > >>> > Hi Gergely, > > >>> > > > >>> > I've uploaded linux packages to a new channel, cctbx-dev, and you > can install it with > > >>> > > > >>> > conda install -c cctbx-dev cctbx > > >>> > > > >>> > in your current environment. You should set your ~/.condarc file > to pull the other dependencies from the conda-forge channel first, so put > conda-forge above cctbx. Mine looks like > > >>> > > > >>> > channels: > > >>> > - conda-forge > > >>> > - defaults > > >>> > - cctbx > > >>> > > > >>> > Do you need dxtbx for your scripts? This package does not build > that part. I think the plan is to build a separate conda package for dxtbx > so that it can be updated more frequently. I can rebuild the packages to > include it for testing, but the one being submitted to conda-forge will not > have it. > > >>> > > > >>> > Also, your error message is probably due to version of HDF5 that > the development build installs. The bootstrap.py script will install > 1.10.4, but your other dependency is looking for 1.10.5. Installing this > cctbx conda package should install 1.10.5, which should fix the issue. > Also, I'm updating those environments and 1.10.5 will be the new default > version. > > >>> > > > >>> > Lastly, the dispatchers will not work in these packages because > the old paths during the build process are still in them and many of them > expect some additional information that has not been updated in the > packages yet. I'm in the process of doing that and will update the > cctbx-dev channel when that's done. However, by starting python, you can > import cctbx modules. So you can run commands like > > >>> > > > >>> > from scitbx.array_family import flex > > >>> > a = flex.random_double(1000000) > > >>> > b = flex.min_max_mean_double(a) > > >>> > b.min > > >>> > b.max > > >>> > b.mean > > >>> > > > >>> > Thanks! > > >>> > > > >>> > -- > > >>> > Billy K. Poon > > >>> > Research Scientist, Molecular Biophysics and Integrated Bioimaging > > >>> > Lawrence Berkeley National Laboratory > > >>> > 1 Cyclotron Road, M/S 33R0345 > > >>> > Berkeley, CA 94720 > > >>> > Tel: (510) 486-5709 > > >>> > Fax: (510) 486-5909 > > >>> > Web: https://phenix-online.org > > >>> > > > >>> > > > >>> > On Tue, Dec 17, 2019 at 5:39 AM Gergely Katona <gkatona(a)gmail.com> > wrote: > > >>> >> > > >>> >> Dear Billy, > > >>> >> > > >>> >> Thank you for the detailed explanation, I look forward to do > further > > >>> >> testing! I aim to pool all modules under the same environment, if > > >>> >> there are conflicts then I just try to reshuffle the order of > imports. > > >>> >> So far this did not cause problems for me even when I was using > system > > >>> >> python, but of course it is not the most prudent thing to do. With > > >>> >> anaconda everything is much more standardized and isolated > already and > > >>> >> without being superuser I can have my familiar environment at any > > >>> >> synchrotron based cluster. It is great that cctbx will be an > integral > > >>> >> part of this ecosystem and this was also the last thing holding me > > >>> >> back from adopting python3. About hdf5, pymc3 requires it and > > >>> >> importing causes a kernel restart with the following error > messages, > > >>> >> curiously if I import h5py first this can be avoided. > > >>> >> > > >>> >> Best wishes, > > >>> >> > > >>> >> Gergely > > >>> >> > > >>> >> import pymc3 as pm > > >>> >> > > >>> >> Warning! ***HDF5 library version mismatched error*** > > >>> >> The HDF5 header files used to compile this application do not > match > > >>> >> the version used by the HDF5 library to which this application is > linked. > > >>> >> Data corruption or segmentation faults may occur if the > application continues. > > >>> >> This can happen when an application was compiled by one version > of HDF5 but > > >>> >> linked with a different version of static or shared HDF5 library. > > >>> >> You should recompile the application or check your shared library > related > > >>> >> settings such as 'LD_LIBRARY_PATH'. > > >>> >> You can, at your own risk, disable this warning by setting the > environment > > >>> >> variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'. > > >>> >> Setting it to 2 or higher will suppress the warning messages > totally. > > >>> >> Headers are 1.10.4, library is 1.10.5 > > >>> >> SUMMARY OF THE HDF5 CONFIGURATION > > >>> >> ================================= > > >>> >> > > >>> >> General Information: > > >>> >> ------------------- > > >>> >> HDF5 Version: 1.10.5 > > >>> >> Configured on: Tue Oct 22 12:02:13 UTC 2019 > > >>> >> Configured by: conda@16247e67ecd5 > > >>> >> Host system: x86_64-conda_cos6-linux-gnu > > >>> >> Uname information: Linux 16247e67ecd5 > 4.15.0-1059-azure > > >>> >> #64-Ubuntu SMP Fri Sep 13 17:02:44 UTC 2019 x86_64 x86_64 x86_64 > > >>> >> GNU/Linux > > >>> >> Byte sex: little-endian > > >>> >> Installation point: /home/gergely/anaconda3 > > >>> >> > > >>> >> Compiling Options: > > >>> >> ------------------ > > >>> >> Build Mode: production > > >>> >> Debugging Symbols: no > > >>> >> Asserts: no > > >>> >> Profiling: no > > >>> >> Optimization Level: high > > >>> >> > > >>> >> Linking Options: > > >>> >> ---------------- > > >>> >> Libraries: static, shared > > >>> >> Statically Linked Executables: > > >>> >> LDFLAGS: -Wl,-O2 -Wl,--sort-common > > >>> >> -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags > > >>> >> -Wl,--gc-sections -Wl,-rpath,/home/gergely/anaconda3/lib > > >>> >> -Wl,-rpath-link,/home/gergely/anaconda3/lib > > >>> >> -L/home/gergely/anaconda3/lib > > >>> >> H5_LDFLAGS: > > >>> >> AM_LDFLAGS: -L/home/gergely/anaconda3/lib > > >>> >> Extra libraries: -lrt -lpthread -lz -ldl -lm > > >>> >> Archiver: > > >>> >> > /home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/_build_env/bin/x86_64-conda_cos6-linux-gnu-ar > > >>> >> AR_FLAGS: cr > > >>> >> Ranlib: > > >>> >> > /home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/_build_env/bin/x86_64-conda_cos6-linux-gnu-ranlib > > >>> >> > > >>> >> Languages: > > >>> >> ---------- > > >>> >> C: yes > > >>> >> C Compiler: > > >>> >> > /home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc > > >>> >> CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 > > >>> >> -I/home/gergely/anaconda3/include > > >>> >> H5_CPPFLAGS: -D_GNU_SOURCE > > >>> >> -D_POSIX_C_SOURCE=200809L -DNDEBUG -UH5_DEBUG_API > > >>> >> AM_CPPFLAGS: > -I/home/gergely/anaconda3/include > > >>> >> C Flags: -march=nocona -mtune=haswell > > >>> >> -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 > > >>> >> -ffunction-sections -pipe -I/home/gergely/anaconda3/include > > >>> >> > -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/work=/usr/local/src/conda/hdf5_split-1.10.5 > > >>> >> > -fdebug-prefix-map=/home/gergely/anaconda3=/usr/local/src/conda-prefix > > >>> >> H5 C Flags: -std=c99 -pedantic -Wall > -Wextra > > >>> >> -Wbad-function-cast -Wc++-compat -Wcast-align -Wcast-qual > -Wconversion > > >>> >> -Wdeclaration-after-statement -Wdisabled-optimization > -Wfloat-equal > > >>> >> -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-declarations > > >>> >> -Wmissing-include-dirs -Wmissing-prototypes -Wnested-externs > > >>> >> -Wold-style-definition -Wpacked -Wpointer-arith -Wredundant-decls > > >>> >> -Wshadow -Wstrict-prototypes -Wswitch-default -Wswitch-enum > -Wundef > > >>> >> -Wunused-macros -Wunsafe-loop-optimizations -Wwrite-strings > > >>> >> -finline-functions -s -Wno-inline -Wno-aggregate-return > > >>> >> -Wno-missing-format-attribute -Wno-missing-noreturn -O > > >>> >> AM C Flags: > > >>> >> Shared C Library: yes > > >>> >> Static C Library: yes > > >>> >> > > >>> >> > > >>> >> Fortran: yes > > >>> >> Fortran Compiler: > > >>> >> > /home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/_build_env/bin/x86_64-conda_cos6-linux-gnu-gfortran > > >>> >> Fortran Flags: > > >>> >> H5 Fortran Flags: -pedantic -Wall -Wextra > -Wunderflow > > >>> >> -Wimplicit-interface -Wsurprising -Wno-c-binding-type -s -O2 > > >>> >> AM Fortran Flags: > > >>> >> Shared Fortran Library: yes > > >>> >> Static Fortran Library: yes > > >>> >> > > >>> >> C++: yes > > >>> >> C++ Compiler: > > >>> >> > /home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/_build_env/bin/x86_64-conda_cos6-linux-gnu-c++ > > >>> >> C++ Flags: -fvisibility-inlines-hidden > > >>> >> -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell > > >>> >> -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 > > >>> >> -ffunction-sections -pipe -I/home/gergely/anaconda3/include > > >>> >> > -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/work=/usr/local/src/conda/hdf5_split-1.10.5 > > >>> >> > -fdebug-prefix-map=/home/gergely/anaconda3=/usr/local/src/conda-prefix > > >>> >> H5 C++ Flags: -pedantic -Wall -W -Wundef > -Wshadow > > >>> >> -Wpointer-arith -Wcast-qual -Wcast-align -Wwrite-strings > -Wconversion > > >>> >> -Wredundant-decls -Winline -Wsign-promo -Woverloaded-virtual > > >>> >> -Wold-style-cast -Weffc++ -Wreorder -Wnon-virtual-dtor > > >>> >> -Wctor-dtor-privacy -Wabi -finline-functions -s -O > > >>> >> AM C++ Flags: > > >>> >> Shared C++ Library: yes > > >>> >> Static C++ Library: yes > > >>> >> > > >>> >> Java: no > > >>> >> > > >>> >> > > >>> >> Features: > > >>> >> --------- > > >>> >> Parallel HDF5: no > > >>> >> Parallel Filtered Dataset Writes: no > > >>> >> Large Parallel I/O: no > > >>> >> High-level library: yes > > >>> >> Threadsafety: yes > > >>> >> Default API mapping: v110 > > >>> >> With deprecated public symbols: yes > > >>> >> I/O filters (external): deflate(zlib) > > >>> >> MPE: no > > >>> >> Direct VFD: no > > >>> >> dmalloc: no > > >>> >> Packages w/ extra debug output: none > > >>> >> API tracing: no > > >>> >> Using memory checker: yes > > >>> >> Memory allocation sanity checks: no > > >>> >> Function stack tracing: no > > >>> >> Strict file format checks: no > > >>> >> Optimization instrumentation: no > > >>> >> > > >>> >> On Tue, Dec 17, 2019 at 8:35 AM Billy Poon <BKPoon(a)lbl.gov> > wrote: > > >>> >> > > > >>> >> > Hi Gergely, > > >>> >> > > > >>> >> > Let me build the test package tomorrow. All the gritty details > for building with conda is being finalized and the official documentation > will be updated to describe the steps. It would be too confusing to keep > changing the documentation as the process evolves. You do have the general > process, though, which is summarized as follows. > > >>> >> > > > >>> >> > 1) Installing dependencies. The cctbx_dependencies metapackage > was an initial approach for managing the CCTBX dependencies, but after > contacting the conda-forge folks, they recommended using the --only-deps > flag. So when the CCTBX conda package is available, you'll be able to get a > set of dependencies with, > > >>> >> > > > >>> >> > conda install -c conda-forge --only-deps cctbx > > >>> >> > > > >>> >> > By default, the bootstrap.py file will automatically install a > set of dependencies in the "conda_base" directory (and a conda installation > if one is not found). It just uses standard conda environment files located > in libtbx/auto_build/conda_envs, so you do not need to install > cctbx_dependencies as a separate step. The environment files avoid channel > issues by explicitly defining the channel to pull the packages from and the > cctbx channel just stores copies of packages from conda-forge. There were > issues earlier where the conda-forge packages would sometimes be moved to a > different label. The --use-conda flag also accepts a path to $CONDA_PREFIX > if you want to use a specific environment for testing. > > >>> >> > > > >>> >> > 2) Building. The bootstrap.py file handles that with SCons. > > >>> >> > > > >>> >> > 3) Running. After building, there should be a setpaths.sh (and > .csh) file that adds build/bin to your path. The build/bin directory has > our dispatchers, which are just scripts that set up the environment > variables for you. This prevents other programs from loading our libraries, > whose versions may conflict. You should see that there is a "python" > dispatcher, which is a convenience for developers. Otherwise, you can use > libtbx.python, which will be able to import CCTBX modules. > > >>> >> > > > >>> >> > The running part is where the conda package for CCTBX will be > different than this build. Since our Python files and extensions modules > will be in the "site-packages" directory for Python, the PYTHONPATH > variable will not be needed (and conda suggests that that variable not be > set). The other CCTBX libraries will be in $CONDA_PREFIX/lib, so > LD_LIBRARY_PATH is not needed. In an active environment, PATH will already > be modified. And then our LIBTBX_BUILD directory can be set to sys.prefix. > > >>> >> > > > >>> >> > So with the conda package, you would only need to activate your > conda environment and CCTBX should integrate with other conda packages. > What is the conflict with hdf5? That's something that should be fixed. > Thanks! > > >>> >> > > > >>> >> > -- > > >>> >> > Billy K. Poon > > >>> >> > Research Scientist, Molecular Biophysics and Integrated > Bioimaging > > >>> >> > Lawrence Berkeley National Laboratory > > >>> >> > 1 Cyclotron Road, M/S 33R0345 > > >>> >> > Berkeley, CA 94720 > > >>> >> > Tel: (510) 486-5709 > > >>> >> > Fax: (510) 486-5909 > > >>> >> > Web: https://phenix-online.org > > >>> >> > > > >>> >> > > > >>> >> > On Mon, Dec 16, 2019 at 2:53 AM Gergely Katona < > gkatona(a)gmail.com> wrote: > > >>> >> >> > > >>> >> >> Dear Billy, > > >>> >> >> > > >>> >> >> Thank you for this update and for your efforts! I found a > solution and > > >>> >> >> indeed most things already work in anaconda3. The steps I took > (even > > >>> >> >> if these instructions will have short expiry date): > > >>> >> >> > > >>> >> >> Modified .condarc with: > > >>> >> >> channels: > > >>> >> >> - cctbx > > >>> >> >> - conda-forge > > >>> >> >> - defaults > > >>> >> >> > > >>> >> >> run > > >>> >> >> conda conda install cctbx_dependencies python=3.6 > > >>> >> >> > > >>> >> >> I expect this will work without python=3.6 in the near future. > > >>> >> >> > > >>> >> >> Then compiling cctbx with anaconda3 python went without any > problem > > >>> >> >> when using these flags: > > >>> >> >> python bootstrap.py --use-conda --python3 --nproc=12 > > >>> >> >> > > >>> >> >> Then I probably did the unorthodox thing and sourced these > directories: > > >>> >> >> > > >>> >> >> setenv LIBTBX_BUILD /home/gergely/cctbx/build > > >>> >> >> setenv PATH ${PATH}:/home/gergely/cctbx/build/bin > > >>> >> >> setenv PYTHONPATH > > >>> >> >> > /home/gergely/cctbx/modules/cctbx_project:/home/gergely/cctbx/modules:/home/gergely/cctbx/modules/cctbx_project/boost_adaptbx:/home/gergely/cctbx/build/lib:/home/gergely/cctbx/conda_base/lib/python3.6/site-packages:$PYTHONPATH > > >>> >> >> setenv LD_LIBRARY_PATH > > >>> >> >> > /home/gergely/cctbx/conda_base/lib:/home/gergely/cctbx/build/lib:$LD_LIBRARY_PATH > > >>> >> >> > > >>> >> >> There is probably a better way to put this into conda > environment. > > >>> >> >> With these steps I could run one of my scripts depending on > cctbx. The > > >>> >> >> only problem I found is that hdf5 library had conflict with > another > > >>> >> >> package in conda, but I does not find this as a showstopper. > > >>> >> >> > > >>> >> >> Best wishes, > > >>> >> >> > > >>> >> >> Gergely > > >>> >> >> > > >>> >> >> > > >>> >> >> > > >>> >> >> > > >>> >> >> > > >>> >> >> > > >>> >> >> On Fri, Dec 13, 2019 at 7:23 PM Billy Poon <BKPoon(a)lbl.gov> > wrote: > > >>> >> >> > > > >>> >> >> > Hi Gergely, > > >>> >> >> > > > >>> >> >> > It's still a work in progress. I'm sorting out some Windows > issues right now. I can probably build a test package on a separate channel > for people that want to test it (let's say next week?). I'll provide > instructions, but basically, the test conda package will be in its own > separate channel and the dependencies will be pulled from the conda-forge > channel. I want most things to be working correctly on Python 2.7, 3.6, > 3.7, and 3.8 on all 3 platforms. > > >>> >> >> > > > >>> >> >> > Thanks! > > >>> >> >> > > > >>> >> >> > -- > > >>> >> >> > Billy K. Poon > > >>> >> >> > Research Scientist, Molecular Biophysics and Integrated > Bioimaging > > >>> >> >> > Lawrence Berkeley National Laboratory > > >>> >> >> > 1 Cyclotron Road, M/S 33R0345 > > >>> >> >> > Berkeley, CA 94720 > > >>> >> >> > Tel: (510) 486-5709 > > >>> >> >> > Fax: (510) 486-5909 > > >>> >> >> > Web: https://phenix-online.org > > >>> >> >> > > > >>> >> >> > > > >>> >> >> > On Fri, Dec 13, 2019 at 5:44 AM Gergely Katona < > gkatona(a)gmail.com> wrote: > > >>> >> >> >> > > >>> >> >> >> Dear Billy, > > >>> >> >> >> > > >>> >> >> >> This sounds very promising and exciting. I am not sure if > cctbx is > > >>> >> >> >> already functional as a conda package in anaconda3 (Linux) > or this is > > >>> >> >> >> still work in progress. My technical expertise does not > allow me to > > >>> >> >> >> tell the difference. What I tried: > > >>> >> >> >> > > >>> >> >> >> Fresh install of anaconda3. Adding - cctbx and - > conda-forge to > > >>> >> >> >> .condarc . Installing pyside2 with conda. Running conda > install > > >>> >> >> >> conda_dependencies . I get a lot package version conflict, > and I > > >>> >> >> >> cannot import cctbx or iotbx to anaconda python. Am I > following the > > >>> >> >> >> right instructions? Or it is too early to expect that cctbx > works when > > >>> >> >> >> installed through conda? > > >>> >> >> >> > > >>> >> >> >> Best wishes, > > >>> >> >> >> > > >>> >> >> >> Gergely > > >>> >> >> >> > > >>> >> >> >> On Wed, Nov 27, 2019 at 3:56 PM Billy Poon <BKPoon(a)lbl.gov> > wrote: > > >>> >> >> >> > > > >>> >> >> >> > Hi all, > > >>> >> >> >> > > > >>> >> >> >> > For a brief update, I have submitted a recipe for > cctbxlite to conda-forge ( > https://github.com/conda-forge/staged-recipes/pull/10021) and support for > Python 3.7 and 3.8 is being added ( > https://github.com/cctbx/cctbx_project/pull/409). With some fixes for > Windows (https://github.com/cctbx/cctbx_project/pull/416), all platforms > (macOS, linux, and Windows) can build for Python 2.7, 3.6, 3.7, and 3.8. > Some additional changes will be needed to get Windows to work with Python 3 > and for tests to pass with Boost 1.70.0. That will enable the conda-forge > recipe to build for all platforms and for all supported versions of Python. > > >>> >> >> >> > > > >>> >> >> >> > Currently, the conda-forge recipe will install into the > conda python and cctbx imports can be done without sourcing the environment > scripts. It looks like a lot of the environment variables being set in the > dispatchers can be removed since the Python files and C++ extensions are in > the right places. I'll update the libtbx_env file so that commands that > load the environment can work correctly. > > >>> >> >> >> > > > >>> >> >> >> > -- > > >>> >> >> >> > Billy K. Poon > > >>> >> >> >> > Research Scientist, Molecular Biophysics and Integrated > Bioimaging > > >>> >> >> >> > Lawrence Berkeley National Laboratory > > >>> >> >> >> > 1 Cyclotron Road, M/S 33R0345 > > >>> >> >> >> > Berkeley, CA 94720 > > >>> >> >> >> > Tel: (510) 486-5709 > > >>> >> >> >> > Fax: (510) 486-5909 > > >>> >> >> >> > Web: https://phenix-online.org > > >>> >> >> >> > > > >>> >> >> >> > > > >>> >> >> >> > On Sun, Aug 25, 2019 at 2:33 PM Tristan Croll < > tic20(a)cam.ac.uk> wrote: > > >>> >> >> >> >> > > >>> >> >> >> >> Hi Luc, > > >>> >> >> >> >> > > >>> >> >> >> >> That sounds promising. From there, I’d need to work out > how to make a fully-packaged installer (basically a modified wheel file) > for the ChimeraX ToolShed - the aim is for the end user to not have to > worry about any of this. That adds a couple of complications - e.g. > $LIBTBX_BUILD would need to be set dynamically before first import - but > doesn’t seem insurmountable. > > >>> >> >> >> >> > > >>> >> >> >> >> Thanks, > > >>> >> >> >> >> > > >>> >> >> >> >> Tristan > > >>> >> >> >> >> > > >>> >> >> >> >> > > >>> >> >> >> >> > > >>> >> >> >> >> Tristan Croll > > >>> >> >> >> >> Research Fellow > > >>> >> >> >> >> Cambridge Institute for Medical Research > > >>> >> >> >> >> University of Cambridge CB2 0XY > > >>> >> >> >> >> > > >>> >> >> >> >> > > >>> >> >> >> >> > > >>> >> >> >> >> > > >>> >> >> >> >> > On 25 Aug 2019, at 18:31, Luc Bourhis < > luc_j_bourhis(a)mac.com> wrote: > > >>> >> >> >> >> > > > >>> >> >> >> >> > Hi Tristan, > > >>> >> >> >> >> > > > >>> >> >> >> >> > cctbx could be built to use your ChimeraX python, now > that cctbx is moving to Python 3. The option —with-python is there for that > with the bootstrap script. The specific environment setup boil down to > setting two environment variable LIBTBX_BUILD and either LD_LIBRARY_PATH on > Linux, PATH on Win32, or DYLIB_LIBRARY_PATH on MacOS. If you work within a > framework such as ChimeraX, that should not be difficult to ensure those > two variables are set. > > >>> >> >> >> >> > > > >>> >> >> >> >> > Best wishes, > > >>> >> >> >> >> > > > >>> >> >> >> >> > Luc > > >>> >> >> >> >> > > > >>> >> >> >> >> > > > >>> >> >> >> >> >> On 23 Aug 2019, at 19:02, Tristan Croll < > tic20(a)cam.ac.uk> wrote: > > >>> >> >> >> >> >> > > >>> >> >> >> >> >> To add my two cents on this: probably the second-most > common question I've had about ISOLDE's implementation is, "why didn't you > use CCTBX?". The honest answer to that is, "I didn't know how." > > >>> >> >> >> >> >> > > >>> >> >> >> >> >> Still don't, really - although the current > developments are rather promising. The problem I've faced is that CCTBX was > designed as its own self-contained Python (2.7, until very recently) > environment, with its own interpreter and a lot of very specific > environment setup. Meanwhile I'm developing ISOLDE in ChimeraX, which is > *also* its own self-contained Python (3.7) environment. To plug one into > the other in that form... well, I don't think I'm a good enough programmer > to really know where to start. > > >>> >> >> >> >> >> > > >>> >> >> >> >> >> The move to Conda and a more modular CCTBX > architecture should make a lot more possible in that direction. Pip would > be even better for me personally (ChimeraX can install directly from the > PyPI, but doesn't interact with Conda) - but I understand pretty well the > substantial challenge that would amount to (not least being that the PyPI > imposes a limit - around 100MB from memory? - on the size of an individual > package). > > >>> >> >> >> >> >> > > >>> >> >> >> >> >> Best regards, > > >>> >> >> >> >> >> > > >>> >> >> >> >> >> Tristan > > >>> >> >> >> >> >> > > >>> >> >> >> >> >>> On 2019-08-23 09:28, Luc Bourhis wrote: > > >>> >> >> >> >> >>> Hi Graeme, > > >>> >> >> >> >> >>> Yes, I know. But “black" is a program doing a very > particular task > > >>> >> >> >> >> >>> (code formatting from the top of my head). Requiring > to use a wrapper > > >>> >> >> >> >> >>> for python itself is another level. But ok, I think > I am mellowing to > > >>> >> >> >> >> >>> the idea after all! Talking with people around me, > and extrapolating, > > >>> >> >> >> >> >>> I would bet that, right now, a great majority of > people interested by > > >>> >> >> >> >> >>> cctbx in pip have already used the cctbx, so they > know about the > > >>> >> >> >> >> >>> Python wrapper, and they would not be too sanguine > about that. My > > >>> >> >> >> >> >>> concern is for the future, when pip will be the > first time some people > > >>> >> >> >> >> >>> use cctbx. Big fat warning notices on PyPI page and > a better error > > >>> >> >> >> >> >>> message when cctbx fails because LIBTBX_BUILD is not > set would be > > >>> >> >> >> >> >>> needed but that could be all right. > > >>> >> >> >> >> >>> If we do a pip installer, we should aim at a minimal > install: cctbx, > > >>> >> >> >> >> >>> iotbx and their dependencies, and that’s it. > > >>> >> >> >> >> >>> Best wishes, > > >>> >> >> >> >> >>> Luc > > >>> >> >> >> >> >>>> On 23 Aug 2019, at 07:17, > Graeme.Winter(a)Diamond.ac.uk <Graeme.Winter(a)diamond.ac.uk> wrote: > > >>> >> >> >> >> >>>> Without discussing the merits of this or whether we > _choose_ to make the move to supporting PIP, I am certain it would be > _possible_ - many other packages make dispatcher scripts when you pip > install them e.g. > > >>> >> >> >> >> >>>> Silver-Surfer rescale_f2 :) $ which black; cat > $(which black) > > >>> >> >> >> >> >>>> > /Library/Frameworks/Python.framework/Versions/3.6/bin/black > > >>> >> >> >> >> >>>> > #!/Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6 > > >>> >> >> >> >> >>>> # -*- coding: utf-8 -*- > > >>> >> >> >> >> >>>> import re > > >>> >> >> >> >> >>>> import sys > > >>> >> >> >> >> >>>> from black import main > > >>> >> >> >> >> >>>> if __name__ == '__main__': > > >>> >> >> >> >> >>>> sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', > '', sys.argv[0]) > > >>> >> >> >> >> >>>> sys.exit(main()) > > >>> >> >> >> >> >>>> So we _could_ work around the absence of > LIBTBX_BUILD etc. in the system. Whether or not we elect to do the work is > a different question, and it seems clear that here are very mixed opinions > on this. > > >>> >> >> >> >> >>>> Best wishes Graeme > > >>> >> >> >> >> >>>> On 23 Aug 2019, at 01:21, Luc Bourhis < > luc_j_bourhis(a)mac.com<mailto:[email protected]>> wrote: > > >>> >> >> >> >> >>>> Hi, > > >>> >> >> >> >> >>>> Even if we managed to ship our the boost dynamic > libraries with pip, it would still not be pip-like, as we would still need > our python wrappers to set LIBTBX_BUILD and LD_LIBRARY_PATH. Normal pip > packages work with the standard python exe. LD_LIBRARY_PATH, we could get > around that by changing the way we compile, using -Wl,-R, which is the > runtime equivalent of build time -L. That’s a significant change that would > need to be tested. But there is no way around setting LIBTBX_BUILD right > now. Leaving that to the user is horrible. Perhaps there is a way to hack > libtbx/env_config.py so that we can hardwire LIBTBX_BUILD in there when pip > installs? > > >>> >> >> >> >> >>>> Best wishes, > > >>> >> >> >> >> >>>> Luc > > >>> >> >> >> >> >>>> On 16 Aug 2019, at 22:47, Luc Bourhis < > luc_j_bourhis(a)mac.com<mailto:[email protected]>> wrote: > > >>> >> >> >> >> >>>> Hi, > > >>> >> >> >> >> >>>> I did look into that many years ago, and even toyed > with building a pip installer. What stopped me is the exact conclusion you > reached too: the user would not have the pip experience he expects. You are > right that it is a lot of effort but is it worth it? Considering that > remark, I don’t think so. Now, Conda was created specifically to go beyond > pip pure-python-only support. Since cctbx has garnered support for Conda, > the best avenue imho is to go the extra length to have a package on > Anaconda.org<http://anaconda.org/>, and then to advertise it hard to > every potential user out there. > > >>> >> >> >> >> >>>> Best wishes, > > >>> >> >> >> >> >>>> Luc > > >>> >> >> >> >> >>>> On 16 Aug 2019, at 21:45, Aaron Brewster < > asbrewster(a)lbl.gov<mailto:[email protected]>> wrote: > > >>> >> >> >> >> >>>> Hi, to avoid clouding Dorothee's documentation > email thread, which I think is a highly useful enterprise, here's some > thoughts about putting cctbx into pip. Pip doesn't install non-python > dependencies well. I don't think boost is available as a package on pip > (at least the package version we use). wxPython4 isn't portable through > pip ( > https://wiki.wxpython.org/How%20to%20install%20wxPython#Installing_wxPython…). > MPI libraries are system dependent. If cctbx were a pure python package, > pip would be fine, but cctbx is not. > > >>> >> >> >> >> >>>> All that said, we could build a manylinux1 version > of cctbx and upload it to PyPi (I'm just learning about this). For a pip > package to be portable (which is a requirement for cctbx), it needs to > conform to PEP513, the manylinux1 standard ( > https://www.python.org/dev/peps/pep-0513/). For example, numpy is built > according to this standard (see https://pypi.org/project/numpy/#files, > where you'll see the manylinux1 wheel). Note, the manylinux1 standard is > built with Centos 5.11 which we no longer support. > > >>> >> >> >> >> >>>> There is also a manylinux2010 standard, which is > based on Centos 6 (https://www.python.org/dev/peps/pep-0571/). This is > likely a more attainable target (note though by default C++11 is not > supported on Centos 6). > > >>> >> >> >> >> >>>> If we built a manylinuxX version of cctbx and > uploaded it to PyPi, the user would need all the non-python dependencies. > There's no way to specify these in pip. For example, cctbx requires boost > 1.63 or better. The user will need to have it in a place their python can > find it, or we could package it ourselves and supply it, similar to how the > pip h5py package now comes with an hd5f library, or how the pip numpy > package includes an openblas library. We'd have to do the same for any > packages we depend on that aren't on pip using the manylinux standards, > such as wxPython4. > > >>> >> >> >> >> >>>> Further, we need to think about how dials and other > cctbx-based packages interact. If pip install cctbx is set up, how does > pip install dials work, such that any dials shared libraries can find the > cctbx libraries? Can shared libraries from one pip package link against > libraries in another pip package? Would each package need to supply its > own boost? Possibly this is well understood in the pip field, but not by > me :) > > >>> >> >> >> >> >>>> Finally, there's the option of providing a source > pip package. This would require the full compiler toolchain for any given > platform (macOS, linux, windows). These are likely available for > developers, but not for general users. > > >>> >> >> >> >> >>>> Anyway, these are some of the obstacles. Not > saying it isn't possible, it's just a lot of effort. > > >>> >> >> >> >> >>>> Thanks, > > >>> >> >> >> >> >>>> -Aaron > > >>> >> >> >> >> >>>> _______________________________________________ > > >>> >> >> >> >> >>>> cctbxbb mailing list > > >>> >> >> >> >> >>>> cctbxbb(a)phenix-online.org<mailto: > cctbxbb(a)phenix-online.org> > > >>> >> >> >> >> >>>> http://phenix-online.org/mailman/listinfo/cctbxbb > > >>> >> >> >> >> >>>> _______________________________________________ > > >>> >> >> >> >> >>>> cctbxbb mailing list > > >>> >> >> >> >> >>>> cctbxbb(a)phenix-online.org<mailto: > cctbxbb(a)phenix-online.org> > > >>> >> >> >> >> >>>> http://phenix-online.org/mailman/listinfo/cctbxbb > > >>> >> >> >> >> >>>> _______________________________________________ > > >>> >> >> >> >> >>>> cctbxbb mailing list > > >>> >> >> >> >> >>>> cctbxbb(a)phenix-online.org<mailto: > cctbxbb(a)phenix-online.org> > > >>> >> >> >> >> >>>> http://phenix-online.org/mailman/listinfo/cctbxbb > > >>> >> >> >> >> >>>> -- > > >>> >> >> >> >> >>>> This e-mail and any attachments may contain > confidential, copyright and or privileged material, and are for the use of > the intended addressee only. If you are not the intended addressee or an > authorised recipient of the addressee please notify us of receipt by > returning the e-mail and do not use, copy, retain, distribute or disclose > the information in or attached to the e-mail. > > >>> >> >> >> >> >>>> Any opinions expressed within this e-mail are those > of the individual and not necessarily of Diamond Light Source Ltd. > > >>> >> >> >> >> >>>> Diamond Light Source Ltd. cannot guarantee that > this e-mail or any attachments are free from viruses and we cannot accept > liability for any damage which you may sustain as a result of software > viruses which may be transmitted in or with the message. > > >>> >> >> >> >> >>>> Diamond Light Source Limited (company no. 4375679). > Registered in England and Wales with its registered office at Diamond > House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 > 0DE, United Kingdom > > >>> >> >> >> >> >>>> _______________________________________________ > > >>> >> >> >> >> >>>> cctbxbb mailing list > > >>> >> >> >> >> >>>> cctbxbb(a)phenix-online.org > > >>> >> >> >> >> >>>> http://phenix-online.org/mailman/listinfo/cctbxbb > > >>> >> >> >> >> >>> _______________________________________________ > > >>> >> >> >> >> >>> cctbxbb mailing list > > >>> >> >> >> >> >>> cctbxbb(a)phenix-online.org > > >>> >> >> >> >> >>> http://phenix-online.org/mailman/listinfo/cctbxbb > > >>> >> >> >> >> >> > > >>> >> >> >> >> >> > > >>> >> >> >> >> >> _______________________________________________ > > >>> >> >> >> >> >> cctbxbb mailing list > > >>> >> >> >> >> >> cctbxbb(a)phenix-online.org > > >>> >> >> >> >> >> http://phenix-online.org/mailman/listinfo/cctbxbb > > >>> >> >> >> >> > > > >>> >> >> >> >> > > > >>> >> >> >> >> > _______________________________________________ > > >>> >> >> >> >> > cctbxbb mailing list > > >>> >> >> >> >> > cctbxbb(a)phenix-online.org > > >>> >> >> >> >> > http://phenix-online.org/mailman/listinfo/cctbxbb > > >>> >> >> >> >> > > >>> >> >> >> >> > > >>> >> >> >> >> _______________________________________________ > > >>> >> >> >> >> cctbxbb mailing list > > >>> >> >> >> >> cctbxbb(a)phenix-online.org > > >>> >> >> >> >> http://phenix-online.org/mailman/listinfo/cctbxbb > > >>> >> >> >> > > > >>> >> >> >> > _______________________________________________ > > >>> >> >> >> > cctbxbb mailing list > > >>> >> >> >> > cctbxbb(a)phenix-online.org > > >>> >> >> >> > http://phenix-online.org/mailman/listinfo/cctbxbb > > >>> >> >> >> > > >>> >> >> >> > > >>> >> >> >> > > >>> >> >> >> -- > > >>> >> >> >> Gergely Katona, PhD > > >>> >> >> >> Associate Professor > > >>> >> >> >> Department of Chemistry and Molecular Biology, University > of Gothenburg > > >>> >> >> >> Box 462, 40530 Göteborg, Sweden > > >>> >> >> >> Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: > +46-31-786-3910 > > >>> >> >> >> Web: http://katonalab.eu, Email: gergely.katona(a)gu.se > > >>> >> >> >> > > >>> >> >> >> _______________________________________________ > > >>> >> >> >> cctbxbb mailing list > > >>> >> >> >> cctbxbb(a)phenix-online.org > > >>> >> >> >> http://phenix-online.org/mailman/listinfo/cctbxbb > > >>> >> >> > > > >>> >> >> > _______________________________________________ > > >>> >> >> > cctbxbb mailing list > > >>> >> >> > cctbxbb(a)phenix-online.org > > >>> >> >> > http://phenix-online.org/mailman/listinfo/cctbxbb > > >>> >> >> > > >>> >> >> > > >>> >> >> > > >>> >> >> -- > > >>> >> >> Gergely Katona, PhD > > >>> >> >> Associate Professor > > >>> >> >> Department of Chemistry and Molecular Biology, University of > Gothenburg > > >>> >> >> Box 462, 40530 Göteborg, Sweden > > >>> >> >> Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: > +46-31-786-3910 > > >>> >> >> Web: http://katonalab.eu, Email: gergely.katona(a)gu.se > > >>> >> >> > > >>> >> >> _______________________________________________ > > >>> >> >> cctbxbb mailing list > > >>> >> >> cctbxbb(a)phenix-online.org > > >>> >> >> http://phenix-online.org/mailman/listinfo/cctbxbb > > >>> >> > > > >>> >> > _______________________________________________ > > >>> >> > cctbxbb mailing list > > >>> >> > cctbxbb(a)phenix-online.org > > >>> >> > http://phenix-online.org/mailman/listinfo/cctbxbb > > >>> >> > > >>> >> > > >>> >> > > >>> >> -- > > >>> >> Gergely Katona, PhD > > >>> >> Associate Professor > > >>> >> Department of Chemistry and Molecular Biology, University of > Gothenburg > > >>> >> Box 462, 40530 Göteborg, Sweden > > >>> >> Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910 > > >>> >> Web: http://katonalab.eu, Email: gergely.katona(a)gu.se > > >>> >> > > >>> >> _______________________________________________ > > >>> >> cctbxbb mailing list > > >>> >> cctbxbb(a)phenix-online.org > > >>> >> http://phenix-online.org/mailman/listinfo/cctbxbb > > >>> > > > >>> > _______________________________________________ > > >>> > cctbxbb mailing list > > >>> > cctbxbb(a)phenix-online.org > > >>> > http://phenix-online.org/mailman/listinfo/cctbxbb > > >>> > > >>> > > >>> > > >>> -- > > >>> Gergely Katona, PhD > > >>> Associate Professor > > >>> Department of Chemistry and Molecular Biology, University of > Gothenburg > > >>> Box 462, 40530 Göteborg, Sweden > > >>> Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910 > > >>> Web: http://katonalab.eu, Email: gergely.katona(a)gu.se > > >>> > > >>> _______________________________________________ > > >>> cctbxbb mailing list > > >>> cctbxbb(a)phenix-online.org > > >>> http://phenix-online.org/mailman/listinfo/cctbxbb > > > > > > _______________________________________________ > > > cctbxbb mailing list > > > cctbxbb(a)phenix-online.org > > > http://phenix-online.org/mailman/listinfo/cctbxbb > > > > > > > > -- > > Gergely Katona, Professor > > Department of Chemistry and Molecular Biology, University of Gothenburg > > Box 462, 40530 Göteborg, Sweden > > Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910 > > Web: http://katonalab.eu, Email: gergely.katona(a)gu.se > > > > -- > Gergely Katona, Professor > Department of Chemistry and Molecular Biology, University of Gothenburg > Box 462, 40530 Göteborg, Sweden > Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910 > Web: http://katonalab.eu, Email: gergely.katona(a)gu.se > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb >

6 years, 1 month

[cctbxbb] conda cctbx on Mac 10.15.2 working with python3.8

by Mooers, Blaine H.M. (HSC)

Hi Billy, Gergely's post yesterday stimulated me to check my conda cctbx setup. I had earlier reported success with conda cctbx for Python3.6, 3.7, and 3.8. This morning I found in my path an earlier python3.6 build of cctbx that may have given me false positives with my conda installs of cctbx. After removing the old build of cctbx from my path, I modified my zshrc file as Gergely suggested. I can confirm that results that Gergely reported yesterday. I used a Mac OS X 10.15.2 with zsh as my shell and anaconda3 installed as /opt/anaconda. I did my testing in a conda env named cctbx38. I added 'export LIBTBX_BUILD=$CONDA_PREFIX' in my .zshrc file. After sourcing my .zshrc file, 'echo $LIBTBX_BUILD' returns '/opt/anaconda/envs/cctbx38' as expected. The toy script below prints the calculated Miller indices as a tuples in a terminal window. It was run using 'python millerSet.py'. Note that the printing of 1 million indices to a jupyter notebook cell is disappointingly slow!! Reduce each unit cell dimension by two orders of magnitude before trying this at home! The following code also worked with Python3.6 and Python3.7 in their corresponding cctbx36 and cctbx37 envs. from cctbx import crystal from cctbx import miller ms = miller.build_set( crystal_symmetry=crystal.symmetry( space_group_symbol='P4', unit_cell=(150.8,150.8,250.4,90.0,90.0,90.0)), anomalous_flag=False, d_min=1.4) [print(hkl) for hkl in ms.indices()] I used conda python3.8.0 built on November 22. Python3.8.1 does not seem to be available yet from Anaconda. Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology College of Medicine University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center (BRC) Rm. 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 ________________________________________ From: cctbxbb-bounces(a)phenix-online.org [cctbxbb-bounces(a)phenix-online.org] on behalf of cctbxbb-request(a)phenix-online.org [cctbxbb-request(a)phenix-online.org] Sent: Saturday, January 04, 2020 2:00 PM To: cctbxbb(a)phenix-online.org Subject: [EXTERNAL] cctbxbb Digest, Vol 130, Issue 2 Send cctbxbb mailing list submissions to cctbxbb(a)phenix-online.org To subscribe or unsubscribe via the World Wide Web, visit https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… or, via email, send a message with subject or body 'help' to cctbxbb-request(a)phenix-online.org You can reach the person managing the list at cctbxbb-owner(a)phenix-online.org When replying, please edit your Subject line so it is more specific than "Re: Contents of cctbxbb digest..." Today's Topics: 1. Re: some thoughts on cctbx and pip (Billy Poon) ---------------------------------------------------------------------- Message: 1 Date: Fri, 3 Jan 2020 21:04:25 +0100 From: Billy Poon <BKPoon(a)lbl.gov> To: cctbx mailing list <cctbxbb(a)phenix-online.org> Subject: Re: [cctbxbb] some thoughts on cctbx and pip Message-ID: <CAHmYUcbWS7FXA6EPUx=AC2X6m6gPY=GqH-MwGD+uzpTaOKSyjQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Gergely, Happy New Year! Can you provide the output to "conda list" for each environment? I suspect that the old version of cctbx might still be around. Is there a file named PYTHON_VERSION_MAJOR_MINOR in "/home/gergely/anaconda3/lib"? If so, delete that file. To make sure you are downloading a new copy of the package, clear the cache where conda keeps copies of all the packages. To do that, you can run "conda clean -y --all". You can remove the "-y" flag if you want to see what will be deleted. The hash for the new linux package should be h8b68381_0. The last error looks like an incompatible version of boost or gcc library was installed. The output from "conda list" should show the boost and boost-cpp packages coming from conda-forge. I would avoid installing into the root or base environment because that usually pulls from the default channels. All the dependencies should be pulled from the conda-forge channel. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://urldefense.proofpoint.com/v2/url?u=https-3A__phenix-2Donline.org&d=… On Fri, Jan 3, 2020 at 2:20 PM Gergely Katona <gkatona(a)gmail.com> wrote: > I found some other errors when using the test environment. > > > --------------------------------------------------------------------------- > RuntimeError Traceback (most recent call last) > <ipython-input-1-fe308b345b3f> in <module> > 10 import scipy as sp > 11 from scipy import linalg > ---> 12 import iotbx.pdb > 13 import cctbx > 14 import pandas as pd > > ~/anaconda3/envs/test/lib/python3.8/site-packages/iotbx/pdb/https://urldefense.proofpoint.com/v2/url?u=http-3A__-5F-5Finit-5F-5F.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=9NiF4LTTyEpDCh-vdb5bXVIJ4i9E6HmD6eWJg_3SjzE&e= > in <module> > 8 > 9 import iotbx.pdb.records > ---> 10 import iotbx.pdb.hierarchy > 11 from scitbx import matrix > 12 > > ~/anaconda3/envs/test/lib/python3.8/site-packages/iotbx/pdb/https://urldefense.proofpoint.com/v2/url?u=http-3A__hierarchy.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=QlonHINbJqyu1vTwlBJWKyChCMCCJxpIWIaT5_rrkLc&e= > in <module> > 14 from six.moves import cStringIO as StringIO > 15 from iotbx.pdb import hy36encode, hy36decode > ---> 16 import iotbx.cif.model > 17 from cctbx import crystal > 18 from libtbx import group_args > > ~/anaconda3/envs/test/lib/python3.8/site-packages/iotbx/cif/https://urldefense.proofpoint.com/v2/url?u=http-3A__-5F-5Finit-5F-5F.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=9NiF4LTTyEpDCh-vdb5bXVIJ4i9E6HmD6eWJg_3SjzE&e= > in <module> > 19 > 20 from cctbx.array_family import flex > ---> 21 from cctbx import miller > 22 from iotbx.cif import model, builders, geometry > 23 from libtbx.containers import OrderedDict > > ~/anaconda3/envs/test/lib/python3.8/site-packages/cctbx/miller/https://urldefense.proofpoint.com/v2/url?u=http-3A__-5F-5Finit-5F-5F.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=9NiF4LTTyEpDCh-vdb5bXVIJ4i9E6HmD6eWJg_3SjzE&e= > in <module> > 11 > 12 from cctbx import crystal > ---> 13 from cctbx import maptbx > 14 from cctbx import sgtbx > 15 from cctbx.sgtbx import lattice_symmetry > > ~/anaconda3/envs/test/lib/python3.8/site-packages/cctbx/maptbx/https://urldefense.proofpoint.com/v2/url?u=http-3A__-5F-5Finit-5F-5F.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=9NiF4LTTyEpDCh-vdb5bXVIJ4i9E6HmD6eWJg_3SjzE&e= > in <module> > 15 from libtbx import adopt_init_args > 16 from libtbx.utils import Sorry > ---> 17 import libtbx.load_env > 18 import math > 19 import sys, os > > ~/anaconda3/envs/test/lib/python3.8/site-packages/libtbx/https://urldefense.proofpoint.com/v2/url?u=http-3A__load-5Fenv.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=rJbfdPr3ymiz7Ir508_VGIhspAKCOwozKhY5I6OXux0&e= in > <module> > 3 import libtbx.env_config > 4 import os > ----> 5 libtbx.env = libtbx.env_config.unpickle() > 6 libtbx.env.set_os_environ_all_dist() > 7 libtbx.env.dispatcher_name = > os.environ.get("LIBTBX_DISPATCHER_NAME") > > ~/anaconda3/envs/test/lib/python3.8/site-packages/libtbx/https://urldefense.proofpoint.com/v2/url?u=http-3A__env-5Fconfig.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=UrsFhQ0dxNNuzXmOT3D6pnGJ5lXko4mfrKceNgBaQV4&e= > in unpickle() > 2736 env = pickle.load(libtbx_env) > 2737 if (env.python_version_major_minor != sys.version_info[:2]): > -> 2738 env.raise_python_version_incompatible() > 2739 if (op.realpath(build_path) != op.realpath(abs(env.build_path))): > 2740 env.build_path.reset(build_path) > > ~/anaconda3/envs/test/lib/python3.8/site-packages/libtbx/https://urldefense.proofpoint.com/v2/url?u=http-3A__env-5Fconfig.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=UrsFhQ0dxNNuzXmOT3D6pnGJ5lXko4mfrKceNgBaQV4&e= > in raise_python_version_incompatible(self, prev_pvmm) > 469 if (prev_pvmm is None): > 470 prev_pvmm = "%d.%d" % self.python_version_major_minor > --> 471 raise RuntimeError("Python version incompatible with this > build:\n" > 472 + " Build directory: %s\n" % > show_string(abs(self.build_path)) > 473 + " Python version used initially: %s\n" % prev_pvmm > > RuntimeError: Python version incompatible with this build: > Build directory: "/home/gergely/anaconda3" > Python version used initially: 3.6 > Python version in use now: 3.8 > > > Interestingly in the base environment all import worked, but I got an > error at: > > > ArgumentError Traceback (most recent call last) > <ipython-input-4-5bc71c36e121> in <module> > 33 atm_odd.set_b(0) > 34 > ---> 35 odd.write_pdb_file("bdiff_in_even_000.pdb") #skriver ny pdb > med dessa inkluderade > 36 dfWBvals=pd.DataFrame(rows_list) > > ~/anaconda3/lib/python3.6/site-packages/iotbx/pdb/https://urldefense.proofpoint.com/v2/url?u=http-3A__-5F-5Finit-5F-5F.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=9NiF4LTTyEpDCh-vdb5bXVIJ4i9E6HmD6eWJg_3SjzE&e= in > write_pdb_file(self, file_name, open_append, crystal_symmetry, > cryst1_z, write_scale_records, append_end, atom_hetatm, sigatm, > anisou, siguij) > 930 siguij=True): > 931 if (crystal_symmetry is Auto): > --> 932 crystal_symmetry = self.crystal_symmetry() > 933 if (cryst1_z is Auto): > 934 cryst1_z = self.extract_cryst1_z_columns() > > ~/anaconda3/lib/python3.6/site-packages/iotbx/pdb/https://urldefense.proofpoint.com/v2/url?u=http-3A__-5F-5Finit-5F-5F.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=9NiF4LTTyEpDCh-vdb5bXVIJ4i9E6HmD6eWJg_3SjzE&e= in > crystal_symmetry(self, crystal_symmetry, weak_symmetry) > 1218 crystal_symmetry=None, > 1219 weak_symmetry=False): > -> 1220 self_symmetry = self.crystal_symmetry_from_cryst1() > 1221 if (self_symmetry is None): > 1222 self_symmetry = self._crystal_symmetry_from_cns_remark_sg() > > ~/anaconda3/lib/python3.6/site-packages/iotbx/pdb/https://urldefense.proofpoint.com/v2/url?u=http-3A__-5F-5Finit-5F-5F.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=9NiF4LTTyEpDCh-vdb5bXVIJ4i9E6HmD6eWJg_3SjzE&e= in > crystal_symmetry_from_cryst1(self) > 1195 for line in self.crystallographic_section(): > 1196 if (line.startswith("CRYST1")): > -> 1197 return > cryst1_interpretation.crystal_symmetry(cryst1_record=line) > 1198 return None > 1199 > > ~/anaconda3/lib/python3.6/site-packages/iotbx/pdb/https://urldefense.proofpoint.com/v2/url?u=http-3A__cryst1-5Finterpretation.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=3OchLb18AMp3YpXOuEb8BDOwhl2XLrV1QAfZByH-l2E&e= > in crystal_symmetry(cryst1_record) > 136 space_group_info=None) > 137 space_group_info = > categorize(cryst1_record.sgroup).space_group_info( > --> 138 unit_cell=u) > 139 return crystal.symmetry(unit_cell=u, > space_group_info=space_group_info) > > ~/anaconda3/lib/python3.6/site-packages/iotbx/pdb/https://urldefense.proofpoint.com/v2/url?u=http-3A__cryst1-5Finterpretation.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=3OchLb18AMp3YpXOuEb8BDOwhl2XLrV1QAfZByH-l2E&e= > in space_group_info(self, unit_cell) > 85 if (self.symbol is None): return None > 86 if (self.category is None): > ---> 87 try: return sgtbx.space_group_info(self.symbol) > 88 except RuntimeError: return None > 89 if (isinstance(unit_cell, uctbx.ext.unit_cell)): > > ~/anaconda3/lib/python3.6/site-packages/cctbx/sgtbx/https://urldefense.proofpoint.com/v2/url?u=http-3A__-5F-5Finit-5F-5F.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=9NiF4LTTyEpDCh-vdb5bXVIJ4i9E6HmD6eWJg_3SjzE&e= in > __init__(self, symbol, table_id, group, number, space_group_t_den) > 100 assert group is None > 101 if (table_id is None): > --> 102 symbols = space_group_symbols(symbol) > 103 else: > 104 if (isinstance(symbol, int)): symbol = str(symbol) > > ArgumentError: Python argument types in > space_group_symbols.__init__(space_group_symbols, str) > did not match C++ signature: > __init__(_object*, int space_group_number) > __init__(_object*, int space_group_number, > std::__cxx11::basic_string<char, std::char_traits<char>, > std::allocator<char> > extension='') > __init__(_object*, int space_group_number, > std::__cxx11::basic_string<char, std::char_traits<char>, > std::allocator<char> > extension='', std::__cxx11::basic_string<char, > std::char_traits<char>, std::allocator<char> > table_id='') > __init__(_object*, std::__cxx11::basic_string<char, > std::char_traits<char>, std::allocator<char> > symbol) > __init__(_object*, std::__cxx11::basic_string<char, > std::char_traits<char>, std::allocator<char> > symbol, > std::__cxx11::basic_string<char, std::char_traits<char>, > std::allocator<char> > table_id='') > > > Gergely > > > > On Fri, Jan 3, 2020 at 1:44 PM Gergely Katona <gkatona(a)gmail.com> wrote: > > > > Dear Billy, > > > > I did some tests installing in my base conda was not troublefree in > > python 3.8. Running iotbx.fetch_pdb --all --mtz 1kp8 resulted in boost > > related error when converting to mtz. Installing into a test > > environment went fine with iotbx.fetch_pdb --all --mtz 1kp8 running > > successfully. I could add pymc3, jupyter and seaborn and iotbx still > > did not break. My LIBTBX_BUILD is not set however in the test > > environment, which breaks miller when I was trying to import it. > > Manually setting the LIBTBX_BUILD to CONDA_PREFIX (setenv LIBTBX_BUILD > > $CONDA_PREFIX) fixes this and one of my script works fine! I will come > > back if I find some problems with my other scripts, but so far this > > looks promising! > > > > > > Happy new year! > > > > Gergely > > > > > > > > > > > > On Fri, Dec 20, 2019 at 8:16 PM Billy Poon <BKPoon(a)lbl.gov> wrote: > > > > > > Hi everyone, > > > > > > I updated the conda packages on the cctbx-dev channel and there are > also now packages for macOS. The old packages have been removed so you can > create a new environment with > > > > > > conda create -n test -c cctbx-dev cctbx python=2.7 > > > conda activate test > > > > > > where "test" is the environment name and 2.7 is the python version. > For the python version, you can also pick 3.6, 3.7, or 3.8. I think the > latest conda will install 3.8 as the default python if the python argument > is not provided. Or install into an existing environment (with python > already installed) with the same command as before, > > > > > > conda install -c cctbx-dev cctbx > > > > > > Again, your .condarc file should have conda-forge as the first channel > so that dependencies can be pulled correctly. > > > > > > The dispatchers should work now and $LIBTBX_BUILD will be set on > activation of an environment (and unset on environment deactivation) or > after installing into an existing environment, so you can do more > interesting things like > > > > > > iotbx.fetch_pdb --all --mtz 1kp8 > > > > > > However, this package does not install databases, so > > > > > > molprobity.molprobity 1kp8.pdb 1kp8.mtz > > > > > > will fail because the database is not available (also probe and reduce > are not built). > > > > > > Some known issues in no particular order, > > > > > > 1) You can run "libtbx.run_tests_parallel module=cctbx nproc=Auto" to > run tests, but not all the test files were copied, so I got 30 failures > here. The final package will probably not have the test files. > > > 2) The other python dispatchers, like "cctbx.python", were not > updated, so those will fail. But you can just run "python" in the active > environment. > > > 3) Parts of mmtbx still need to be updated for Python 3. > > > 4) The LIBTBX_BUILD variable should be set for sh and csh shells. Let > me know if it's not working for your shell (i.e. "echo $LIBTBX_BUILD" > should show the same thing as $CONDA_PREFIX). > > > 5) One future step is to enable building other CCTBX-like modules with > this conda package. This will require some bookkeeping updates so that > modules in the conda environment and the modules being built are tracked > properly. Also, making sure that all the necessary headers exist in > $PREFIX/include. > > > > > > Gergely, let me know if your scripts are working. > > > > > > Happy holidays! > > > > > > -- > > > Billy K. Poon > > > Research Scientist, Molecular Biophysics and Integrated Bioimaging > > > Lawrence Berkeley National Laboratory > > > 1 Cyclotron Road, M/S 33R0345 > > > Berkeley, CA 94720 > > > Tel: (510) 486-5709 > > > Fax: (510) 486-5909 > > > Web: https://urldefense.proofpoint.com/v2/url?u=https-3A__phenix-2Donline.org&d=… > > > > > > > > > On Wed, Dec 18, 2019 at 11:25 AM Billy Poon <BKPoon(a)lbl.gov> wrote: > > >> > > >> Hi Gergely, > > >> > > >> That's the other information that hasn't been updated yet in the > conda package. :) > > >> > > >> For LIBTBX_BUILD, I can set up environment variables sort of how the > conda gcc package sets up environment variables. I have to double check to > see if they're set after installation of the package and after activation > of an environment. The variable will just be a copy of $CONDA_PREFIX. > > >> > > >> The libtbx_env file is a file that exists in $LIBTBX_BUILD that > basically stores configuration information. I'll have to modify the > contents to update the locations of the different modules since the conda > package will not have a "modules" directory. > > >> > > >> -- > > >> Billy K. Poon > > >> Research Scientist, Molecular Biophysics and Integrated Bioimaging > > >> Lawrence Berkeley National Laboratory > > >> 1 Cyclotron Road, M/S 33R0345 > > >> Berkeley, CA 94720 > > >> Tel: (510) 486-5709 > > >> Fax: (510) 486-5909 > > >> Web: https://urldefense.proofpoint.com/v2/url?u=https-3A__phenix-2Donline.org&d=… > > >> > > >> > > >> On Wed, Dec 18, 2019 at 2:08 AM Gergely Katona <gkatona(a)gmail.com> > wrote: > > >>> > > >>> Hi Billy, > > >>> > > >>> Conda install went fine with your instructions after rearranging the > > >>> channels by putting cctbx last. I removed all environmental variables > > >>> and previous build of cctbx. > > >>> > > >>> import sys > > >>> print (sys.path, sys.prefix) > > >>> > > >>> ['/home/gergely/anaconda3/lib/https://urldefense.proofpoint.com/v2/url?u=http-3A__python36.zip&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=cUHL8qgeloeUO3oYTQcr9d56RegJk01wJ2i-c3Zo6oE&e= ', > > >>> '/home/gergely/anaconda3/lib/python3.6', > > >>> '/home/gergely/anaconda3/lib/python3.6/lib-dynload', '', > > >>> '/home/gergely/anaconda3/lib/python3.6/site-packages', > > >>> > '/home/gergely/anaconda3/lib/python3.6/site-packages/IPython/extensions', > > >>> '/home/gergely/.ipython'] /home/gergely/anaconda3 > > >>> > > >>> Many imports went fine including pymc3, but I encountered problems > > >>> with these three: > > >>> > > >>> from cctbx import miller > > >>> import iotbx.pdb > > >>> from iotbx import reflection_file_reader, mtz > > >>> > > >>> > > >>> I also got type error when handling space groups. > > >>> > > >>> > > >>> > > >>> > --------------------------------------------------------------------------- > > >>> KeyError Traceback (most recent > call last) > > >>> <ipython-input-5-cedbd4f84f3d> in <module> > > >>> 25 from cctbx import uctbx > > >>> 26 from cctbx import sgtbx > > >>> ---> 27 from cctbx import miller > > >>> 28 #from iotbx import reflection_file_reader, mtz > > >>> 29 sns.set_context("poster") > > >>> > > >>> ~/anaconda3/lib/python3.6/site-packages/cctbx/miller/https://urldefense.proofpoint.com/v2/url?u=http-3A__-5F-5Finit-5F-5F.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=9NiF4LTTyEpDCh-vdb5bXVIJ4i9E6HmD6eWJg_3SjzE&e= in > <module> > > >>> 11 > > >>> 12 from cctbx import crystal > > >>> ---> 13 from cctbx import maptbx > > >>> 14 from cctbx import sgtbx > > >>> 15 from cctbx.sgtbx import lattice_symmetry > > >>> > > >>> ~/anaconda3/lib/python3.6/site-packages/cctbx/maptbx/https://urldefense.proofpoint.com/v2/url?u=http-3A__-5F-5Finit-5F-5F.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=9NiF4LTTyEpDCh-vdb5bXVIJ4i9E6HmD6eWJg_3SjzE&e= in > <module> > > >>> 15 from libtbx import adopt_init_args > > >>> 16 from libtbx.utils import Sorry > > >>> ---> 17 import libtbx.load_env > > >>> 18 import math > > >>> 19 import sys, os > > >>> > > >>> ~/anaconda3/lib/python3.6/site-packages/libtbx/https://urldefense.proofpoint.com/v2/url?u=http-3A__load-5Fenv.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=rJbfdPr3ymiz7Ir508_VGIhspAKCOwozKhY5I6OXux0&e= in > <module> > > >>> 3 import libtbx.env_config > > >>> 4 import os > > >>> ----> 5 libtbx.env = libtbx.env_config.unpickle() > > >>> 6 libtbx.env.set_os_environ_all_dist() > > >>> 7 libtbx.env.dispatcher_name = > os.environ.get("LIBTBX_DISPATCHER_NAME") > > >>> > > >>> ~/anaconda3/lib/python3.6/site-packages/libtbx/https://urldefense.proofpoint.com/v2/url?u=http-3A__env-5Fconfig.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=UrsFhQ0dxNNuzXmOT3D6pnGJ5lXko4mfrKceNgBaQV4&e= in > unpickle() > > >>> 2603 > > >>> 2604 def unpickle(): > > >>> -> 2605 build_path = os.environ["LIBTBX_BUILD"] > > >>> 2606 > set_preferred_sys_prefix_and_sys_executable(build_path=build_path) > > >>> 2607 libtbx_env = open(op.join(build_path, "libtbx_env"), "rb") > > >>> > > >>> ~/anaconda3/lib/python3.6/https://urldefense.proofpoint.com/v2/url?u=http-3A__os.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=hA1zo5wap0c9wK3DrlWIKqYBIqqbfKXca5jQ9aX5pYU&e= in __getitem__(self, key) > > >>> 667 except KeyError: > > >>> 668 # raise KeyError with the original key value > > >>> --> 669 raise KeyError(key) from None > > >>> 670 return self.decodevalue(value) > > >>> 671 > > >>> > > >>> KeyError: 'LIBTBX_BUILD' > > >>> > > >>> > > >>> > > >>> > --------------------------------------------------------------------------- > > >>> ArgumentError Traceback (most recent > call last) > > >>> <ipython-input-7-2acd3a9ce26a> in <module> > > >>> 26 return > ms,msnam,mscent,msacent,msnamacent,msnamcent,msnamacent_dstar > > >>> 27 > > >>> ---> 28 > ms,msnam,mscent,msacent,msnamacent,msnamcent,msnamacent_dstar=initializecrystal() > > >>> > > >>> <ipython-input-7-2acd3a9ce26a> in initializecrystal() > > >>> 11 uc = uctbx.unit_cell(unit_cell) > > >>> 12 wavelength = 1.54980 > > >>> ---> 13 xtal_symm = crystal.symmetry(unit_cell=unit_cell, > > >>> space_group_symbol="P 43 21 2") > > >>> 14 > > >>> 15 ms = > > >>> miller.build_set(crystal_symmetry=xtal_symm,anomalous_flag=True, > > >>> d_min=1.61) > > >>> > > >>> ~/anaconda3/lib/python3.6/site-packages/cctbx/crystal/https://urldefense.proofpoint.com/v2/url?u=http-3A__-5F-5Finit-5F-5F.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=9NiF4LTTyEpDCh-vdb5bXVIJ4i9E6HmD6eWJg_3SjzE&e= in > > >>> __init__(self, unit_cell, space_group_symbol, space_group_info, > > >>> space_group, correct_rhombohedral_setting_if_necessary, > > >>> assert_is_compatible_unit_cell, > raise_sorry_if_incompatible_unit_cell, > > >>> force_compatible_unit_cell) > > >>> 74 if (space_group_symbol is not None): > > >>> 75 self._space_group_info = sgtbx.space_group_info( > > >>> ---> 76 symbol=space_group_symbol) > > >>> 77 elif (space_group is not None): > > >>> 78 if (isinstance(space_group, sgtbx.space_group)): > > >>> > > >>> ~/anaconda3/lib/python3.6/site-packages/cctbx/sgtbx/https://urldefense.proofpoint.com/v2/url?u=http-3A__-5F-5Finit-5F-5F.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=9NiF4LTTyEpDCh-vdb5bXVIJ4i9E6HmD6eWJg_3SjzE&e= in > > >>> __init__(self, symbol, table_id, group, number, space_group_t_den) > > >>> 100 assert group is None > > >>> 101 if (table_id is None): > > >>> --> 102 symbols = space_group_symbols(symbol) > > >>> 103 else: > > >>> 104 if (isinstance(symbol, int)): symbol = str(symbol) > > >>> > > >>> ArgumentError: Python argument types in > > >>> space_group_symbols.__init__(space_group_symbols, str) > > >>> did not match C++ signature: > > >>> __init__(_object*, int space_group_number) > > >>> __init__(_object*, int space_group_number, > > >>> std::__cxx11::basic_string<char, std::char_traits<char>, > > >>> std::allocator<char> > extension='') > > >>> __init__(_object*, int space_group_number, > > >>> std::__cxx11::basic_string<char, std::char_traits<char>, > > >>> std::allocator<char> > extension='', std::__cxx11::basic_string<char, > > >>> std::char_traits<char>, std::allocator<char> > table_id='') > > >>> __init__(_object*, std::__cxx11::basic_string<char, > > >>> std::char_traits<char>, std::allocator<char> > symbol) > > >>> __init__(_object*, std::__cxx11::basic_string<char, > > >>> std::char_traits<char>, std::allocator<char> > symbol, > > >>> std::__cxx11::basic_string<char, std::char_traits<char>, > > >>> std::allocator<char> > table_id='') > > >>> > > >>> > > >>> When I tried to set LIBTBX_BUILD to /home/gergely/anaconda3 (this is > > >>> sys.prefix on my system), I got other problems when importing. Can > > >>> LIBTBX_BUILD be set in the conda package? > > >>> > > >>> > > >>> > > >>> > --------------------------------------------------------------------------- > > >>> FileNotFoundError Traceback (most recent > call last) > > >>> <ipython-input-1-7e2b144826cc> in <module> > > >>> 26 from cctbx import sgtbx > > >>> 27 #from cctbx import miller > > >>> ---> 28 from iotbx import reflection_file_reader, mtz > > >>> 29 sns.set_context("poster") > > >>> 30 plt.rcParams.update({'figure.autolayout': True}) > > >>> > > >>> > ~/anaconda3/lib/python3.6/site-packages/iotbx/https://urldefense.proofpoint.com/v2/url?u=http-3A__reflection-5Ffile-5Freader.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=U5BvLmuCgufvN_LRxQw9n78p33jNaRrXVbH1BRSXgxg&e= > > >>> in <module> > > >>> 53 > > >>> 54 from __future__ import absolute_import, division, > print_function > > >>> ---> 55 from iotbx import mtz > > >>> 56 from iotbx.scalepack import merge as scalepack_merge > > >>> 57 from iotbx.scalepack import no_merge_original_index as > > >>> scalepack_no_merge > > >>> > > >>> ~/anaconda3/lib/python3.6/site-packages/iotbx/mtz/https://urldefense.proofpoint.com/v2/url?u=http-3A__-5F-5Finit-5F-5F.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=9NiF4LTTyEpDCh-vdb5bXVIJ4i9E6HmD6eWJg_3SjzE&e= in > <module> > > >>> 9 import iotbx_mtz_ext as ext > > >>> 10 > > >>> ---> 11 from iotbx.mtz import extract_from_symmetry_lib > > >>> 12 from cctbx import xray > > >>> 13 import cctbx.xray.observation_types > > >>> > > >>> > ~/anaconda3/lib/python3.6/site-packages/iotbx/mtz/https://urldefense.proofpoint.com/v2/url?u=http-3A__extract-5Ffrom-5Fsymmetry-5Flib.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=k3WR6VZd4-PDULPXl4O0Vwz9q3LCaocUUhK_ehTn9UE&e= > > >>> in <module> > > >>> 1 from __future__ import absolute_import, division, > print_function > > >>> 2 from cctbx import sgtbx > > >>> ----> 3 import libtbx.load_env > > >>> 4 import os.path as op > > >>> 5 from six.moves import range > > >>> > > >>> ~/anaconda3/lib/python3.6/site-packages/libtbx/https://urldefense.proofpoint.com/v2/url?u=http-3A__load-5Fenv.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=rJbfdPr3ymiz7Ir508_VGIhspAKCOwozKhY5I6OXux0&e= in > <module> > > >>> 3 import libtbx.env_config > > >>> 4 import os > > >>> ----> 5 libtbx.env = libtbx.env_config.unpickle() > > >>> 6 libtbx.env.set_os_environ_all_dist() > > >>> 7 libtbx.env.dispatcher_name = > os.environ.get("LIBTBX_DISPATCHER_NAME") > > >>> > > >>> ~/anaconda3/lib/python3.6/site-packages/libtbx/https://urldefense.proofpoint.com/v2/url?u=http-3A__env-5Fconfig.py&d=DwICAg&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=9IjF95nqsrMq_R_HHQ4nsTpGpSpiU2e4ynF8kN3qTHY&s=UrsFhQ0dxNNuzXmOT3D6pnGJ5lXko4mfrKceNgBaQV4&e= in > unpickle() > > >>> 2605 build_path = os.environ["LIBTBX_BUILD"] > > >>> 2606 > set_preferred_sys_prefix_and_sys_executable(build_path=build_path) > > >>> -> 2607 libtbx_env = open(op.join(build_path, "libtbx_env"), "rb") > > >>> 2608 env = pickle.load(libtbx_env) > > >>> 2609 if (env.python_version_major_minor != > sys.version_info[:2]): > > >>> > > >>> FileNotFoundError: [Errno 2] No such file or directory: > > >>> '/home/gergely/anaconda3/libtbx_env' > > >>> > > >>> On Wed, Dec 18, 2019 at 9:10 AM Billy Poon <BKPoon(a)lbl.gov> wrote: > > >>> > > > >>> > Hi Gergely, > > >>> > > > >>> > I've uploaded linux packages to a new channel, cctbx-dev, and you > can install it with > > >>> > > > >>> > conda install -c cctbx-dev cctbx > > >>> > > > >>> > in your current environment. You should set your ~/.condarc file > to pull the other dependencies from the conda-forge channel first, so put > conda-forge above cctbx. Mine looks like > > >>> > > > >>> > channels: > > >>> > - conda-forge > > >>> > - defaults > > >>> > - cctbx > > >>> > > > >>> > Do you need dxtbx for your scripts? This package does not build > that part. I think the plan is to build a separate conda package for dxtbx > so that it can be updated more frequently. I can rebuild the packages to > include it for testing, but the one being submitted to conda-forge will not > have it. > > >>> > > > >>> > Also, your error message is probably due to version of HDF5 that > the development build installs. The https://urldefense.proofpoint.com/v2/url?u=http-3A__bootstrap.py&d=DwICAg&c… script will install > 1.10.4, but your other dependency is looking for 1.10.5. Installing this > cctbx conda package should install 1.10.5, which should fix the issue. > Also, I'm updating those environments and 1.10.5 will be the new default > version. > > >>> > > > >>> > Lastly, the dispatchers will not work in these packages because > the old paths during the build process are still in them and many of them > expect some additional information that has not been updated in the > packages yet. I'm in the process of doing that and will update the > cctbx-dev channel when that's done. However, by starting python, you can > import cctbx modules. So you can run commands like > > >>> > > > >>> > from scitbx.array_family import flex > > >>> > a = flex.random_double(1000000) > > >>> > b = flex.min_max_mean_double(a) > > >>> > b.min > > >>> > b.max > > >>> > b.mean > > >>> > > > >>> > Thanks! > > >>> > > > >>> > -- > > >>> > Billy K. Poon > > >>> > Research Scientist, Molecular Biophysics and Integrated Bioimaging > > >>> > Lawrence Berkeley National Laboratory > > >>> > 1 Cyclotron Road, M/S 33R0345 > > >>> > Berkeley, CA 94720 > > >>> > Tel: (510) 486-5709 > > >>> > Fax: (510) 486-5909 > > >>> > Web: https://urldefense.proofpoint.com/v2/url?u=https-3A__phenix-2Donline.org&d=… > > >>> > > > >>> > > > >>> > On Tue, Dec 17, 2019 at 5:39 AM Gergely Katona <gkatona(a)gmail.com> > wrote: > > >>> >> > > >>> >> Dear Billy, > > >>> >> > > >>> >> Thank you for the detailed explanation, I look forward to do > further > > >>> >> testing! I aim to pool all modules under the same environment, if > > >>> >> there are conflicts then I just try to reshuffle the order of > imports. > > >>> >> So far this did not cause problems for me even when I was using > system > > >>> >> python, but of course it is not the most prudent thing to do. With > > >>> >> anaconda everything is much more standardized and isolated > already and > > >>> >> without being superuser I can have my familiar environment at any > > >>> >> synchrotron based cluster. It is great that cctbx will be an > integral > > >>> >> part of this ecosystem and this was also the last thing holding me > > >>> >> back from adopting python3. About hdf5, pymc3 requires it and > > >>> >> importing causes a kernel restart with the following error > messages, > > >>> >> curiously if I import h5py first this can be avoided. > > >>> >> > > >>> >> Best wishes, > > >>> >> > > >>> >> Gergely > > >>> >> > > >>> >> import pymc3 as pm > > >>> >> > > >>> >> Warning! ***HDF5 library version mismatched error*** > > >>> >> The HDF5 header files used to compile this application do not > match > > >>> >> the version used by the HDF5 library to which this application is > linked. > > >>> >> Data corruption or segmentation faults may occur if the > application continues. > > >>> >> This can happen when an application was compiled by one version > of HDF5 but > > >>> >> linked with a different version of static or shared HDF5 library. > > >>> >> You should recompile the application or check your shared library > related > > >>> >> settings such as 'LD_LIBRARY_PATH'. > > >>> >> You can, at your own risk, disable this warning by setting the > environment > > >>> >> variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'. > > >>> >> Setting it to 2 or higher will suppress the warning messages > totally. > > >>> >> Headers are 1.10.4, library is 1.10.5 > > >>> >> SUMMARY OF THE HDF5 CONFIGURATION > > >>> >> ================================= > > >>> >> > > >>> >> General Information: > > >>> >> ------------------- > > >>> >> HDF5 Version: 1.10.5 > > >>> >> Configured on: Tue Oct 22 12:02:13 UTC 2019 > > >>> >> Configured by: conda@16247e67ecd5 > > >>> >> Host system: x86_64-conda_cos6-linux-gnu > > >>> >> Uname information: Linux 16247e67ecd5 > 4.15.0-1059-azure > > >>> >> #64-Ubuntu SMP Fri Sep 13 17:02:44 UTC 2019 x86_64 x86_64 x86_64 > > >>> >> GNU/Linux > > >>> >> Byte sex: little-endian > > >>> >> Installation point: /home/gergely/anaconda3 > > >>> >> > > >>> >> Compiling Options: > > >>> >> ------------------ > > >>> >> Build Mode: production > > >>> >> Debugging Symbols: no > > >>> >> Asserts: no > > >>> >> Profiling: no > > >>> >> Optimization Level: high > > >>> >> > > >>> >> Linking Options: > > >>> >> ---------------- > > >>> >> Libraries: static, shared > > >>> >> Statically Linked Executables: > > >>> >> LDFLAGS: -Wl,-O2 -Wl,--sort-common > > >>> >> -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags > > >>> >> -Wl,--gc-sections -Wl,-rpath,/home/gergely/anaconda3/lib > > >>> >> -Wl,-rpath-link,/home/gergely/anaconda3/lib > > >>> >> -L/home/gergely/anaconda3/lib > > >>> >> H5_LDFLAGS: > > >>> >> AM_LDFLAGS: -L/home/gergely/anaconda3/lib > > >>> >> Extra libraries: -lrt -lpthread -lz -ldl -lm > > >>> >> Archiver: > > >>> >> > /home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/_build_env/bin/x86_64-conda_cos6-linux-gnu-ar > > >>> >> AR_FLAGS: cr > > >>> >> Ranlib: > > >>> >> > /home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/_build_env/bin/x86_64-conda_cos6-linux-gnu-ranlib > > >>> >> > > >>> >> Languages: > > >>> >> ---------- > > >>> >> C: yes > > >>> >> C Compiler: > > >>> >> > /home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc > > >>> >> CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 > > >>> >> -I/home/gergely/anaconda3/include > > >>> >> H5_CPPFLAGS: -D_GNU_SOURCE > > >>> >> -D_POSIX_C_SOURCE=200809L -DNDEBUG -UH5_DEBUG_API > > >>> >> AM_CPPFLAGS: > -I/home/gergely/anaconda3/include > > >>> >> C Flags: -march=nocona -mtune=haswell > > >>> >> -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 > > >>> >> -ffunction-sections -pipe -I/home/gergely/anaconda3/include > > >>> >> > -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/work=/usr/local/src/conda/hdf5_split-1.10.5 > > >>> >> > -fdebug-prefix-map=/home/gergely/anaconda3=/usr/local/src/conda-prefix > > >>> >> H5 C Flags: -std=c99 -pedantic -Wall > -Wextra > > >>> >> -Wbad-function-cast -Wc++-compat -Wcast-align -Wcast-qual > -Wconversion > > >>> >> -Wdeclaration-after-statement -Wdisabled-optimization > -Wfloat-equal > > >>> >> -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-declarations > > >>> >> -Wmissing-include-dirs -Wmissing-prototypes -Wnested-externs > > >>> >> -Wold-style-definition -Wpacked -Wpointer-arith -Wredundant-decls > > >>> >> -Wshadow -Wstrict-prototypes -Wswitch-default -Wswitch-enum > -Wundef > > >>> >> -Wunused-macros -Wunsafe-loop-optimizations -Wwrite-strings > > >>> >> -finline-functions -s -Wno-inline -Wno-aggregate-return > > >>> >> -Wno-missing-format-attribute -Wno-missing-noreturn -O > > >>> >> AM C Flags: > > >>> >> Shared C Library: yes > > >>> >> Static C Library: yes > > >>> >> > > >>> >> > > >>> >> Fortran: yes > > >>> >> Fortran Compiler: > > >>> >> > /home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/_build_env/bin/x86_64-conda_cos6-linux-gnu-gfortran > > >>> >> Fortran Flags: > > >>> >> H5 Fortran Flags: -pedantic -Wall -Wextra > -Wunderflow > > >>> >> -Wimplicit-interface -Wsurprising -Wno-c-binding-type -s -O2 > > >>> >> AM Fortran Flags: > > >>> >> Shared Fortran Library: yes > > >>> >> Static Fortran Library: yes > > >>> >> > > >>> >> C++: yes > > >>> >> C++ Compiler: > > >>> >> > /home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/_build_env/bin/x86_64-conda_cos6-linux-gnu-c++ > > >>> >> C++ Flags: -fvisibility-inlines-hidden > > >>> >> -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell > > >>> >> -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 > > >>> >> -ffunction-sections -pipe -I/home/gergely/anaconda3/include > > >>> >> > -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/hdf5_split_1571745596770/work=/usr/local/src/conda/hdf5_split-1.10.5 > > >>> >> > -fdebug-prefix-map=/home/gergely/anaconda3=/usr/local/src/conda-prefix > > >>> >> H5 C++ Flags: -pedantic -Wall -W -Wundef > -Wshadow > > >>> >> -Wpointer-arith -Wcast-qual -Wcast-align -Wwrite-strings > -Wconversion > > >>> >> -Wredundant-decls -Winline -Wsign-promo -Woverloaded-virtual > > >>> >> -Wold-style-cast -Weffc++ -Wreorder -Wnon-virtual-dtor > > >>> >> -Wctor-dtor-privacy -Wabi -finline-functions -s -O > > >>> >> AM C++ Flags: > > >>> >> Shared C++ Library: yes > > >>> >> Static C++ Library: yes > > >>> >> > > >>> >> Java: no > > >>> >> > > >>> >> > > >>> >> Features: > > >>> >> --------- > > >>> >> Parallel HDF5: no > > >>> >> Parallel Filtered Dataset Writes: no > > >>> >> Large Parallel I/O: no > > >>> >> High-level library: yes > > >>> >> Threadsafety: yes > > >>> >> Default API mapping: v110 > > >>> >> With deprecated public symbols: yes > > >>> >> I/O filters (external): deflate(zlib) > > >>> >> MPE: no > > >>> >> Direct VFD: no > > >>> >> dmalloc: no > > >>> >> Packages w/ extra debug output: none > > >>> >> API tracing: no > > >>> >> Using memory checker: yes > > >>> >> Memory allocation sanity checks: no > > >>> >> Function stack tracing: no > > >>> >> Strict file format checks: no > > >>> >> Optimization instrumentation: no > > >>> >> > > >>> >> On Tue, Dec 17, 2019 at 8:35 AM Billy Poon <BKPoon(a)lbl.gov> > wrote: > > >>> >> > > > >>> >> > Hi Gergely, > > >>> >> > > > >>> >> > Let me build the test package tomorrow. All the gritty details > for building with conda is being finalized and the official documentation > will be updated to describe the steps. It would be too confusing to keep > changing the documentation as the process evolves. You do have the general > process, though, which is summarized as follows. > > >>> >> > > > >>> >> > 1) Installing dependencies. The cctbx_dependencies metapackage > was an initial approach for managing the CCTBX dependencies, but after > contacting the conda-forge folks, they recommended using the --only-deps > flag. So when the CCTBX conda package is available, you'll be able to get a > set of dependencies with, > > >>> >> > > > >>> >> > conda install -c conda-forge --only-deps cctbx > > >>> >> > > > >>> >> > By default, the https://urldefense.proofpoint.com/v2/url?u=http-3A__bootstrap.py&d=DwICAg&c… file will automatically install a > set of dependencies in the "conda_base" directory (and a conda installation > if one is not found). It just uses standard conda environment files located > in libtbx/auto_build/conda_envs, so you do not need to install > cctbx_dependencies as a separate step. The environment files avoid channel > issues by explicitly defining the channel to pull the packages from and the > cctbx channel just stores copies of packages from conda-forge. There were > issues earlier where the conda-forge packages would sometimes be moved to a > different label. The --use-conda flag also accepts a path to $CONDA_PREFIX > if you want to use a specific environment for testing. > > >>> >> > > > >>> >> > 2) Building. The https://urldefense.proofpoint.com/v2/url?u=http-3A__bootstrap.py&d=DwICAg&c… file handles that with SCons. > > >>> >> > > > >>> >> > 3) Running. After building, there should be a https://urldefense.proofpoint.com/v2/url?u=http-3A__setpaths.sh&d=DwICAg&c=… (and > .csh) file that adds build/bin to your path. The build/bin directory has > our dispatchers, which are just scripts that set up the environment > variables for you. This prevents other programs from loading our libraries, > whose versions may conflict. You should see that there is a "python" > dispatcher, which is a convenience for developers. Otherwise, you can use > libtbx.python, which will be able to import CCTBX modules. > > >>> >> > > > >>> >> > The running part is where the conda package for CCTBX will be > different than this build. Since our Python files and extensions modules > will be in the "site-packages" directory for Python, the PYTHONPATH > variable will not be needed (and conda suggests that that variable not be > set). The other CCTBX libraries will be in $CONDA_PREFIX/lib, so > LD_LIBRARY_PATH is not needed. In an active environment, PATH will already > be modified. And then our LIBTBX_BUILD directory can be set to sys.prefix. > > >>> >> > > > >>> >> > So with the conda package, you would only need to activate your > conda environment and CCTBX should integrate with other conda packages. > What is the conflict with hdf5? That's something that should be fixed. > Thanks! > > >>> >> > > > >>> >> > -- > > >>> >> > Billy K. Poon > > >>> >> > Research Scientist, Molecular Biophysics and Integrated > Bioimaging > > >>> >> > Lawrence Berkeley National Laboratory > > >>> >> > 1 Cyclotron Road, M/S 33R0345 > > >>> >> > Berkeley, CA 94720 > > >>> >> > Tel: (510) 486-5709 > > >>> >> > Fax: (510) 486-5909 > > >>> >> > Web: https://urldefense.proofpoint.com/v2/url?u=https-3A__phenix-2Donline.org&d=… > > >>> >> > > > >>> >> > > > >>> >> > On Mon, Dec 16, 2019 at 2:53 AM Gergely Katona < > gkatona(a)gmail.com> wrote: > > >>> >> >> > > >>> >> >> Dear Billy, > > >>> >> >> > > >>> >> >> Thank you for this update and for your efforts! I found a > solution and > > >>> >> >> indeed most things already work in anaconda3. The steps I took > (even > > >>> >> >> if these instructions will have short expiry date): > > >>> >> >> > > >>> >> >> Modified .condarc with: > > >>> >> >> channels: > > >>> >> >> - cctbx > > >>> >> >> - conda-forge > > >>> >> >> - defaults > > >>> >> >> > > >>> >> >> run > > >>> >> >> conda conda install cctbx_dependencies python=3.6 > > >>> >> >> > > >>> >> >> I expect this will work without python=3.6 in the near future. > > >>> >> >> > > >>> >> >> Then compiling cctbx with anaconda3 python went without any > problem > > >>> >> >> when using these flags: > > >>> >> >> python https://urldefense.proofpoint.com/v2/url?u=http-3A__bootstrap.py&d=DwICAg&c… --use-conda --python3 --nproc=12 > > >>> >> >> > > >>> >> >> Then I probably did the unorthodox thing and sourced these > directories: > > >>> >> >> > > >>> >> >> setenv LIBTBX_BUILD /home/gergely/cctbx/build > > >>> >> >> setenv PATH ${PATH}:/home/gergely/cctbx/build/bin > > >>> >> >> setenv PYTHONPATH > > >>> >> >> > /home/gergely/cctbx/modules/cctbx_project:/home/gergely/cctbx/modules:/home/gergely/cctbx/modules/cctbx_project/boost_adaptbx:/home/gergely/cctbx/build/lib:/home/gergely/cctbx/conda_base/lib/python3.6/site-packages:$PYTHONPATH > > >>> >> >> setenv LD_LIBRARY_PATH > > >>> >> >> > /home/gergely/cctbx/conda_base/lib:/home/gergely/cctbx/build/lib:$LD_LIBRARY_PATH > > >>> >> >> > > >>> >> >> There is probably a better way to put this into conda > environment. > > >>> >> >> With these steps I could run one of my scripts depending on > cctbx. The > > >>> >> >> only problem I found is that hdf5 library had conflict with > another > > >>> >> >> package in conda, but I does not find this as a showstopper. > > >>> >> >> > > >>> >> >> Best wishes, > > >>> >> >> > > >>> >> >> Gergely > > >>> >> >> > > >>> >> >> > > >>> >> >> > > >>> >> >> > > >>> >> >> > > >>> >> >> > > >>> >> >> On Fri, Dec 13, 2019 at 7:23 PM Billy Poon <BKPoon(a)lbl.gov> > wrote: > > >>> >> >> > > > >>> >> >> > Hi Gergely, > > >>> >> >> > > > >>> >> >> > It's still a work in progress. I'm sorting out some Windows > issues right now. I can probably build a test package on a separate channel > for people that want to test it (let's say next week?). I'll provide > instructions, but basically, the test conda package will be in its own > separate channel and the dependencies will be pulled from the conda-forge > channel. I want most things to be working correctly on Python 2.7, 3.6, > 3.7, and 3.8 on all 3 platforms. > > >>> >> >> > > > >>> >> >> > Thanks! > > >>> >> >> > > > >>> >> >> > -- > > >>> >> >> > Billy K. Poon > > >>> >> >> > Research Scientist, Molecular Biophysics and Integrated > Bioimaging > > >>> >> >> > Lawrence Berkeley National Laboratory > > >>> >> >> > 1 Cyclotron Road, M/S 33R0345 > > >>> >> >> > Berkeley, CA 94720 > > >>> >> >> > Tel: (510) 486-5709 > > >>> >> >> > Fax: (510) 486-5909 > > >>> >> >> > Web: https://urldefense.proofpoint.com/v2/url?u=https-3A__phenix-2Donline.org&d=… > > >>> >> >> > > > >>> >> >> > > > >>> >> >> > On Fri, Dec 13, 2019 at 5:44 AM Gergely Katona < > gkatona(a)gmail.com> wrote: > > >>> >> >> >> > > >>> >> >> >> Dear Billy, > > >>> >> >> >> > > >>> >> >> >> This sounds very promising and exciting. I am not sure if > cctbx is > > >>> >> >> >> already functional as a conda package in anaconda3 (Linux) > or this is > > >>> >> >> >> still work in progress. My technical expertise does not > allow me to > > >>> >> >> >> tell the difference. What I tried: > > >>> >> >> >> > > >>> >> >> >> Fresh install of anaconda3. Adding - cctbx and - > conda-forge to > > >>> >> >> >> .condarc . Installing pyside2 with conda. Running conda > install > > >>> >> >> >> conda_dependencies . I get a lot package version conflict, > and I > > >>> >> >> >> cannot import cctbx or iotbx to anaconda python. Am I > following the > > >>> >> >> >> right instructions? Or it is too early to expect that cctbx > works when > > >>> >> >> >> installed through conda? > > >>> >> >> >> > > >>> >> >> >> Best wishes, > > >>> >> >> >> > > >>> >> >> >> Gergely > > >>> >> >> >> > > >>> >> >> >> On Wed, Nov 27, 2019 at 3:56 PM Billy Poon <BKPoon(a)lbl.gov> > wrote: > > >>> >> >> >> > > > >>> >> >> >> > Hi all, > > >>> >> >> >> > > > >>> >> >> >> > For a brief update, I have submitted a recipe for > cctbxlite to conda-forge ( > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_conda-2Dfor… ) and support for > Python 3.7 and 3.8 is being added ( > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_cctbx_cctbx… ). With some fixes for > Windows (https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_cctbx_cctbx… ), all platforms > (macOS, linux, and Windows) can build for Python 2.7, 3.6, 3.7, and 3.8. > Some additional changes will be needed to get Windows to work with Python 3 > and for tests to pass with Boost 1.70.0. That will enable the conda-forge > recipe to build for all platforms and for all supported versions of Python. > > >>> >> >> >> > > > >>> >> >> >> > Currently, the conda-forge recipe will install into the > conda python and cctbx imports can be done without sourcing the environment > scripts. It looks like a lot of the environment variables being set in the > dispatchers can be removed since the Python files and C++ extensions are in > the right places. I'll update the libtbx_env file so that commands that > load the environment can work correctly. > > >>> >> >> >> > > > >>> >> >> >> > -- > > >>> >> >> >> > Billy K. Poon > > >>> >> >> >> > Research Scientist, Molecular Biophysics and Integrated > Bioimaging > > >>> >> >> >> > Lawrence Berkeley National Laboratory > > >>> >> >> >> > 1 Cyclotron Road, M/S 33R0345 > > >>> >> >> >> > Berkeley, CA 94720 > > >>> >> >> >> > Tel: (510) 486-5709 > > >>> >> >> >> > Fax: (510) 486-5909 > > >>> >> >> >> > Web: https://urldefense.proofpoint.com/v2/url?u=https-3A__phenix-2Donline.org&d=… > > >>> >> >> >> > > > >>> >> >> >> > > > >>> >> >> >> > On Sun, Aug 25, 2019 at 2:33 PM Tristan Croll < > tic20(a)cam.ac.uk> wrote: > > >>> >> >> >> >> > > >>> >> >> >> >> Hi Luc, > > >>> >> >> >> >> > > >>> >> >> >> >> That sounds promising. From there, I?d need to work out > how to make a fully-packaged installer (basically a modified wheel file) > for the ChimeraX ToolShed - the aim is for the end user to not have to > worry about any of this. That adds a couple of complications - e.g. > $LIBTBX_BUILD would need to be set dynamically before first import - but > doesn?t seem insurmountable. > > >>> >> >> >> >> > > >>> >> >> >> >> Thanks, > > >>> >> >> >> >> > > >>> >> >> >> >> Tristan > > >>> >> >> >> >> > > >>> >> >> >> >> > > >>> >> >> >> >> > > >>> >> >> >> >> Tristan Croll > > >>> >> >> >> >> Research Fellow > > >>> >> >> >> >> Cambridge Institute for Medical Research > > >>> >> >> >> >> University of Cambridge CB2 0XY > > >>> >> >> >> >> > > >>> >> >> >> >> > > >>> >> >> >> >> > > >>> >> >> >> >> > > >>> >> >> >> >> > On 25 Aug 2019, at 18:31, Luc Bourhis < > luc_j_bourhis(a)mac.com> wrote: > > >>> >> >> >> >> > > > >>> >> >> >> >> > Hi Tristan, > > >>> >> >> >> >> > > > >>> >> >> >> >> > cctbx could be built to use your ChimeraX python, now > that cctbx is moving to Python 3. The option ?with-python is there for that > with the bootstrap script. The specific environment setup boil down to > setting two environment variable LIBTBX_BUILD and either LD_LIBRARY_PATH on > Linux, PATH on Win32, or DYLIB_LIBRARY_PATH on MacOS. If you work within a > framework such as ChimeraX, that should not be difficult to ensure those > two variables are set. > > >>> >> >> >> >> > > > >>> >> >> >> >> > Best wishes, > > >>> >> >> >> >> > > > >>> >> >> >> >> > Luc > > >>> >> >> >> >> > > > >>> >> >> >> >> > > > >>> >> >> >> >> >> On 23 Aug 2019, at 19:02, Tristan Croll < > tic20(a)cam.ac.uk> wrote: > > >>> >> >> >> >> >> > > >>> >> >> >> >> >> To add my two cents on this: probably the second-most > common question I've had about ISOLDE's implementation is, "why didn't you > use CCTBX?". The honest answer to that is, "I didn't know how." > > >>> >> >> >> >> >> > > >>> >> >> >> >> >> Still don't, really - although the current > developments are rather promising. The problem I've faced is that CCTBX was > designed as its own self-contained Python (2.7, until very recently) > environment, with its own interpreter and a lot of very specific > environment setup. Meanwhile I'm developing ISOLDE in ChimeraX, which is > *also* its own self-contained Python (3.7) environment. To plug one into > the other in that form... well, I don't think I'm a good enough programmer > to really know where to start. > > >>> >> >> >> >> >> > > >>> >> >> >> >> >> The move to Conda and a more modular CCTBX > architecture should make a lot more possible in that direction. Pip would > be even better for me personally (ChimeraX can install directly from the > PyPI, but doesn't interact with Conda) - but I understand pretty well the > substantial challenge that would amount to (not least being that the PyPI > imposes a limit - around 100MB from memory? - on the size of an individual > package). > > >>> >> >> >> >> >> > > >>> >> >> >> >> >> Best regards, > > >>> >> >> >> >> >> > > >>> >> >> >> >> >> Tristan > > >>> >> >> >> >> >> > > >>> >> >> >> >> >>> On 2019-08-23 09:28, Luc Bourhis wrote: > > >>> >> >> >> >> >>> Hi Graeme, > > >>> >> >> >> >> >>> Yes, I know. But ?black" is a program doing a very > particular task > > >>> >> >> >> >> >>> (code formatting from the top of my head). Requiring > to use a wrapper > > >>> >> >> >> >> >>> for python itself is another level. But ok, I think > I am mellowing to > > >>> >> >> >> >> >>> the idea after all! Talking with people around me, > and extrapolating, > > >>> >> >> >> >> >>> I would bet that, right now, a great majority of > people interested by > > >>> >> >> >> >> >>> cctbx in pip have already used the cctbx, so they > know about the > > >>> >> >> >> >> >>> Python wrapper, and they would not be too sanguine > about that. My > > >>> >> >> >> >> >>> concern is for the future, when pip will be the > first time some people > > >>> >> >> >> >> >>> use cctbx. Big fat warning notices on PyPI page and > a better error > > >>> >> >> >> >> >>> message when cctbx fails because LIBTBX_BUILD is not > set would be > > >>> >> >> >> >> >>> needed but that could be all right. > > >>> >> >> >> >> >>> If we do a pip installer, we should aim at a minimal > install: cctbx, > > >>> >> >> >> >> >>> iotbx and their dependencies, and that?s it. > > >>> >> >> >> >> >>> Best wishes, > > >>> >> >> >> >> >>> Luc > > >>> >> >> >> >> >>>> On 23 Aug 2019, at 07:17, > Graeme.Winter(a)Diamond.ac.uk <Graeme.Winter(a)diamond.ac.uk> wrote: > > >>> >> >> >> >> >>>> Without discussing the merits of this or whether we > _choose_ to make the move to supporting PIP, I am certain it would be > _possible_ - many other packages make dispatcher scripts when you pip > install them e.g. > > >>> >> >> >> >> >>>> Silver-Surfer rescale_f2 :) $ which black; cat > $(which black) > > >>> >> >> >> >> >>>> > /Library/Frameworks/Python.framework/Versions/3.6/bin/black > > >>> >> >> >> >> >>>> > #!/Library/Frameworks/Python.framework/Versions/3.6/bin/python3.6 > > >>> >> >> >> >> >>>> # -*- coding: utf-8 -*- > > >>> >> >> >> >> >>>> import re > > >>> >> >> >> >> >>>> import sys > > >>> >> >> >> >> >>>> from black import main > > >>> >> >> >> >> >>>> if __name__ == '__main__': > > >>> >> >> >> >> >>>> sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', > '', sys.argv[0]) > > >>> >> >> >> >> >>>> sys.exit(main()) > > >>> >> >> >> >> >>>> So we _could_ work around the absence of > LIBTBX_BUILD etc. in the system. Whether or not we elect to do the work is > a different question, and it seems clear that here are very mixed opinions > on this. > > >>> >> >> >> >> >>>> Best wishes Graeme > > >>> >> >> >> >> >>>> On 23 Aug 2019, at 01:21, Luc Bourhis < > luc_j_bourhis(a)mac.com<mailto:[email protected]>> wrote: > > >>> >> >> >> >> >>>> Hi, > > >>> >> >> >> >> >>>> Even if we managed to ship our the boost dynamic > libraries with pip, it would still not be pip-like, as we would still need > our python wrappers to set LIBTBX_BUILD and LD_LIBRARY_PATH. Normal pip > packages work with the standard python exe. LD_LIBRARY_PATH, we could get > around that by changing the way we compile, using -Wl,-R, which is the > runtime equivalent of build time -L. That?s a significant change that would > need to be tested. But there is no way around setting LIBTBX_BUILD right > now. Leaving that to the user is horrible. Perhaps there is a way to hack > libtbx/https://urldefense.proofpoint.com/v2/url?u=http-3A__env-5Fconfig.py&… so that we can hardwire LIBTBX_BUILD in there when pip > installs? > > >>> >> >> >> >> >>>> Best wishes, > > >>> >> >> >> >> >>>> Luc > > >>> >> >> >> >> >>>> On 16 Aug 2019, at 22:47, Luc Bourhis < > luc_j_bourhis(a)mac.com<mailto:[email protected]>> wrote: > > >>> >> >> >> >> >>>> Hi, > > >>> >> >> >> >> >>>> I did look into that many years ago, and even toyed > with building a pip installer. What stopped me is the exact conclusion you > reached too: the user would not have the pip experience he expects. You are > right that it is a lot of effort but is it worth it? Considering that > remark, I don?t think so. Now, Conda was created specifically to go beyond > pip pure-python-only support. Since cctbx has garnered support for Conda, > the best avenue imho is to go the extra length to have a package on > https://urldefense.proofpoint.com/v2/url?u=http-3A__Anaconda.org&d=DwICAg&c… <https://urldefense.proofpoint.com/v2/url?u=http-3A__anaconda.org_&d=DwICAg&… >, and then to advertise it hard to > every potential user out there. > > >>> >> >> >> >> >>>> Best wishes, > > >>> >> >> >> >> >>>> Luc > > >>> >> >> >> >> >>>> On 16 Aug 2019, at 21:45, Aaron Brewster < > asbrewster(a)lbl.gov<mailto:[email protected]>> wrote: > > >>> >> >> >> >> >>>> Hi, to avoid clouding Dorothee's documentation > email thread, which I think is a highly useful enterprise, here's some > thoughts about putting cctbx into pip. Pip doesn't install non-python > dependencies well. I don't think boost is available as a package on pip > (at least the package version we use). wxPython4 isn't portable through > pip ( > https://urldefense.proofpoint.com/v2/url?u=https-3A__wiki.wxpython.org_How-… ). > MPI libraries are system dependent. If cctbx were a pure python package, > pip would be fine, but cctbx is not. > > >>> >> >> >> >> >>>> All that said, we could build a manylinux1 version > of cctbx and upload it to PyPi (I'm just learning about this). For a pip > package to be portable (which is a requirement for cctbx), it needs to > conform to PEP513, the manylinux1 standard ( > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.python.org_dev_pep… ). For example, numpy is built > according to this standard (see https://urldefense.proofpoint.com/v2/url?u=https-3A__pypi.org_project_numpy… , > where you'll see the manylinux1 wheel). Note, the manylinux1 standard is > built with Centos 5.11 which we no longer support. > > >>> >> >> >> >> >>>> There is also a manylinux2010 standard, which is > based on Centos 6 (https://urldefense.proofpoint.com/v2/url?u=https-3A__www.python.org_dev_pep… ). This is > likely a more attainable target (note though by default C++11 is not > supported on Centos 6). > > >>> >> >> >> >> >>>> If we built a manylinuxX version of cctbx and > uploaded it to PyPi, the user would need all the non-python dependencies. > There's no way to specify these in pip. For example, cctbx requires boost > 1.63 or better. The user will need to have it in a place their python can > find it, or we could package it ourselves and supply it, similar to how the > pip h5py package now comes with an hd5f library, or how the pip numpy > package includes an openblas library. We'd have to do the same for any > packages we depend on that aren't on pip using the manylinux standards, > such as wxPython4. > > >>> >> >> >> >> >>>> Further, we need to think about how dials and other > cctbx-based packages interact. If pip install cctbx is set up, how does > pip install dials work, such that any dials shared libraries can find the > cctbx libraries? Can shared libraries from one pip package link against > libraries in another pip package? Would each package need to supply its > own boost? Possibly this is well understood in the pip field, but not by > me :) > > >>> >> >> >> >> >>>> Finally, there's the option of providing a source > pip package. This would require the full compiler toolchain for any given > platform (macOS, linux, windows). These are likely available for > developers, but not for general users. > > >>> >> >> >> >> >>>> Anyway, these are some of the obstacles. Not > saying it isn't possible, it's just a lot of effort. > > >>> >> >> >> >> >>>> Thanks, > > >>> >> >> >> >> >>>> -Aaron > > >>> >> >> >> >> >>>> _______________________________________________ > > >>> >> >> >> >> >>>> cctbxbb mailing list > > >>> >> >> >> >> >>>> cctbxbb(a)phenix-online.org<mailto: > cctbxbb(a)phenix-online.org> > > >>> >> >> >> >> >>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… > > >>> >> >> >> >> >>>> _______________________________________________ > > >>> >> >> >> >> >>>> cctbxbb mailing list > > >>> >> >> >> >> >>>> cctbxbb(a)phenix-online.org<mailto: > cctbxbb(a)phenix-online.org> > > >>> >> >> >> >> >>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… > > >>> >> >> >> >> >>>> _______________________________________________ > > >>> >> >> >> >> >>>> cctbxbb mailing list > > >>> >> >> >> >> >>>> cctbxbb(a)phenix-online.org<mailto: > cctbxbb(a)phenix-online.org> > > >>> >> >> >> >> >>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… > > >>> >> >> >> >> >>>> -- > > >>> >> >> >> >> >>>> This e-mail and any attachments may contain > confidential, copyright and or privileged material, and are for the use of > the intended addressee only. If you are not the intended addressee or an > authorised recipient of the addressee please notify us of receipt by > returning the e-mail and do not use, copy, retain, distribute or disclose > the information in or attached to the e-mail. > > >>> >> >> >> >> >>>> Any opinions expressed within this e-mail are those > of the individual and not necessarily of Diamond Light Source Ltd. > > >>> >> >> >> >> >>>> Diamond Light Source Ltd. cannot guarantee that > this e-mail or any attachments are free from viruses and we cannot accept > liability for any damage which you may sustain as a result of software > viruses which may be transmitted in or with the message. > > >>> >> >> >> >> >>>> Diamond Light Source Limited (company no. 4375679). > Registered in England and Wales with its registered office at Diamond > House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 > 0DE, United Kingdom > > >>> >> >> >> >> >>>> _______________________________________________ > > >>> >> >> >> >> >>>> cctbxbb mailing list > > >>> >> >> >> >> >>>> cctbxbb(a)phenix-online.org > > >>> >> >> >> >> >>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… > > >>> >> >> >> >> >>> _______________________________________________ > > >>> >> >> >> >> >>> cctbxbb mailing list > > >>> >> >> >> >> >>> cctbxbb(a)phenix-online.org > > >>> >> >> >> >> >>> https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… > > >>> >> >> >> >> >> > > >>> >> >> >> >> >> > > >>> >> >> >> >> >> _______________________________________________ > > >>> >> >> >> >> >> cctbxbb mailing list > > >>> >> >> >> >> >> cctbxbb(a)phenix-online.org > > >>> >> >> >> >> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… > > >>> >> >> >> >> > > > >>> >> >> >> >> > > > >>> >> >> >> >> > _______________________________________________ > > >>> >> >> >> >> > cctbxbb mailing list > > >>> >> >> >> >> > cctbxbb(a)phenix-online.org > > >>> >> >> >> >> > https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… > > >>> >> >> >> >> > > >>> >> >> >> >> > > >>> >> >> >> >> _______________________________________________ > > >>> >> >> >> >> cctbxbb mailing list > > >>> >> >> >> >> cctbxbb(a)phenix-online.org > > >>> >> >> >> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… > > >>> >> >> >> > > > >>> >> >> >> > _______________________________________________ > > >>> >> >> >> > cctbxbb mailing list > > >>> >> >> >> > cctbxbb(a)phenix-online.org > > >>> >> >> >> > https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… > > >>> >> >> >> > > >>> >> >> >> > > >>> >> >> >> > > >>> >> >> >> -- > > >>> >> >> >> Gergely Katona, PhD > > >>> >> >> >> Associate Professor > > >>> >> >> >> Department of Chemistry and Molecular Biology, University > of Gothenburg > > >>> >> >> >> Box 462, 40530 G?teborg, Sweden > > >>> >> >> >> Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: > +46-31-786-3910 > > >>> >> >> >> Web: https://urldefense.proofpoint.com/v2/url?u=http-3A__katonalab.eu&d=DwICAg&c… , Email: gergely.katona(a)gu.se > > >>> >> >> >> > > >>> >> >> >> _______________________________________________ > > >>> >> >> >> cctbxbb mailing list > > >>> >> >> >> cctbxbb(a)phenix-online.org > > >>> >> >> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… > > >>> >> >> > > > >>> >> >> > _______________________________________________ > > >>> >> >> > cctbxbb mailing list > > >>> >> >> > cctbxbb(a)phenix-online.org > > >>> >> >> > https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… > > >>> >> >> > > >>> >> >> > > >>> >> >> > > >>> >> >> -- > > >>> >> >> Gergely Katona, PhD > > >>> >> >> Associate Professor > > >>> >> >> Department of Chemistry and Molecular Biology, University of > Gothenburg > > >>> >> >> Box 462, 40530 G?teborg, Sweden > > >>> >> >> Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: > +46-31-786-3910 > > >>> >> >> Web: https://urldefense.proofpoint.com/v2/url?u=http-3A__katonalab.eu&d=DwICAg&c… , Email: gergely.katona(a)gu.se > > >>> >> >> > > >>> >> >> _______________________________________________ > > >>> >> >> cctbxbb mailing list > > >>> >> >> cctbxbb(a)phenix-online.org > > >>> >> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… > > >>> >> > > > >>> >> > _______________________________________________ > > >>> >> > cctbxbb mailing list > > >>> >> > cctbxbb(a)phenix-online.org > > >>> >> > https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… > > >>> >> > > >>> >> > > >>> >> > > >>> >> -- > > >>> >> Gergely Katona, PhD > > >>> >> Associate Professor > > >>> >> Department of Chemistry and Molecular Biology, University of > Gothenburg > > >>> >> Box 462, 40530 G?teborg, Sweden > > >>> >> Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910 > > >>> >> Web: https://urldefense.proofpoint.com/v2/url?u=http-3A__katonalab.eu&d=DwICAg&c… , Email: gergely.katona(a)gu.se > > >>> >> > > >>> >> _______________________________________________ > > >>> >> cctbxbb mailing list > > >>> >> cctbxbb(a)phenix-online.org > > >>> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… > > >>> > > > >>> > _______________________________________________ > > >>> > cctbxbb mailing list > > >>> > cctbxbb(a)phenix-online.org > > >>> > https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… > > >>> > > >>> > > >>> > > >>> -- > > >>> Gergely Katona, PhD > > >>> Associate Professor > > >>> Department of Chemistry and Molecular Biology, University of > Gothenburg > > >>> Box 462, 40530 G?teborg, Sweden > > >>> Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910 > > >>> Web: https://urldefense.proofpoint.com/v2/url?u=http-3A__katonalab.eu&d=DwICAg&c… , Email: gergely.katona(a)gu.se > > >>> > > >>> _______________________________________________ > > >>> cctbxbb mailing list > > >>> cctbxbb(a)phenix-online.org > > >>> https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… > > > > > > _______________________________________________ > > > cctbxbb mailing list > > > cctbxbb(a)phenix-online.org > > > https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… > > > > > > > > -- > > Gergely Katona, Professor > > Department of Chemistry and Molecular Biology, University of Gothenburg > > Box 462, 40530 G?teborg, Sweden > > Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910 > > Web: https://urldefense.proofpoint.com/v2/url?u=http-3A__katonalab.eu&d=DwICAg&c… , Email: gergely.katona(a)gu.se > > > > -- > Gergely Katona, Professor > Department of Chemistry and Molecular Biology, University of Gothenburg > Box 462, 40530 G?teborg, Sweden > Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910 > Web: https://urldefense.proofpoint.com/v2/url?u=http-3A__katonalab.eu&d=DwICAg&c… , Email: gergely.katona(a)gu.se > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > https://urldefense.proofpoint.com/v2/url?u=http-3A__phenix-2Donline.org_mai… >

6 years, 1 month

Re: [phenixbb] phenix.map_to_model input mtz file failure --caution on using map_to_model with X-ray data

by Edward A. Berry

On 06/13/2017 07:44 PM, Dale Tronrud wrote: > > First we have to agree on exactly what we are talking about. I > presumed we were talking about real space refinement against an > experimental map such as one gets in cryo-EM. In that case there are no > Fobs. Reciprocal space is a fiction and should be avoided. > > If you are working, instead, with a 2Fo-Fc map then just do > reciprocal space refinement. I don't know of any reason to do > whole-molecule real space refinement when you are working with crystal > diffraction data. Reciprocal space is where the experiment lives and > the analysis should be done there. > > In cases of model building it is computationally quicker to do a > local real space refinement to touch up a model just so you can see if > it looks reasonable before going back into reciprocal space. This real > space refinement is quick-and-dirty and any flaws will be erased by the > proper reciprocal space refinement that follows. I have no argument with that! And I do realize how significant cryo-EM has become to structural biology with the advent of direct electron detectors. I was still stuck on the perhaps not so important theoretical question of "to exclude or not to exclude" the free-R set in real-space refinement prior to reciprocal space refinement. > As for "neighborhood correlation" I was thinking of cryo-EM maps. > Since the individual measurements (pictures) are real space in nature, I > can't imagine an experimental error in the voltage of one voxel wouldn't > tend to show up similarly in its neighbors. The whole group of voxels > will be illuminated by electrons who all had very similar histories > passing through the microscope. > > We have similar situations with diffraction data. A reflection whose > neighbor is in a shadow has a much higher chance of being shadowed > itself. Our spots, however, are much further apart on the detector than > the voxels of an EM image. > > There is another type of correlation that is probably more important. > Our diffraction spots are separated enough that you cannot predict the > intensity of a reflection based on its neighbors. You can make a very > good prediction of the darkness of a voxel based on its neighbors. If > you leave out one voxel, as a test set member, you could easily deduce > its hidden value without even building a molecular model - just > interpolate. You can't do that with diffraction data. > > This means if you want to leave out a chunk of map data for a test > set you have to pull out a big enough piece (many contiguous voxels) > that you can't deduce anything about their opaqueness from the remaining > image. To do this you have to know something about how the microscope > works. > > Dale Tronrud > > On 6/13/2017 4:08 PM, Edward A. Berry wrote: >>> To unbias you would have to calculate a >>> new map with current Fcalc's for every iteration of the model, but this >>> method would not take into account the neighborhood correlation present >>> in experimental maps.) >> >> Thanks, Dale, >> Could you explain this "neighborhood correlation"? >> >> My very simple (maybe too simple) understanding of how real space would >> bias reflections is as follows: >> >> You make a map using phases (and Fc?) from the current model and Fobs. >> But you omit the free set. >> >> Now if you take the fourier transform of that unmodified map, you would >> get back >> exactly the coefficients you put in: 2Fo-Fc (?) for the working >> reflections, >> and zero for the free set. >> >> Then you make modifications to the model to make its density match as >> nearly >> as possible the density of the map. If you were able to make the density of >> the model exactly match that of the map, then the Fc for the model would >> be that of the map. >> >> Of course you can never make the density of the model exactly match that of >> the map - modelization is the severest form of density modification. >> But, to the extent that you make the model's density more nearly like that >> of the map, the Fourier transform of the new model will be more >> like that of the map. >> >> That means for the working reflections, Fc will get closer to 2Fo-Fc >> which brings them closer to Fo; and the R-work improves. >> (If there is error in the Fobs, that will be reflected in the map, >> and the Fcalc of the model will tend toward these eromeous Fobs >> (fitting the error) and Rwork will get better than it should (bias).) >> Free reflections will move closer to zero, and most likely Rfree >> will get worse. >> >> I think that's all consistent with what you wrote, but then >> I had the impression that the bias could be prevented by making the >> map with Fc for the test set (proposed in an old paper by Ivan >> Rayment. That way the free reflections get are following the >> process by their coupling to neighboring reflections in reciprocal >> space (neighborhood correlation?), the same way they do in reciprocal >> space refinement, rather than the Fobs being used. The information >> in these free Fcalc is coming from the neighboring working reflections >> due to redundancy of information in a finely sampled molecular transform. >> >> Ed >> >> >> >> On 06/13/2017 05:40 PM, Dale Tronrud wrote: >>> >>> >>> On 6/13/2017 12:30 PM, Edward A. Berry wrote: >>>> Thanks, Pavel, >>>> I really appreciate your taking the time to generate the example. >>>> >>>> While I agree with Tim and Ian that refinement to convergence should >>>> remove the bias making it perhaps not a serious problem, my question was >>>> in fact whether there is any bias immediately after the refinement. >>>> >>>> I will need to study this example a bit, but one thing I notice is >>>> that you are doing exactly what I was guessing, comparing Rfree >>>> after real-space refinement with and without using the free set. >>>> Then, I still think, we >>>>>>> have to think about how much of that difference results from >>>>>>> bias towards the observed values (when the reflections are included) >>>>>>> and >>>>>>> how much is from bias towards zero (when the free set is excluded). >>>> >>> Of course the model is refined as though the test set Fourier >>> components were equal to zero. In reciprocal space refinement when you >>> leave a reflection out of the "sum over all reflections" when >>> calculating the difference map you are saying that you have no opinion >>> about the amplitude of that reflection. When you calculate a real space >>> map from Fourier coefficients you can't not have an opinion, i.e. you >>> can't leave a term out of the sum you can only set that term to zero. >>> If your model produces a prediction for that term which is not equal to >>> zero it will be penalized. (If you set that term to Fcalc you tie your >>> model to its starting point. To unbias you would have to calculate a >>> new map with current Fcalc's for every iteration of the model, but this >>> method would not take into account the neighborhood correlation present >>> in experimental maps.) >>> >>> What this means is that Rfree is not a meaningful stat for assessing >>> overfitting of real space refinement. This is hardly a surprise. A >>> test of a refinement protocol has to be based on the mathematics of that >>> protocol, not the protocol you happened to have used yesterday. If you >>> want an unbiased estimate of the quality of a real space refinement you >>> have to leave out a region of the map and then see how well the model >>> fits that region. This is harder to do in an automated fashion and >>> there will be a lot of caveats about your results (e.g. you know about >>> the ability to fit one region but does that generalize to other areas?). >>> If you recall there are a lot of caveats about Rfree too - we have just >>> stopped worrying about them. (e.g. low resolution vrs high resolution >>> reflections, choosing based on shells or randomly, what to do about >>> ncs...) >>> >>> I think you should consider yourself on the wrong track if you come >>> up with a statistical test, but haven't given any thought to the actual >>> experiment that produced your map. >>> >>> Dale Tronrud >>> >>>> Things I need to look at- >>>> What are R and R-free for the original refined model >>>> What are R and R-free after shaking (did RSR lower R but not Rfree, or >>>> did it raise Rfree? >>>> What if RSR is done using a map made with fill-in strategy? >>>> >>>> Ed >>>> >>>> On 06/13/2017 02:15 PM, Pavel Afonine wrote: >>>>> Hi Ed, >>>>> >>>>> Including free-r reflections into map calculation and then using such >>>>> map in real-space refinement of entire model will affect Rfree. Here >>>>> is a simple example that illustrates my statement, step-by-step: >>>>> >>>>> 1) Get data and model from PDB: >>>>> >>>>> phenix.fetch_pdb 1f8t --mtz >>>>> >>>>> 2) Compute two 2mFo-DFc maps: one includes all reflections the other >>>>> one has no free-r terms: >>>>> >>>>> phenix.python run.py 1f8t.{pdb,mtz} >>>>> >>>>> This will create an MTZ file (map_coeffs.mtz) that contains Fourier >>>>> map coefficients for both maps. >>>>> >>>>> 3) Shake model a bit: >>>>> >>>>> phenix.dynamics 1f8t.pdb number_of_steps=500 >>>>> >>>>> 4) Run real-space refinement using two maps: >>>>> >>>>> phenix.real_space_refine map_coeffs.mtz 1f8t_shaken.pdb >>>>> label="work,PHIwork" ncs_constraints=false output.file_name_prefix=work >>>>> >>>>> phenix.real_space_refine map_coeffs.mtz 1f8t_shaken.pdb >>>>> label="all,PHIall" ncs_constraints=false output.file_name_prefix=all >>>>> >>>>> 5) Compute R-factors using data and real-space refined models: >>>>> >>>>> phenix.model_vs_data 1f8t.mtz all_real_space_refined.pdb >>>>> r_work(re-computed) : 0.2419 >>>>> r_free(re-computed) : 0.2441 >>>>> >>>>> phenix.model_vs_data 1f8t.mtz work_real_space_refined.pdb >>>>> r_work(re-computed) : 0.2444 >>>>> r_free(re-computed) : 0.2756 >>>>> >>>>> The result is self-explicable and is inline with Tom's reply to Wei. >>>>> >>>>> All files necessary to reproduce calculations above are here: >>>>> http://cci.lbl.gov/~afonine/tmp/ >>>>> >>>>> All the best, >>>>> Pavel >>>>> >>>>> >>>>> On 6/8/17 10:05, Tim Gruene wrote: >>>>>> Hi Ed, >>>>>> >>>>>> including the 'free' reflections in the map for modelling does not >>>>>> taint the >>>>>> value of Rfree. That is a misconception that i s very persistent (as >>>>>> prejudice >>>>>> usually are). I believe it was Ian Tickle who formulated that when >>>>>> you simply >>>>>> refine long enough towards convergence, all reflections excluded from >>>>>> refinement >>>>>> will become independent, i.e. you can assign a new set for Rfree >>>>>> every time >>>>>> you refine, if you wish so. >>>>>> >>>>>> This concept is the reason why Rcomplete (the "better" equivalent to >>>>>> Rfree for >>>>>> small data sets with < 10,000 unique reflections), introduced by Axel >>>>>> Brunger, >>>>>> works, as we could demonstrate in doi: 10.1073/pnas.1502136112 >>>>>> >>>>>> So nothing to worry about when including all reflections in map >>>>>> calculations. >>>>>> >>>>>> Cheers, >>>>>> Tim >>>>>> >>>>>> On Thursday, June 8, 2017 12:42:53 PM CEST Edward A. Berry wrote: >>>>>>> Hi, Tom, >>>>>>> Please forgive what may be a silly question from an outsider who >>>>>>> hasn't >>>>>>> really kept up with the crystallography literature or even all the >>>>>>> Phenix >>>>>>> newsletters- What is the evidence that including the free set in >>>>>>> real space >>>>>>> refinement biases R-free of the resulting model? Is this Rfree also >>>>>>> biased >>>>>>> when map coefficients use "fill-in" for the excluded free >>>>>>> reflections (and >>>>>>> is that what phenix.remove_free_from_map does?). >>>>>>> >>>>>>> My point is that literally excluding the free reflections, as >>>>>>> opposed to >>>>>>> substituting their values with Fc, will bias the free set toward >>>>>>> grossly >>>>>>> incorrect values (namely zero) and therefore greatly worsen R-free. >>>>>>> Thus if >>>>>>> the evidence for bias is that you get worse R-free when you >>>>>>> exclude the >>>>>>> free set, you have to think about how much of that difference >>>>>>> results from >>>>>>> bias towards the observed values (when the reflections are included) >>>>>>> and >>>>>>> how much is from bias towards zero (when the free set is excluded). >>>>>>> (Again, I realize this may be all very well understood by the >>>>>>> crystallography community and properly taken care of in phenix; I'm >>>>>>> just >>>>>>> asking for my own information) eab >>>>>>> >>>>>>> On 06/08/2017 07:28 AM, Terwilliger, Thomas Charles wrote: >>>>>>>> Hi Wei, >>>>>>>> >>>>>>>> >>>>>>>> I want to give a word of caution about how to use >>>>>>>> phenix.map_to_model on >>>>>>>> crystallographic data...The bottom line is you should remove the >>>>>>>> test set >>>>>>>> from your map coefficients before running phenix.map_to model on >>>>>>>> X-ray >>>>>>>> data. Here is why: >>>>>>>> >>>>>>>> >>>>>>>> phenix.map_to_model uses real-space refinement, which is refinement >>>>>>>> against the map. If you supply map coefficients that include your >>>>>>>> test >>>>>>>> reflections, then you will be refining against data that is in your >>>>>>>> test >>>>>>>> set. This will make your Rfree invalid when you go back and >>>>>>>> refine your >>>>>>>> model against the original crystallographic data. >>>>>>>> >>>>>>>> >>>>>>>> To remove the test set from your map coefficients you can use: >>>>>>>> >>>>>>>> >>>>>>>> phenix.remove_free_from_map map_coeffs=my_map_coeffs.mtz >>>>>>>> free_in=my_data_file_with_freeR_flags.mtz >>>>>>>> mtz_out=my_map_coeffs_no_free.mtz >>>>>>>> >>>>>>>> >>>>>>>> Also note that phenix.map_to_model uses a fixed map (it does not do >>>>>>>> density modification). Consequently for most crystallographic >>>>>>>> data at >>>>>>>> moderate resolution or higher phenix.autobuild is going to do much >>>>>>>> better >>>>>>>> than phenix.map_to_model. >>>>>>>> >>>>>>>> >>>>>>>> All the best, >>>>>>>> >>>>>>>> Tom T >>>>>>>> >>>>>>>> >>>>>>>> -------------------------------------------------------------------------- >>>>>>>> >>>>>>>> >>>>>>>> -------------------------------------------------------------------------- >>>>>>>> >>>>>>>> >>>>>>>> -------------------------------------------------------------------------- >>>>>>>> >>>>>>>> >>>>>>>> -------------------------------------------------------------------------- >>>>>>>> >>>>>>>> >>>>>>>> -------------------------------------------------------------------------- >>>>>>>> >>>>>>>> >>>>>>>> -------------------------------------------------------------------------- >>>>>>>> >>>>>>>> >>>>>>>> -------------------------------------------------------------------------- >>>>>>>> >>>>>>>> >>>>>>>> -------------------------------------------------------------------------- >>>>>>>> >>>>>>>> >>>>>>>> -------------------------------------------------------------------------- >>>>>>>> >>>>>>>> >>>>>>>> -------------------------------------------------------------------------- >>>>>>>> >>>>>>>> >>>>>>>> -------------------------------------------------------------------------- >>>>>>>> >>>>>>>> >>>>>>>> -------------------------------------------------------------------------- >>>>>>>> >>>>>>>> >>>>>>>> -------------------------------------------------------------------------- >>>>>>>> >>>>>>>> >>>>>>>> ---------------------------- *From:*[email protected] >>>>>>>> <dingding830106(a)163.com> on behalf ofdancingdream(a)163.com >>>>>>>> <dancingdream(a)163.com> *Sent:* Tuesday, June 6, 2017 9:16 PM >>>>>>>> *To:* Terwilliger, Thomas Charles >>>>>>>> *Cc:*[email protected] >>>>>>>> *Subject:* Re:Re: [phenixbb] phenix.map_to_model input mtz file >>>>>>>> failure >>>>>>>> Dear Thomas, >>>>>>>> I use CAD to convert the labels from FDM->FWT, PHIDM->PHFWT, then >>>>>>>> submit >>>>>>>> this job again (without map_coeffs_labels=... ), and everything >>>>>>>> seems ok. >>>>>>>> Thank you very much for you help. >>>>>>>> Best! >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> Wei Ding >>>>>>>> P.O.Box 603 >>>>>>>> The Institute of Physics,Chinese Academy of Sciences >>>>>>>> Beijing,China >>>>>>>> 100190 >>>>>>>> Tel: +86-10-82649083 >>>>>>>> >>>>>>>> E-mail:[email protected] <mailto:[email protected]> >>>>>>>> >>>>>>>> At 2017-06-07 10:32:14, "Terwilliger, Thomas Charles" >>>>>> <terwilliger(a)lanl.gov> wrote: >>>>>>>> Hi Wei, >>>>>>>> >>>>>>>> >>>>>>>> I'm sorry for the trouble! >>>>>>>> >>>>>>>> >>>>>>>> If you supply an MTZ file that has FWT,PHFWT or similar >>>>>>>> labels, then >>>>>>>> you can skip the "labels=...." statement and it should run. >>>>>>>> >>>>>>>> >>>>>>>> Let me know if that does not work! >>>>>>>> All the best, >>>>>>>> >>>>>>>> Tom T >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> ---------------------------------------------------------------------- >>>>>>>> >>>>>>>> >>>>>>>> ---------------------------------------------------------------------- >>>>>>>> >>>>>>>> >>>>>>>> ---------------------------------------------------------------------- >>>>>>>> >>>>>>>> >>>>>>>> ---------------------------------------------------------------------- >>>>>>>> >>>>>>>> >>>>>>>> ---------------------------------------------------------------------- >>>>>>>> >>>>>>>> >>>>>>>> ---------------------------------------------------------------------- >>>>>>>> >>>>>>>> >>>>>>>> ---------------------------------------------------------------------- >>>>>>>> >>>>>>>> >>>>>>>> ---------------------------------------------------------------------- >>>>>>>> >>>>>>>> >>>>>>>> ---------------------------------------------------------------------- >>>>>>>> >>>>>>>> >>>>>>>> ---------------------------------------------------------------------- >>>>>>>> >>>>>>>> >>>>>>>> ---------------------------------------------------------------------- >>>>>>>> >>>>>>>> >>>>>>>> ---------------------------------------------------------------------- >>>>>>>> >>>>>>>> >>>>>>>> ---------------------------------------------------------------------- >>>>>>>> >>>>>>>> >>>>>>>> ---------------------------------------------------------------------- >>>>>>>> >>>>>>>> ---------- *From:*[email protected] >>>>>>>> <mailto:[email protected]> >>>>>>>> <phenixbb-bounces(a)phenix-online.org >>>>>>>> <mailto:[email protected]>> on behalf of >>>>>>>> dancingdream(a)163.com <mailto:[email protected]> >>>>>>>> <dancingdream(a)163.com <mailto:[email protected]>> *Sent:* >>>>>>>> Tuesday, >>>>>>>> June 6, 2017 8:19 PM >>>>>>>> *To:*[email protected] >>>>>>>> <mailto:[email protected]> >>>>>>>> *Subject:* [phenixbb] phenix.map_to_model input mtz file >>>>>>>> failure >>>>>>>> Dear Phenix bb, >>>>>>>> I intend to build a initial model by phenix.map_to_model. >>>>>>>> And the >>>>>>>> command line is as follows: phenix.map_to_model_1.12rc0-2787 >>>>>>>> map_coeffs_file=../rep_dm.mtz map_coeffs_labels="'FP,SIGFP' >>>>>>>> 'PHIDM' >>>>>>>> 'FOMDM'" seq_file=../resolve.seq is_crystal=True >>>>>>>> use_sg_symmetry=True density_select=False >>>>>>>> truncate_at_d_min=True >>>>>>>> and the feedback like this: >>>>>>>> Sorry: No initial assignment made for map_coeffs. Labels used: >>>>>>>> FP,SIGFP PHIDM FOMDM. Available labels: ['PHIB', 'FOM', >>>>>>>> 'HLA,HLB,HLC,HLD', 'FP,SIGFP', 'PHIDM', 'FOMDM', 'FDM', >>>>>>>> 'HLADM,HLBDM,HLCDM,HLDDM'] NOTE: grouped labels like >>>>>>>> 'FP,SIGFP' must >>>>>>>> stay together, >>>>>>>> have commas, and have no spaces. If they come from an MTZ >>>>>>>> file, >>>>>>>> they must be in adjacent columns as well. >>>>>>>> Suggested labels to use: PHIDM FOMDM >>>>>>>> I try many other input format of map_coeffs_labels, such as >>>>>>>> map_coeffs_labels="FP,SIGFP PHIDM FOMDM" >>>>>>>> map_coeffs_labels=["FP,SIGFP PHIDM FOMDM"] >>>>>>>> ... ... >>>>>>>> but the result is the same. Dose anyone can tell me how to fix >>>>>>>> this >>>>>>>> problem? Thank a lot. >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> Wei Ding >>>>>>>> P.O.Box 603 >>>>>>>> The Institute of Physics,Chinese Academy of Sciences >>>>>>>> Beijing,China >>>>>>>> 100190 >>>>>>>> Tel: +86-10-82649083 >>>>>>>> E-mail:[email protected] <mailto:[email protected]> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> phenixbb mailing list >>>>>>>> phenixbb(a)phenix-online.org >>>>>>>> http://phenix-online.org/mailman/listinfo/phenixbb >>>>>>>> Unsubscribe:[email protected] >>>>>>> _______________________________________________ >>>>>>> phenixbb mailing list >>>>>>> phenixbb(a)phenix-online.org >>>>>>> http://phenix-online.org/mailman/listinfo/phenixbb >>>>>>> Unsubscribe:[email protected] >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> phenixbb mailing list >>>>>> phenixbb(a)phenix-online.org >>>>>> http://phenix-online.org/mailman/listinfo/phenixbb >>>>>> Unsubscribe:[email protected] >>>>> >>>> _______________________________________________ >>>> phenixbb mailing list >>>> phenixbb(a)phenix-online.org >>>> http://phenix-online.org/mailman/listinfo/phenixbb >>>> Unsubscribe: phenixbb-leave(a)phenix-online.org >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://phenix-online.org/mailman/listinfo/phenixbb >>> Unsubscribe: phenixbb-leave(a)phenix-online.org >>> >> >

8 years, 7 months

Jump to page: