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conda cctbx on Mac 10.15.2 working with python3.8
by Mooers, Blaine H.M. (HSC) 05 Jan '20

05 Jan '20

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… >

2 1

Re: [cctbxbb] [EXTERNAL] cctbxbb Digest, Vol 129, Issue 6
by Mooers, Blaine H.M. (HSC) 20 Dec '19

20 Dec '19

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… >> >

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Emergency power test at Berkeley this weekend (12/13-12/16)
by Billy Poon 16 Dec '19

16 Dec '19

Hi everyone, To mitigate disruptions from future power shut offs due to wildfire concerns, we are performing an emergency power test for our web servers. This will affect the phenix-online.org and cci.lbl.gov servers. The websites, mailing lists, and repositories will remain available, but the servers will be running on emergency power instead. The servers will be switched to emergency power at around 2 pm Pacific time on Friday (12/13) and switched back to main power around 10 am Pacific time on Monday (12/16). Please let me know if you experience 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

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Postdoc position in Berkeley
by Petrus Zwart 08 Nov '19

08 Nov '19

Dear All, We have two postdoc positions open in LBNL's Center for Advanced Mathematics in Energy Research Applications (CAMERA; https://www.camera.lbl.gov/) to work on a diverse set of problems in managing, cleaning and interpreting biophysical data ranging from microscopy to crystallography. https://lbl.taleo.net/careersection/2/jobdetail.ftl?job=88805 https://lbl.taleo.net/careersection/2/jobdetail.ftl?job=88480 Feel free to contact me for more information. Regards Peter Zwart -- ------------------------------------------------------------------------ P.H. Zwart Staff Scientist Molecular Biophysics and Integrated Bioimaging & Center for Advanced Mathematics for Energy Research Applications Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 PHENIX: http://www.phenix-online.org CAMERA: http://camera.lbl.gov/ -------------------------------------------------------------------------

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Fwd: Target platform with conda
by Winter, Graeme (DLSLtd,RAL,LSCI) 06 Nov '19

06 Nov '19

Hello all Looking at the commits relating to conda, what are the target platforms now? Looks like 3.7 is valid? I’m asking as it would be good to know what language features we can adopt without causing incompatible code problems. We’ve clearly nearly got up to date on Python 3 now... Do we have guidelines somewhere? Thanks Graeme -- 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

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Potential Berkeley Server Outage (October 25)
by Billy Poon 29 Oct '19

29 Oct '19

Hi everyone, As a result of the increased frequency of wildfires in California the power company is taking steps to reduce risk under certain weather conditions. This entails shutting down electricity to regions that are experiencing dry windy conditions. We have been informed that the weather this weekend meets their criteria for a shutdown in our part of the Bay Area. Therefore several of the Berkeley servers will probably be shut down today and will return next week. This will affect: - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience. -- 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

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Berkeley Server Outage (Starting October 26th)
by Paul Adams 25 Oct '19

25 Oct '19

Dear Colleagues, yet again, as a result of the increased frequency of wildfires in California the power company is taking steps to reduce risk under certain weather conditions. This entails shutting down electricity to regions that are experiencing dry windy conditions. We have been informed that the weather this weekend meets their criteria for a shutdown in our part of the Bay Area. Therefore several of the Berkeley servers will be shut down this weekend and will return later the following week. This will affect: - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience. Cheers, Paul -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Berkeley Lab (http://biosciences.lbl.gov/divisions/mbib) Division Deputy for Biosciences, Advanced Light Source, Berkeley Lab (https://als.lbl.gov) Principal Investigator, ALS-ENABLE, Advanced Light Source, Berkeley Lab (http://als-enable.lbl.gov) Group Leader, Computational Crystallography Initiative, Berkeley Lab (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 347 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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sgtbx.space_group and sgtbx.space_group_info query
by Ben Williams 14 Oct '19

14 Oct '19

Dear CCTBX devs, What is a sgtbx.space_group_info object, and why does it do something subtly different to sgtbx.space_group? >>> from cctbx import sgtbx >>> print(sgtbx.space_group('C2').type().universal_hermann_mauguin_symbol()) P 1 2 1 (c,2*a+c,b) >>> print(sgtbx.space_group_info('C2').group().type().universal_hermann_mauguin_symbol()) C 1 2 1 sgtbx.space_group_info is notably lacking in docstring (or indeed comments in the code). sgtbx.space_group isn't too hot on the documentation either... Cheers, Ben -- Ben Williams Post-doctoral research associate Scientific Software Diamond Light Source -- 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

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Berkeley Server Outage (Starting October evening 8th)
by Paul Adams 12 Oct '19

12 Oct '19

Dear Colleagues, as a result of the increased frequency of wildfires in California the power company is taking steps to reduce risk under certain weather conditions. This entails shutting down electricity to regions that are experiencing dry windy conditions. We have been informed that the weather this week meets their criteria for a shutdown in our part of the Bay Area. Therefore several of the Berkeley servers will be shut down today and will return later in the week. This will affect: - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience. Cheers, Paul -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Berkeley Lab (http://biosciences.lbl.gov/divisions/mbib) Division Deputy for Biosciences, Advanced Light Source, Berkeley Lab (https://als.lbl.gov) Principal Investigator, ALS-ENABLE, Advanced Light Source, Berkeley Lab (http://als-enable.lbl.gov) Group Leader, Computational Crystallography Initiative, Berkeley Lab (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 347 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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Potential Berkeley Server Outage (September 23/24)
by Paul Adams 21 Sep '19

21 Sep '19

Dear Colleagues, as a result of the increased frequency of wildfires in California the power company is taking steps to reduce risk under certain weather conditions. This entails shutting down electricity to regions that are experiencing dry windy conditions. They are predicting that Monday or Tuesday this coming week (September 23/24) might meet their criteria for a shutdown in the Bay Area. Hopefully this is just a worst case prediction and nothing will happen. However, there is a possibility that the Berkeley servers will be down for some time during that period (duration unknown). This will affect: - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience. Cheers, Paul -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Berkeley Lab (http://biosciences.lbl.gov/divisions/mbib) Division Deputy for Biosciences, Advanced Light Source, Berkeley Lab (https://als.lbl.gov) Principal Investigator, ALS-ENABLE, Advanced Light Source, Berkeley Lab (http://als-enable.lbl.gov) Group Leader, Computational Crystallography Initiative, Berkeley Lab (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 347 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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Re: [cctbxbb] cctbx.python readline issue
by Mooers, Blaine H.M. (HSC) 24 Aug '19

24 Aug '19

In response to Wolfram Tempel's trouble with backspace in interactive sessions, I found the same problem with backspace in interactive sessions in cctbx.python version 1723 on Mac OS 10.14.6. I solved the problem by installing readline with pip using the command below (I did not try using conda) and sourcing the again $HOME/local/cctbx-dev-1723/cctbx_env.sh. $HOME/local/cctbx-dev-1723/build/bin/libtbx.pip install --upgrade readline 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, August 24, 2019 2:00 PM To: cctbxbb(a)phenix-online.org Subject: [EXTERNAL] cctbxbb Digest, Vol 125, Issue 22 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. interactive cctbx.python backspace behavior (on linux) (wtempel) 2. Re: some thoughts on cctbx and pip (Billy Poon) 3. Re: interactive cctbx.python backspace behavior (on linux) (Billy Poon) 4. Re: interactive cctbx.python backspace behavior (on linux) (Billy Poon) 5. Re: some thoughts on cctbx and pip (Tristan Croll) ---------------------------------------------------------------------- Message: 1 Date: Fri, 23 Aug 2019 15:54:09 -0400 From: wtempel <wtempel(a)gmail.com> To: cctbxbb(a)phenix-online.org Subject: [cctbxbb] interactive cctbx.python backspace behavior (on linux) Message-ID: <CAGjFzmBj3m_Uez1Siz6HPrjxAdOJqSczO-udnJo7C2W5Od4Q8A(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi, Currently, cctbx.python behaves like described in this stackoverflow post: https://urldefense.proofpoint.com/v2/url?u=https-3A__stackoverflow.com_ques… . I am missing the convenience of backspace delete, which is available on /usr/bin/python interactive sessions. Could that feature be added during compilation of the pre-built cctbx distributions? Regards. Wolfram Tempel

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interactive cctbx.python backspace behavior (on linux)
by wtempel 23 Aug '19

23 Aug '19

Hi, Currently, cctbx.python behaves like described in this stackoverflow post: https://stackoverflow.com/questions/893053/seeing-escape-characters-when-pr…. I am missing the convenience of backspace delete, which is available on /usr/bin/python interactive sessions. Could that feature be added during compilation of the pre-built cctbx distributions? Regards. Wolfram Tempel

2 2

cls parameter
by Graeme.Winter＠Diamond.ac.uk 22 Aug '19

22 Aug '19

Folks, For reading shelxl .res files I need to define a cls parameter - it is not _used_ for anything though - so 0 works fine e.g. from iotbx import shelx import sys s = shelx.cctbx_xray_structure_from(0, filename=sys.argv[1]) will work fine. I based this on the documentation at https://cci.lbl.gov/cctbx_docs/iotbx/iotbx.shelx.html What have I missed? Thanks Graeme -- 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

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Re: [cctbxbb] Molprobity / CCTBX incompatibility
by Nigel Moriarty 19 Aug '19

19 Aug '19

That is the correct directory for the general Phenix install. @Christopher Williams <christopher.sci.williams(a)gmail.com> Does the script run bootstrap.py from the current directory or does it cd elsewhere. I have noticed that accessing the repos at Duke can be a problem but I just did so the servers are fine. I still think the "running the install script with bootstrap.py in the current directory" could still be the problem. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov On Mon, Aug 19, 2019 at 10:49 AM Charitha Belluru Shetty < charitha-belluru.b.shetty(a)gsk.com> wrote: > Hi Nigel, > > > > Can you please let us know which directory? Since the Molprobity directory > is not created after running > > *. install_via_bootstrap.sh 10* > > > > The steps to install ideally would be as below: > > ./install_via_bootstrap.sh 4 > > cd/molprobity > > ./setup.sh > > > > > > But in our case “modules” directory got created. > > > > -bash-4.2$ ls -l > > total 131 > > -rw-r--r-- 1 cbs72396 appmgmt 90799 Aug 14 18:26 bootstrap.py > > -rw-r--r-- 1 cbs72396 appmgmt 82015 Aug 16 13:38 bootstrap.pyc > > -rw-r--r-- 1 cbs72396 appmgmt 1817 Aug 14 14:03 install_via_bootstrap.sh > > drwxr-sr-x 12 cbs72396 appmgmt 22 Aug 16 13:38 modules > > > > -bash-4.2$ ls -l modules > > total 2913 > > drwxr-xr-x 11 cbs72396 appmgmt 17 Nov 27 2012 annlib > > drwxr-sr-x 8 cbs72396 appmgmt 15 Aug 16 13:38 annlib_adaptbx > > -rw-r--r-- 1 cbs72396 appmgmt 519563 Aug 16 05:13 annlib.gz > > drwxr-sr-x 5 cbs72396 appmgmt 6 Aug 16 13:38 boost > > drwxr-sr-x 20 cbs72396 appmgmt 48 Aug 16 13:38 cbflib > > drwxr-xr-x 5 cbs72396 appmgmt 6 Oct 30 2013 ccp4io > > drwxr-xr-x 5 cbs72396 appmgmt 30 May 19 17:56 ccp4io_adaptbx > > -rw-r--r-- 1 cbs72396 appmgmt 208764 Aug 16 05:13 ccp4io_adaptbx.gz > > -rw-r--r-- 1 cbs72396 appmgmt 1417443 Aug 16 05:13 ccp4io.gz > > drwxr-sr-x 38 cbs72396 appmgmt 45 Aug 16 13:38 cctbx_project > > drwxr-sr-x 5 cbs72396 appmgmt 5 Aug 16 13:37 chem_data > > drwxrwxr-x 4 cbs72396 appmgmt 15 Sep 18 2017 scons > > -rw-r--r-- 1 cbs72396 appmgmt 636186 Aug 16 05:13 scons.gz > > drwxr-xr-x 4 cbs72396 appmgmt 11 Aug 19 2009 tntbx > > -rw-r--r-- 1 cbs72396 appmgmt 38909 Aug 16 05:13 tntbx.gz > > > > Best Regards, > > Charitha Shetty > > > > > > *From:* Nigel Moriarty <nwmoriarty(a)lbl.gov> > *Sent:* Monday, August 19, 2019 1:08 PM > *To:* Christopher Williams <christopher.sci.williams(a)gmail.com> > *Cc:* Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com>; Robert > Nolte <robert.t.nolte(a)gsk.com>; cctbxbb(a)phenix-online.org > *Subject:* Re: Molprobity / CCTBX incompatibility > > > > *EXTERNAL* > > Sorry guy, I was on holidays and the maintenance was a problem. > > > > Try putting the bootstrap.py in the directory that the command is being > run. > > > Cheers > > > > Nigel > > > > --- > > Nigel W. Moriarty > Building 33R0349, Molecular Biophysics and Integrated Bioimaging > > Lawrence Berkeley National Laboratory > Berkeley, CA 94720-8235 > Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov > Fax : 510-486-5909 Web : CCI.LBL.gov > > > > > > On Fri, Aug 16, 2019 at 7:27 PM Christopher Williams < > christopher.sci.williams(a)gmail.com> wrote: > > Hmm. Nigel, I may need some of your expertise here. It looks like > there's a consistent problem with svn checkouts. > > > > "git clone" operations seem to have been successful, so it probably isn't > a matter of GitHub being down. Especially since the svn checkout of geostd > from Sourceforge also failed. > > > > Do you know if your system has problems with svn? Our svn checkouts > generally take this form: " svn co > https://github.com/rlabduke/MolProbity.git/trunk molprobity > --non-interactive --trust-server-cert " Is there perhaps a security > issue with the --trust-server-cert flag? > > > > I believe that the cci machines at Berkeley are under maintenance until > Sunday, so there are other reasons the script won't work until then. > > > > Good luck, > > -Christopher Williams > > ---Richardson Lab, Duke University > > > > > > On Fri, Aug 16, 2019 at 5:45 PM Charitha Belluru Shetty < > charitha-belluru.b.shetty(a)gsk.com> wrote: > > Hi Christopher, > > > > I ran the installer script twice and this is what I got… > > > > *When I ran it first time, only the modules directory was created* > > bash-4.2$ *. install_via_bootstrap.sh 10* > > ++++++++++ creating build directories ... > > svn: E000110: Unable to connect to a repository at URL 'svn:// > svn.code.sf.net/p/geostd/code/trunk' > > svn: E000110: Can't read from connection: Connection timed out > > svn: E175002: Unable to connect to a repository at URL ' > https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_rotame… > ' > > svn: E175002: OPTIONS of ' > https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_rotame…': > SSL handshake failed: SSL socket read failed (https://github.com) > > svn: E175002: Unable to connect to a repository at URL ' > https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_ramach… > ' > > svn: E175002: OPTIONS of ' > https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_ramach…': > SSL handshake failed: SSL socket read failed (https://github.com) > > svn: E175002: Unable to connect to a repository at URL ' > https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_cablam… > ' > > svn: E175002: OPTIONS of ' > https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_cablam…': > SSL handshake failed: SSL socket read failed (https://github.com) > > svn: E175002: Unable to connect to a repository at URL ' > https://github.com/cctbx/cctbx_project.git/trunk/libtbx/auto_build/bootstra… > ' > > svn: E175002: OPTIONS of ' > https://github.com/cctbx/cctbx_project.git/trunk/libtbx/auto_build/bootstra…': > SSL handshake failed: SSL socket read failed (https://github.com) > > python: can't open file 'bootstrap.py': [Errno 2] No such file or directory > > -bash: build/setpaths.sh: No such file or directory > > python: can't open file > 'modules/chem_data/cablam_data/rebuild_cablam_cache.py': [Errno 2] No such > file or directory > > ++++++++++ MolProbity configure.sh finished. > > ++++++++++ Run molprobity/setup.sh to complete installation. > > -bash-4.2$ > > > > -bash-4.2$ pwd > > /hpc/apps/current/molprobity/v4.4.app > > -bash-4.2$ ls -l > > total 31 > > *-rw-r--r-- 1 cbs72396 appmgmt 1817 Aug 14 14:03 install_via_bootstrap.sh* > > *drwxr-sr-x 3 cbs72396 appmgmt 3 Aug 15 17:58 modules* > > > > > > *Second time when I ran..bootstap.py and bootstrap.pyc was crated and the > modules directory…* > > > > -bash-4.2$ *. install_via_bootstrap.sh 4* > > ++++++++++ creating build directories ... > > > > > > svn: E000110: Unable to connect to a repository at URL 'svn:// > svn.code.sf.net/p/geostd/code/trunk' > > svn: E000110: Can't read from connection: Connection timed out > > Performing actions: hot update base build > > Installing base packages using: > > python modules/cctbx_project/libtbx/auto_build/install_conda.py > --builder=molprobity --install_conda > > ===== Downloading http://cci.lbl.gov/repositories/annlib.gz: 0.5 MB > > [0%.........20%.........40%.........60%.........80%.........100%] > > ===== Running in modules: extracting files from annlib.gz > > ===== Downloading http://cci.lbl.gov/repositories/scons.gz: 0.6 MB > > [0%.........20%.........40%.........60%.........80%.........100%] > > ===== Running in modules: extracting files from scons.gz > > ===== Downloading http://cci.lbl.gov/repositories/ccp4io.gz: 1.4 MB > > [0%.........20%.........40%.........60%.........80%.........100%] > > ===== Running in modules: extracting files from ccp4io.gz > > ===== Running in modules: git clone --recursive > https://github.com/cctbx/boost.git boost --progress --verbose > > Cloning into 'boost'... > > POST git-upload-pack (942 bytes) > > remote: Enumerating objects: 27664, done. > > remote: Total 27664 (delta 0), reused 0 (delta 0), pack-reused 27664 > > Receiving objects: 100% (27664/27664), 20.47 MiB | 14.72 MiB/s, done. > > Resolving deltas: 100% (15913/15913), done. > > Checking out files: 100% (14245/14245), done. > > setting branch master to rebase > > ===== Running in modules/boost: git rev-parse HEAD > > 72edfa007c73dd3dd01f5530205f7ca14cda7420 > > ===== Running in modules: git clone --recursive > https://github.com/yayahjb/cbflib.git cbflib --progress --verbose > > Cloning into 'cbflib'... > > POST git-upload-pack (gzip 2442 to 1233 bytes) > > remote: Enumerating objects: 7463, done. > > remote: Total 7463 (delta 0), reused 0 (delta 0), pack-reused 7463 > > Receiving objects: 100% (7463/7463), 24.84 MiB | 13.21 MiB/s, done. > > Resolving deltas: 100% (5380/5380), done. > > setting branch master to rebase > > ===== Running in modules/cbflib: git rev-parse HEAD > > 611f21bbef81c5104954aaab9b72e4e55ec3e70d > > ===== Running in modules: git clone --recursive > https://github.com/cctbx/cctbx_project.git cctbx_project --progress > --verbose > > Cloning into 'cctbx_project'... > > POST git-upload-pack (gzip 1842 to 958 bytes) > > remote: Enumerating objects: 61, done. > > remote: Counting objects: 100% (61/61), done. > > remote: Compressing objects: 100% (52/52), done. > > remote: Total 243691 (delta 14), reused 22 (delta 9), pack-reused 243630 > > Receiving objects: 100% (243691/243691), 91.05 MiB | 14.77 MiB/s, done. > > Resolving deltas: 100% (192566/192566), done. > > Checking out files: 100% (6173/6173), done. > > setting branch master to rebase > > ===== Running in modules/cctbx_project: git rev-parse HEAD > > bd3139c85312f5f43009e1eb31baa34f41734fbb > > ===== Downloading http://cci.lbl.gov/repositories/ccp4io_adaptbx.gz: > 203.9 kB > > [0%.........20%.........40%.........60%.........80%.........100%] > > ===== Running in modules: extracting files from ccp4io_adaptbx.gz > > ===== Running in modules: git clone --recursive > https://github.com/cctbx/annlib_adaptbx.git annlib_adaptbx --progress > --verbose > > Cloning into 'annlib_adaptbx'... > > POST git-upload-pack (842 bytes) > > remote: Enumerating objects: 175, done. > > remote: Total 175 (delta 0), reused 0 (delta 0), pack-reused 175 > > Receiving objects: 100% (175/175), 162.09 KiB | 0 bytes/s, done. > > Resolving deltas: 100% (77/77), done. > > setting branch master to rebase > > ===== Running in modules/annlib_adaptbx: git rev-parse HEAD > > 3ca66b2dd77eacd7524f915fce0705ac0764b46f > > ===== Downloading http://cci.lbl.gov/repositories/tntbx.gz: 38.0 kB > > [0%.........20%.........40%.........60%.........80%.........100%] > > ===== Running in modules: extracting files from tntbx.gz > > ===== Running in .: svn co > https://github.com/rlabduke/MolProbity.git/trunk molprobity > --non-interactive --trust-server-cert > > svn: E175002: Unable to connect to a repository at URL ' > https://github.com/rlabduke/MolProbity.git/trunk' > > svn: E175002: OPTIONS of 'https://github.com/rlabduke/MolProbity.git/trunk': > SSL handshake failed: SSL socket read failed (https://github.com) > > Process failed with return code 1 > > -bash: build/setpaths.sh: No such file or directory > > Traceback (most recent call last): > > File "modules/chem_data/cablam_data/rebuild_cablam_cache.py", line 2, in > <module> > > import libtbx.load_env > > ImportError: No module named libtbx.load_env > > ++++++++++ MolProbity configure.sh finished. > > ++++++++++ Run molprobity/setup.sh to complete installation. > > -bash-4.2$ > > -bash-4.2$ > > *-bash-4.2$ ls -l* > > *total 131* > > *-rw-r--r-- 1 cbs72396 appmgmt 90799 Aug 14 18:26 bootstrap.py* > > *-rw-r--r-- 1 cbs72396 appmgmt 82015 Aug 16 13:38 bootstrap.pyc* > > *-rw-r--r-- 1 cbs72396 appmgmt 1817 Aug 14 14:03 > install_via_bootstrap.sh* > > *drwxr-sr-x 12 cbs72396 appmgmt 22 Aug 16 13:38 modules* > > > > > > Best Regards, > > Charitha Shetty > > > > *From:* Christopher Williams <christopher.sci.williams(a)gmail.com> > *Sent:* Wednesday, August 14, 2019 2:23 PM > *To:* Robert Nolte <robert.t.nolte(a)gsk.com> > *Cc:* Nigel Moriarty <nwmoriarty(a)lbl.gov>; Charitha Belluru Shetty < > charitha-belluru.b.shetty(a)gsk.com>; cctbxbb(a)phenix-online.org > *Subject:* Re: Molprobity / CCTBX incompatibility > > > > *EXTERNAL* > > Hi All, > > > > Okay looks like the new installer works. It uses the conda mode of the > cctbx bootstrap builder for everything except chem_data, which it builds on > its own. > > > > Get the new installer from our GitHub here: > > svn --quiet --non-interactive --trust-server-cert export > https://github.com/rlabduke/MolProbity.git/trunk/install_via_bootstrap.sh > > > > Place it in the dir where you want to install MolProbity, then run it. > > . install_via_bootstrap.sh > > The script optionally accepts a single integer argument to set the number > of processors that the bootstrap builder will use. > > . install_via_bootstrap.sh 4 > > > > When this is complete, cd to the molprobity dir it created and run > setup.sh, as usual. > > > > Good luck, > > -Christopher Williams > > ---Richardson Lab, Duke University > > > > > > On Wed, Aug 14, 2019 at 1:33 PM Christopher Williams < > christopher.sci.williams(a)gmail.com> wrote: > > Hi Bob, > > > > I am currently doing one more test build to make sure that the new > installer works. It looks promising. > > > > Regards, > > -Christopher Williams > > ---Richardson Lab, Duke University > > > > On Wed, Aug 14, 2019 at 11:17 AM Robert Nolte <robert.t.nolte(a)gsk.com> > wrote: > > Folks, > > Any progress on sorting out our issue, or cleaning up the installer? > > Bob > > > > > > *From:* Christopher Williams <christopher.sci.williams(a)gmail.com> > *Sent:* Monday, August 12, 2019 7:48 PM > *To:* Nigel Moriarty <nwmoriarty(a)lbl.gov> > *Cc:* Robert Nolte <robert.t.nolte(a)gsk.com>; Charitha Belluru Shetty < > charitha-belluru.b.shetty(a)gsk.com>; cctbxbb(a)phenix-online.org > *Subject:* Re: Molprobity / CCTBX incompatibility > > > > *EXTERNAL* > > The dispatcher should be using both phenix.reduce and molprobity.reduce > interchangeably in all cases. Ditto for all the validations that > MolProbity runs like phenix.rotalyze/molprobity.rotalyze. > > > > My current install of MolProbity is successfully accessing Reduce via > phenix.reduce, so I don't *think* this is the issue. > > > > -Christopher Williams > > ---Richardson Lab, Duke University > > > > On Mon, Aug 12, 2019 at 6:07 PM Nigel Moriarty <nwmoriarty(a)lbl.gov> wrote: > > But maybe the installation of cctbx has molprobity.reduce and not > phenix.reduce so if that is the case we can change the script to look for > molprobity.reduce instead of phenix.reduce. > > > Cheers > > > > Nigel > > > > --- > > Nigel W. Moriarty > Building 33R0349, Molecular Biophysics and Integrated Bioimaging > > Lawrence Berkeley National Laboratory > Berkeley, CA 94720-8235 > Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov > Fax : 510-486-5909 Web : CCI.LBL.gov > > > > > > On Mon, Aug 12, 2019 at 2:58 PM Robert Nolte <robert.t.nolte(a)gsk.com> > wrote: > > According to the log file when I just tried to run it, it is phenix.reduce > that it can’t find. > > Bob > > > > > > *From:* Nigel Moriarty <nwmoriarty(a)lbl.gov> > *Sent:* Monday, August 12, 2019 5:55 PM > *To:* Robert Nolte <robert.t.nolte(a)gsk.com> > *Cc:* Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com>; > Christopher Williams <christopher.sci.williams(a)gmail.com>; > cctbxbb(a)phenix-online.org > *Subject:* Re: Molprobity / CCTBX incompatibility > > > > *EXTERNAL* > > I'm just trying to find out if, at the command line, whether it is > phenix.reduce or molprobity.reduce. Charitha just needs to type one or the > other to see what happens. > > > Cheers > > > > Nigel > > > > --- > > Nigel W. Moriarty > Building 33R0349, Molecular Biophysics and Integrated Bioimaging > > Lawrence Berkeley National Laboratory > Berkeley, CA 94720-8235 > Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov > Fax : 510-486-5909 Web : CCI.LBL.gov > > > > > > On Mon, Aug 12, 2019 at 2:44 PM Robert Nolte <robert.t.nolte(a)gsk.com> > wrote: > > Nigel, > > Currently it is not running. This was working from the scratch > install last week. I am not sure what is going on now. > > Bob > > > > > > *From:* Nigel Moriarty <nwmoriarty(a)lbl.gov> > *Sent:* Monday, August 12, 2019 4:52 PM > *To:* Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com> > *Cc:* Christopher Williams <christopher.sci.williams(a)gmail.com>; > cctbxbb(a)phenix-online.org; Robert Nolte <robert.t.nolte(a)gsk.com> > *Subject:* Re: Molprobity / CCTBX incompatibility > > > > *EXTERNAL* > > Does molprobity.reduce run? > > > Cheers > > > > Nigel > > > > --- > > Nigel W. Moriarty > Building 33R0349, Molecular Biophysics and Integrated Bioimaging > > Lawrence Berkeley National Laboratory > Berkeley, CA 94720-8235 > Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov > Fax : 510-486-5909 Web : CCI.LBL.gov > > > > > > On Mon, Aug 12, 2019 at 1:14 PM Charitha Belluru Shetty < > charitha-belluru.b.shetty(a)gsk.com> wrote: > > Hi Nigel, > > > > I hit the send button too soon..Ignore my previous email 😊 > > > > -bash-4.2$ source setpaths.sh > > -bash-4.2$ > > -bash-4.2$ env |grep -i reduce > > -bash-4.2$ > > > > So the “setpath.sh” has the below contents… > > > > $ cat /hpc/apps/current/molprobity/v4.4.app/MolProbity/build/setpaths.sh > > # THIS IS AN AUTOMATICALLY GENERATED FILE. > > # DO NOT EDIT! CHANGES WILL BE LOST. > > ocwd="`pwd`" > > if [ -n "$LIBTBX_BUILD_RELOCATION_HINT" ]; then > > cd "$LIBTBX_BUILD_RELOCATION_HINT" > > LIBTBX_BUILD_RELOCATION_HINT= > > export LIBTBX_BUILD_RELOCATION_HINT > > elif [ -n "$BASH_SOURCE" ]; then > > LIBTBX_BUILD=`dirname "$BASH_SOURCE[0]"` > > cd "$LIBTBX_BUILD" > > else > > cd "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build" > > fi > > LIBTBX_BUILD=`pwd -P` > > export LIBTBX_BUILD > > LIBTBX_OPATH="$PATH" > > export LIBTBX_OPATH > > PATH="$LIBTBX_BUILD/bin:$PATH" > > export PATH > > cd "$ocwd" > > ocwd= > > alias libtbx.setpaths_all=". \"$LIBTBX_BUILD/setpaths_all.sh\"" > > alias libtbx.unsetpaths=". \"$LIBTBX_BUILD/unsetpaths.sh\"" > > if [ -n "$LIBTBX_OPATH" ]; then > > LIBTBX_TMPVAL="$LIBTBX_OPATH" > > else > > LIBTBX_TMPVAL= > > fi > > export LIBTBX_TMPVAL > > PATH=`libtbx.path_utility prepend LIBTBX_TMPVAL "$LIBTBX_BUILD/bin" < > /dev/null` > > export PATH > > if [ "$PATH" = "L_I_B_T_B_X_E_M_P_T_Y" ]; then unset PATH; fi > > LIBTBX_TMPVAL= > > LIBTBX_OPATH= > > LIBTBX_BUILD= > > > > > > Best Regards, > > Charitha Shetty > > > > *From:* Nigel Moriarty <nwmoriarty(a)lbl.gov> > *Sent:* Monday, August 12, 2019 4:08 PM > *To:* Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com> > *Cc:* Christopher Williams <christopher.sci.williams(a)gmail.com>; > cctbxbb(a)phenix-online.org; Robert Nolte <robert.t.nolte(a)gsk.com> > *Subject:* Re: Molprobity / CCTBX incompatibility > > > > *EXTERNAL* > > Once you source the setpaths.sh file in the build directory do you have > phenix.reduce or molprobity.reduce? > > Cheers > > > > Nigel > > > > --- > > Nigel W. Moriarty > Building 33R0349, Molecular Biophysics and Integrated Bioimaging > > Lawrence Berkeley National Laboratory > Berkeley, CA 94720-8235 > Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov > Fax : 510-486-5909 Web : CCI.LBL.gov > > > > > > On Mon, Aug 12, 2019 at 12:43 PM Charitha Belluru Shetty < > charitha-belluru.b.shetty(a)gsk.com> wrote: > > Hi Christopher/ Nigel, > > > > Thank you for your quick reply. > > > > The build process was completed without any error. Pasting few of the > lines from it… > > > > > > ===== Running in build: rebuild rotarama > > Processing data files in > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/chem_data/rotarama_data": > > rota8000-cys.data -> rota8000-cys.pickle: converting ... done. > > rota8000-asp.data -> rota8000-asp.pickle: converting ... done. > > rota8000-ser.data -> rota8000-ser.pickle: converting ... done. > > rota8000-gln.data -> rota8000-gln.pickle: converting ... done. > > rota8000-ile.data -> rota8000-ile.pickle: converting ... done. > > rota8000-pro.data -> rota8000-pro.pickle: converting ... done. > > rota8000-lys.data -> rota8000-lys.pickle: converting ... done. > > rota8000-thr.data -> rota8000-thr.pickle: converting ... done. > > rota8000-phetyr.data -> rota8000-phetyr.pickle: converting ... done. > > rota8000-glu.data -> rota8000-glu.pickle: converting ... done. > > rota8000-met.data -> rota8000-met.pickle: converting ... done. > > rota8000-his.data -> rota8000-his.pickle: converting ... done. > > rota8000-leu.data -> rota8000-leu.pickle: converting ... done. > > rota8000-arg.data -> rota8000-arg.pickle: converting ... done. > > rota8000-trp.data -> rota8000-trp.pickle: converting ... done. > > rota8000-asn.data -> rota8000-asn.pickle: converting ... done. > > rota8000-phetyr.data -> rota8000-phetyr.pickle: already up to date. > > rota8000-val.data -> rota8000-val.pickle: converting ... done. > > Processing data files in > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/chem_data/rotarama_data": > > rama8000-ileval-nopreP.data -> rama8000-ileval-nopreP.pickle: converting > ... done. > > rama8000-gly-sym.data -> rama8000-gly-sym.pickle: converting ... done. > > rama8000-cispro.data -> rama8000-cispro.pickle: converting ... done. > > rama8000-general-noGPIVpreP.data -> rama8000-general-noGPIVpreP.pickle: > converting ... done. > > rama8000-transpro.data -> rama8000-transpro.pickle: converting ... done. > > rama8000-prepro-noGP.data -> rama8000-prepro-noGP.pickle: converting ... > done. > > u+s,u,s: 10.06 9.83 0.23 > > ===== Running in .: libtbx.refresh > > Python: 2.7.16 > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/bin/python2.7" > > Compiler: default > > Build mode: release > > Warning level: 0 > > Precompiled Headers: False > > Static libraries: False > > Static exe: False > > Scan Boost headers: False > > Write full flex_fwd.h files: False > > Build Boost.Python extensions: True > > Define BOOST_PYTHON_NO_PY_SIGNATURES: False > > Define BOOST_PYTHON_BOOL_INT_STRICT: True > > Enable OpenMP if possible: False > > Boost threads enabled: True > > Enable CUDA: False > > Use conda: False > > Use opt_resources if available: False > > Use environment flags: False > > Enable C++11: False > > Python3 migration warning policy: None > > command_version_suffix: None > > Relocatable paths anchored at: > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/build > > Top-down list of all modules involved: > > mmtbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx" > > iotbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx" > > ccp4io+adaptbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/ccp4io" > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/ccp4io_adaptbx" > > smtbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx" > > ucif > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/ucif" > > cctbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx" > > scitbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx" > > fable > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/fable" > > omptbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/omptbx" > > boost+adaptbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/boost" > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx" > > tbxx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/tbxx" > > chiltbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/chiltbx" > > libtbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/libtbx" > > Creating files in build directory: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build" > > dispatcher_include_template.sh > > dispatcher_head.sh > > setpaths.sh > > setpaths.csh > > setpaths_all.sh > > setpaths_all.csh > > setpaths_debug.sh > > unsetpaths.sh > > setpaths_debug.csh > > unsetpaths.csh > > SConstruct > > Makefile > > run_tests.csh > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/libtbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/fable/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx/libtbx_refresh.py" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx/libtbx_refresh.py" > > Generating C++ header files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/scitbx/array_family" > > Generating C++ files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/scitbx/array_family/boost_python" > > Using fable to convert scitbx/lbfgs.f > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx/libtbx_refresh.py" > > Generating C++ files in: > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/cctbx/eltbx" > > Generating C++ files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/cctbx/boost_python" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx/libtbx_refresh.py" > > Generating C++ files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/smtbx/boost_python" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx/libtbx_refresh.py" > > Using fable to convert iotbx/pdb/hybrid_36_f.f > > Writing: iotbx/pdb/hybrid_36_fem.cpp > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx/libtbx_refresh.py" > > Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/exe_dev" > > Regenerating module files in > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base > > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/pango not present, > could not regenerate pango files > > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/gtk-2.0 not > present, could not regenerate gdk-pixbuf.loaders > > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/fonts not present, > could not rebuild fonts > > generating index.theme file > > Done. > > > > *Bootstrap success: build* > > *++++++++++ MolProbity configure.sh finished.* > > > > > > > > [tm375568@uptus060-3 MolProbity]$ ./setup.sh > > ++++++++++ creating directories ... > > ++++++++++ setting permisions ... > > *Couldn't get a file descriptor referring to the console **à I assume > this can be ignored. * > > [tm375568@uptus060-3 MolProbity]$ > > > > Best Regards, > > Charitha Shetty > > > > *From:* Christopher Williams <christopher.sci.williams(a)gmail.com> > *Sent:* Monday, August 12, 2019 3:34 PM > *To:* Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com> > *Cc:* Nigel Moriarty (nwmoriarty(a)lbl.gov) <nwmoriarty(a)lbl.gov>; > cctbxbb(a)phenix-online.org; Robert Nolte <robert.t.nolte(a)gsk.com> > *Subject:* Re: Molprobity / CCTBX incompatibility > > > > *EXTERNAL* > > Hmm. It looks like Reduce and/or Probe has failed to install correctly. > Most likely an early call to Reduce has resulted in an empty file, which is > then passed into other programs, resulting in error messages. > > > > The configure script ran a build process. Do you know if that process > finished successfully or if it ended with errors? If the build exited > early, it may have never reached the part where Reduce gets compiled. Some > dependencies have changed, and I have been having trouble with my own > builds lately. > > > > It is also possible that there was just a network hiccup that prevented > something from downloading correctly, and a second attempt will work. > > > > I am working on a new configure/install script for more consistent > handling of dependencies. Hopefully it will be ready in about a day. > > > > Good luck, > > -Christopher Williams > > ---Richardson Lab, Duke University > > > > > > > > > > > > *GSK monitors email communications sent to and from GSK in order to > protect GSK, our employees, customers, suppliers and business partners, > from cyber threats and loss of GSK Information. GSK monitoring is conducted > with appropriate confidentiality controls and in accordance with local laws > and after appropriate consultation.* > > *GSK monitors email communications sent to and from GSK in order to > protect GSK, our employees, customers, suppliers and business partners, > from cyber threats and loss of GSK Information. GSK monitoring is conducted > with appropriate confidentiality controls and in accordance with local laws > and after appropriate consultation.* > > *GSK monitors email communications sent to and from GSK in order to > protect GSK, our employees, customers, suppliers and business partners, > from cyber threats and loss of GSK Information. GSK monitoring is conducted > with appropriate confidentiality controls and in accordance with local laws > and after appropriate consultation.* > > *GSK monitors email communications sent to and from GSK in order to > protect GSK, our employees, customers, suppliers and business partners, > from cyber threats and loss of GSK Information. GSK monitoring is conducted > with appropriate confidentiality controls and in accordance with local laws > and after appropriate consultation.* > > *GSK monitors email communications sent to and from GSK in order to > protect GSK, our employees, customers, suppliers and business partners, > from cyber threats and loss of GSK Information. GSK monitoring is conducted > with appropriate confidentiality controls and in accordance with local laws > and after appropriate consultation.* > > *GSK monitors email communications sent to and from GSK in order to > protect GSK, our employees, customers, suppliers and business partners, > from cyber threats and loss of GSK Information. GSK monitoring is conducted > with appropriate confidentiality controls and in accordance with local laws > and after appropriate consultation.* > > *GSK monitors email communications sent to and from GSK in order to > protect GSK, our employees, customers, suppliers and business partners, > from cyber threats and loss of GSK Information. GSK monitoring is conducted > with appropriate confidentiality controls and in accordance with local laws > and after appropriate consultation.* >

1 0

Re: [cctbxbb] Molprobity / CCTBX incompatibility
by Nigel Moriarty 19 Aug '19

19 Aug '19

Sorry guy, I was on holidays and the maintenance was a problem. Try putting the bootstrap.py in the directory that the command is being run. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov On Fri, Aug 16, 2019 at 7:27 PM Christopher Williams < christopher.sci.williams(a)gmail.com> wrote: > Hmm. Nigel, I may need some of your expertise here. It looks like > there's a consistent problem with svn checkouts. > > "git clone" operations seem to have been successful, so it probably isn't > a matter of GitHub being down. Especially since the svn checkout of geostd > from Sourceforge also failed. > > Do you know if your system has problems with svn? Our svn checkouts > generally take this form: " svn co > https://github.com/rlabduke/MolProbity.git/trunk molprobity > --non-interactive --trust-server-cert " Is there perhaps a security > issue with the --trust-server-cert flag? > > I believe that the cci machines at Berkeley are under maintenance until > Sunday, so there are other reasons the script won't work until then. > > Good luck, > -Christopher Williams > ---Richardson Lab, Duke University > > > On Fri, Aug 16, 2019 at 5:45 PM Charitha Belluru Shetty < > charitha-belluru.b.shetty(a)gsk.com> wrote: > >> Hi Christopher, >> >> >> >> I ran the installer script twice and this is what I got… >> >> >> >> *When I ran it first time, only the modules directory was created* >> >> bash-4.2$ *. install_via_bootstrap.sh 10* >> >> ++++++++++ creating build directories ... >> >> svn: E000110: Unable to connect to a repository at URL 'svn:// >> svn.code.sf.net/p/geostd/code/trunk' >> >> svn: E000110: Can't read from connection: Connection timed out >> >> svn: E175002: Unable to connect to a repository at URL ' >> https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_rotame… >> ' >> >> svn: E175002: OPTIONS of ' >> https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_rotame…': >> SSL handshake failed: SSL socket read failed (https://github.com) >> >> svn: E175002: Unable to connect to a repository at URL ' >> https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_ramach… >> ' >> >> svn: E175002: OPTIONS of ' >> https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_ramach…': >> SSL handshake failed: SSL socket read failed (https://github.com) >> >> svn: E175002: Unable to connect to a repository at URL ' >> https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_cablam… >> ' >> >> svn: E175002: OPTIONS of ' >> https://github.com/rlabduke/reference_data.git/trunk/Top8000/Top8000_cablam…': >> SSL handshake failed: SSL socket read failed (https://github.com) >> >> svn: E175002: Unable to connect to a repository at URL ' >> https://github.com/cctbx/cctbx_project.git/trunk/libtbx/auto_build/bootstra… >> ' >> >> svn: E175002: OPTIONS of ' >> https://github.com/cctbx/cctbx_project.git/trunk/libtbx/auto_build/bootstra…': >> SSL handshake failed: SSL socket read failed (https://github.com) >> >> python: can't open file 'bootstrap.py': [Errno 2] No such file or >> directory >> >> -bash: build/setpaths.sh: No such file or directory >> >> python: can't open file >> 'modules/chem_data/cablam_data/rebuild_cablam_cache.py': [Errno 2] No such >> file or directory >> >> ++++++++++ MolProbity configure.sh finished. >> >> ++++++++++ Run molprobity/setup.sh to complete installation. >> >> -bash-4.2$ >> >> >> >> -bash-4.2$ pwd >> >> /hpc/apps/current/molprobity/v4.4.app >> >> -bash-4.2$ ls -l >> >> total 31 >> >> *-rw-r--r-- 1 cbs72396 appmgmt 1817 Aug 14 14:03 >> install_via_bootstrap.sh* >> >> *drwxr-sr-x 3 cbs72396 appmgmt 3 Aug 15 17:58 modules* >> >> >> >> >> >> *Second time when I ran..bootstap.py and bootstrap.pyc was crated and the >> modules directory…* >> >> >> >> -bash-4.2$ *. install_via_bootstrap.sh 4* >> >> ++++++++++ creating build directories ... >> >> >> >> >> >> svn: E000110: Unable to connect to a repository at URL 'svn:// >> svn.code.sf.net/p/geostd/code/trunk' >> >> svn: E000110: Can't read from connection: Connection timed out >> >> Performing actions: hot update base build >> >> Installing base packages using: >> >> python modules/cctbx_project/libtbx/auto_build/install_conda.py >> --builder=molprobity --install_conda >> >> ===== Downloading http://cci.lbl.gov/repositories/annlib.gz: 0.5 MB >> >> [0%.........20%.........40%.........60%.........80%.........100%] >> >> ===== Running in modules: extracting files from annlib.gz >> >> ===== Downloading http://cci.lbl.gov/repositories/scons.gz: 0.6 MB >> >> [0%.........20%.........40%.........60%.........80%.........100%] >> >> ===== Running in modules: extracting files from scons.gz >> >> ===== Downloading http://cci.lbl.gov/repositories/ccp4io.gz: 1.4 MB >> >> [0%.........20%.........40%.........60%.........80%.........100%] >> >> ===== Running in modules: extracting files from ccp4io.gz >> >> ===== Running in modules: git clone --recursive >> https://github.com/cctbx/boost.git boost --progress --verbose >> >> Cloning into 'boost'... >> >> POST git-upload-pack (942 bytes) >> >> remote: Enumerating objects: 27664, done. >> >> remote: Total 27664 (delta 0), reused 0 (delta 0), pack-reused 27664 >> >> Receiving objects: 100% (27664/27664), 20.47 MiB | 14.72 MiB/s, done. >> >> Resolving deltas: 100% (15913/15913), done. >> >> Checking out files: 100% (14245/14245), done. >> >> setting branch master to rebase >> >> ===== Running in modules/boost: git rev-parse HEAD >> >> 72edfa007c73dd3dd01f5530205f7ca14cda7420 >> >> ===== Running in modules: git clone --recursive >> https://github.com/yayahjb/cbflib.git cbflib --progress --verbose >> >> Cloning into 'cbflib'... >> >> POST git-upload-pack (gzip 2442 to 1233 bytes) >> >> remote: Enumerating objects: 7463, done. >> >> remote: Total 7463 (delta 0), reused 0 (delta 0), pack-reused 7463 >> >> Receiving objects: 100% (7463/7463), 24.84 MiB | 13.21 MiB/s, done. >> >> Resolving deltas: 100% (5380/5380), done. >> >> setting branch master to rebase >> >> ===== Running in modules/cbflib: git rev-parse HEAD >> >> 611f21bbef81c5104954aaab9b72e4e55ec3e70d >> >> ===== Running in modules: git clone --recursive >> https://github.com/cctbx/cctbx_project.git cctbx_project --progress >> --verbose >> >> Cloning into 'cctbx_project'... >> >> POST git-upload-pack (gzip 1842 to 958 bytes) >> >> remote: Enumerating objects: 61, done. >> >> remote: Counting objects: 100% (61/61), done. >> >> remote: Compressing objects: 100% (52/52), done. >> >> remote: Total 243691 (delta 14), reused 22 (delta 9), pack-reused 243630 >> >> Receiving objects: 100% (243691/243691), 91.05 MiB | 14.77 MiB/s, done. >> >> Resolving deltas: 100% (192566/192566), done. >> >> Checking out files: 100% (6173/6173), done. >> >> setting branch master to rebase >> >> ===== Running in modules/cctbx_project: git rev-parse HEAD >> >> bd3139c85312f5f43009e1eb31baa34f41734fbb >> >> ===== Downloading http://cci.lbl.gov/repositories/ccp4io_adaptbx.gz: >> 203.9 kB >> >> [0%.........20%.........40%.........60%.........80%.........100%] >> >> ===== Running in modules: extracting files from ccp4io_adaptbx.gz >> >> ===== Running in modules: git clone --recursive >> https://github.com/cctbx/annlib_adaptbx.git annlib_adaptbx --progress >> --verbose >> >> Cloning into 'annlib_adaptbx'... >> >> POST git-upload-pack (842 bytes) >> >> remote: Enumerating objects: 175, done. >> >> remote: Total 175 (delta 0), reused 0 (delta 0), pack-reused 175 >> >> Receiving objects: 100% (175/175), 162.09 KiB | 0 bytes/s, done. >> >> Resolving deltas: 100% (77/77), done. >> >> setting branch master to rebase >> >> ===== Running in modules/annlib_adaptbx: git rev-parse HEAD >> >> 3ca66b2dd77eacd7524f915fce0705ac0764b46f >> >> ===== Downloading http://cci.lbl.gov/repositories/tntbx.gz: 38.0 kB >> >> [0%.........20%.........40%.........60%.........80%.........100%] >> >> ===== Running in modules: extracting files from tntbx.gz >> >> ===== Running in .: svn co >> https://github.com/rlabduke/MolProbity.git/trunk molprobity >> --non-interactive --trust-server-cert >> >> svn: E175002: Unable to connect to a repository at URL ' >> https://github.com/rlabduke/MolProbity.git/trunk' >> >> svn: E175002: OPTIONS of ' >> https://github.com/rlabduke/MolProbity.git/trunk': SSL handshake failed: >> SSL socket read failed (https://github.com) >> >> Process failed with return code 1 >> >> -bash: build/setpaths.sh: No such file or directory >> >> Traceback (most recent call last): >> >> File "modules/chem_data/cablam_data/rebuild_cablam_cache.py", line 2, >> in <module> >> >> import libtbx.load_env >> >> ImportError: No module named libtbx.load_env >> >> ++++++++++ MolProbity configure.sh finished. >> >> ++++++++++ Run molprobity/setup.sh to complete installation. >> >> -bash-4.2$ >> >> -bash-4.2$ >> >> *-bash-4.2$ ls -l* >> >> *total 131* >> >> *-rw-r--r-- 1 cbs72396 appmgmt 90799 Aug 14 18:26 bootstrap.py* >> >> *-rw-r--r-- 1 cbs72396 appmgmt 82015 Aug 16 13:38 bootstrap.pyc* >> >> *-rw-r--r-- 1 cbs72396 appmgmt 1817 Aug 14 14:03 >> install_via_bootstrap.sh* >> >> *drwxr-sr-x 12 cbs72396 appmgmt 22 Aug 16 13:38 modules* >> >> >> >> >> >> Best Regards, >> >> Charitha Shetty >> >> >> >> *From:* Christopher Williams <christopher.sci.williams(a)gmail.com> >> *Sent:* Wednesday, August 14, 2019 2:23 PM >> *To:* Robert Nolte <robert.t.nolte(a)gsk.com> >> *Cc:* Nigel Moriarty <nwmoriarty(a)lbl.gov>; Charitha Belluru Shetty < >> charitha-belluru.b.shetty(a)gsk.com>; cctbxbb(a)phenix-online.org >> *Subject:* Re: Molprobity / CCTBX incompatibility >> >> >> >> *EXTERNAL* >> >> Hi All, >> >> >> >> Okay looks like the new installer works. It uses the conda mode of the >> cctbx bootstrap builder for everything except chem_data, which it builds on >> its own. >> >> >> >> Get the new installer from our GitHub here: >> >> svn --quiet --non-interactive --trust-server-cert export >> https://github.com/rlabduke/MolProbity.git/trunk/install_via_bootstrap.sh >> >> >> >> Place it in the dir where you want to install MolProbity, then run it. >> >> . install_via_bootstrap.sh >> >> The script optionally accepts a single integer argument to set the number >> of processors that the bootstrap builder will use. >> >> . install_via_bootstrap.sh 4 >> >> >> >> When this is complete, cd to the molprobity dir it created and run >> setup.sh, as usual. >> >> >> >> Good luck, >> >> -Christopher Williams >> >> ---Richardson Lab, Duke University >> >> >> >> >> >> On Wed, Aug 14, 2019 at 1:33 PM Christopher Williams < >> christopher.sci.williams(a)gmail.com> wrote: >> >> Hi Bob, >> >> >> >> I am currently doing one more test build to make sure that the new >> installer works. It looks promising. >> >> >> >> Regards, >> >> -Christopher Williams >> >> ---Richardson Lab, Duke University >> >> >> >> On Wed, Aug 14, 2019 at 11:17 AM Robert Nolte <robert.t.nolte(a)gsk.com> >> wrote: >> >> Folks, >> >> Any progress on sorting out our issue, or cleaning up the installer? >> >> Bob >> >> >> >> >> >> *From:* Christopher Williams <christopher.sci.williams(a)gmail.com> >> *Sent:* Monday, August 12, 2019 7:48 PM >> *To:* Nigel Moriarty <nwmoriarty(a)lbl.gov> >> *Cc:* Robert Nolte <robert.t.nolte(a)gsk.com>; Charitha Belluru Shetty < >> charitha-belluru.b.shetty(a)gsk.com>; cctbxbb(a)phenix-online.org >> *Subject:* Re: Molprobity / CCTBX incompatibility >> >> >> >> *EXTERNAL* >> >> The dispatcher should be using both phenix.reduce and molprobity.reduce >> interchangeably in all cases. Ditto for all the validations that >> MolProbity runs like phenix.rotalyze/molprobity.rotalyze. >> >> >> >> My current install of MolProbity is successfully accessing Reduce via >> phenix.reduce, so I don't *think* this is the issue. >> >> >> >> -Christopher Williams >> >> ---Richardson Lab, Duke University >> >> >> >> On Mon, Aug 12, 2019 at 6:07 PM Nigel Moriarty <nwmoriarty(a)lbl.gov> >> wrote: >> >> But maybe the installation of cctbx has molprobity.reduce and not >> phenix.reduce so if that is the case we can change the script to look for >> molprobity.reduce instead of phenix.reduce. >> >> >> Cheers >> >> >> >> Nigel >> >> >> >> --- >> >> Nigel W. Moriarty >> Building 33R0349, Molecular Biophysics and Integrated Bioimaging >> >> Lawrence Berkeley National Laboratory >> Berkeley, CA 94720-8235 >> Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov >> Fax : 510-486-5909 Web : CCI.LBL.gov >> >> >> >> >> >> On Mon, Aug 12, 2019 at 2:58 PM Robert Nolte <robert.t.nolte(a)gsk.com> >> wrote: >> >> According to the log file when I just tried to run it, it is >> phenix.reduce that it can’t find. >> >> Bob >> >> >> >> >> >> *From:* Nigel Moriarty <nwmoriarty(a)lbl.gov> >> *Sent:* Monday, August 12, 2019 5:55 PM >> *To:* Robert Nolte <robert.t.nolte(a)gsk.com> >> *Cc:* Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com>; >> Christopher Williams <christopher.sci.williams(a)gmail.com>; >> cctbxbb(a)phenix-online.org >> *Subject:* Re: Molprobity / CCTBX incompatibility >> >> >> >> *EXTERNAL* >> >> I'm just trying to find out if, at the command line, whether it is >> phenix.reduce or molprobity.reduce. Charitha just needs to type one or the >> other to see what happens. >> >> >> Cheers >> >> >> >> Nigel >> >> >> >> --- >> >> Nigel W. Moriarty >> Building 33R0349, Molecular Biophysics and Integrated Bioimaging >> >> Lawrence Berkeley National Laboratory >> Berkeley, CA 94720-8235 >> Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov >> Fax : 510-486-5909 Web : CCI.LBL.gov >> >> >> >> >> >> On Mon, Aug 12, 2019 at 2:44 PM Robert Nolte <robert.t.nolte(a)gsk.com> >> wrote: >> >> Nigel, >> >> Currently it is not running. This was working from the scratch >> install last week. I am not sure what is going on now. >> >> Bob >> >> >> >> >> >> *From:* Nigel Moriarty <nwmoriarty(a)lbl.gov> >> *Sent:* Monday, August 12, 2019 4:52 PM >> *To:* Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com> >> *Cc:* Christopher Williams <christopher.sci.williams(a)gmail.com>; >> cctbxbb(a)phenix-online.org; Robert Nolte <robert.t.nolte(a)gsk.com> >> *Subject:* Re: Molprobity / CCTBX incompatibility >> >> >> >> *EXTERNAL* >> >> Does molprobity.reduce run? >> >> >> Cheers >> >> >> >> Nigel >> >> >> >> --- >> >> Nigel W. Moriarty >> Building 33R0349, Molecular Biophysics and Integrated Bioimaging >> >> Lawrence Berkeley National Laboratory >> Berkeley, CA 94720-8235 >> Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov >> Fax : 510-486-5909 Web : CCI.LBL.gov >> >> >> >> >> >> On Mon, Aug 12, 2019 at 1:14 PM Charitha Belluru Shetty < >> charitha-belluru.b.shetty(a)gsk.com> wrote: >> >> Hi Nigel, >> >> >> >> I hit the send button too soon..Ignore my previous email 😊 >> >> >> >> -bash-4.2$ source setpaths.sh >> >> -bash-4.2$ >> >> -bash-4.2$ env |grep -i reduce >> >> -bash-4.2$ >> >> >> >> So the “setpath.sh” has the below contents… >> >> >> >> $ cat /hpc/apps/current/molprobity/v4.4.app/MolProbity/build/setpaths.sh >> >> # THIS IS AN AUTOMATICALLY GENERATED FILE. >> >> # DO NOT EDIT! CHANGES WILL BE LOST. >> >> ocwd="`pwd`" >> >> if [ -n "$LIBTBX_BUILD_RELOCATION_HINT" ]; then >> >> cd "$LIBTBX_BUILD_RELOCATION_HINT" >> >> LIBTBX_BUILD_RELOCATION_HINT= >> >> export LIBTBX_BUILD_RELOCATION_HINT >> >> elif [ -n "$BASH_SOURCE" ]; then >> >> LIBTBX_BUILD=`dirname "$BASH_SOURCE[0]"` >> >> cd "$LIBTBX_BUILD" >> >> else >> >> cd "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build" >> >> fi >> >> LIBTBX_BUILD=`pwd -P` >> >> export LIBTBX_BUILD >> >> LIBTBX_OPATH="$PATH" >> >> export LIBTBX_OPATH >> >> PATH="$LIBTBX_BUILD/bin:$PATH" >> >> export PATH >> >> cd "$ocwd" >> >> ocwd= >> >> alias libtbx.setpaths_all=". \"$LIBTBX_BUILD/setpaths_all.sh\"" >> >> alias libtbx.unsetpaths=". \"$LIBTBX_BUILD/unsetpaths.sh\"" >> >> if [ -n "$LIBTBX_OPATH" ]; then >> >> LIBTBX_TMPVAL="$LIBTBX_OPATH" >> >> else >> >> LIBTBX_TMPVAL= >> >> fi >> >> export LIBTBX_TMPVAL >> >> PATH=`libtbx.path_utility prepend LIBTBX_TMPVAL "$LIBTBX_BUILD/bin" < >> /dev/null` >> >> export PATH >> >> if [ "$PATH" = "L_I_B_T_B_X_E_M_P_T_Y" ]; then unset PATH; fi >> >> LIBTBX_TMPVAL= >> >> LIBTBX_OPATH= >> >> LIBTBX_BUILD= >> >> >> >> >> >> Best Regards, >> >> Charitha Shetty >> >> >> >> *From:* Nigel Moriarty <nwmoriarty(a)lbl.gov> >> *Sent:* Monday, August 12, 2019 4:08 PM >> *To:* Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com> >> *Cc:* Christopher Williams <christopher.sci.williams(a)gmail.com>; >> cctbxbb(a)phenix-online.org; Robert Nolte <robert.t.nolte(a)gsk.com> >> *Subject:* Re: Molprobity / CCTBX incompatibility >> >> >> >> *EXTERNAL* >> >> Once you source the setpaths.sh file in the build directory do you have >> phenix.reduce or molprobity.reduce? >> >> Cheers >> >> >> >> Nigel >> >> >> >> --- >> >> Nigel W. Moriarty >> Building 33R0349, Molecular Biophysics and Integrated Bioimaging >> >> Lawrence Berkeley National Laboratory >> Berkeley, CA 94720-8235 >> Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov >> Fax : 510-486-5909 Web : CCI.LBL.gov >> >> >> >> >> >> On Mon, Aug 12, 2019 at 12:43 PM Charitha Belluru Shetty < >> charitha-belluru.b.shetty(a)gsk.com> wrote: >> >> Hi Christopher/ Nigel, >> >> >> >> Thank you for your quick reply. >> >> >> >> The build process was completed without any error. Pasting few of the >> lines from it… >> >> >> >> >> >> ===== Running in build: rebuild rotarama >> >> Processing data files in >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/chem_data/rotarama_data": >> >> rota8000-cys.data -> rota8000-cys.pickle: converting ... done. >> >> rota8000-asp.data -> rota8000-asp.pickle: converting ... done. >> >> rota8000-ser.data -> rota8000-ser.pickle: converting ... done. >> >> rota8000-gln.data -> rota8000-gln.pickle: converting ... done. >> >> rota8000-ile.data -> rota8000-ile.pickle: converting ... done. >> >> rota8000-pro.data -> rota8000-pro.pickle: converting ... done. >> >> rota8000-lys.data -> rota8000-lys.pickle: converting ... done. >> >> rota8000-thr.data -> rota8000-thr.pickle: converting ... done. >> >> rota8000-phetyr.data -> rota8000-phetyr.pickle: converting ... done. >> >> rota8000-glu.data -> rota8000-glu.pickle: converting ... done. >> >> rota8000-met.data -> rota8000-met.pickle: converting ... done. >> >> rota8000-his.data -> rota8000-his.pickle: converting ... done. >> >> rota8000-leu.data -> rota8000-leu.pickle: converting ... done. >> >> rota8000-arg.data -> rota8000-arg.pickle: converting ... done. >> >> rota8000-trp.data -> rota8000-trp.pickle: converting ... done. >> >> rota8000-asn.data -> rota8000-asn.pickle: converting ... done. >> >> rota8000-phetyr.data -> rota8000-phetyr.pickle: already up to date. >> >> rota8000-val.data -> rota8000-val.pickle: converting ... done. >> >> Processing data files in >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/chem_data/rotarama_data": >> >> rama8000-ileval-nopreP.data -> rama8000-ileval-nopreP.pickle: >> converting ... done. >> >> rama8000-gly-sym.data -> rama8000-gly-sym.pickle: converting ... done. >> >> rama8000-cispro.data -> rama8000-cispro.pickle: converting ... done. >> >> rama8000-general-noGPIVpreP.data -> rama8000-general-noGPIVpreP.pickle: >> converting ... done. >> >> rama8000-transpro.data -> rama8000-transpro.pickle: converting ... done. >> >> rama8000-prepro-noGP.data -> rama8000-prepro-noGP.pickle: converting >> ... done. >> >> u+s,u,s: 10.06 9.83 0.23 >> >> ===== Running in .: libtbx.refresh >> >> Python: 2.7.16 >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/bin/python2.7" >> >> Compiler: default >> >> Build mode: release >> >> Warning level: 0 >> >> Precompiled Headers: False >> >> Static libraries: False >> >> Static exe: False >> >> Scan Boost headers: False >> >> Write full flex_fwd.h files: False >> >> Build Boost.Python extensions: True >> >> Define BOOST_PYTHON_NO_PY_SIGNATURES: False >> >> Define BOOST_PYTHON_BOOL_INT_STRICT: True >> >> Enable OpenMP if possible: False >> >> Boost threads enabled: True >> >> Enable CUDA: False >> >> Use conda: False >> >> Use opt_resources if available: False >> >> Use environment flags: False >> >> Enable C++11: False >> >> Python3 migration warning policy: None >> >> command_version_suffix: None >> >> Relocatable paths anchored at: >> /hpc/apps/2018/molprobity/v4.4.app/MolProbity/build >> >> Top-down list of all modules involved: >> >> mmtbx >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx" >> >> iotbx >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx" >> >> ccp4io+adaptbx >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/ccp4io" >> >> >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/ccp4io_adaptbx" >> >> smtbx >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx" >> >> ucif >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/ucif" >> >> cctbx >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx" >> >> scitbx >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx" >> >> fable >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/fable" >> >> omptbx >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/omptbx" >> >> boost+adaptbx >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/boost" >> >> >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx" >> >> tbxx >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/tbxx" >> >> chiltbx >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/chiltbx" >> >> libtbx >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/libtbx" >> >> Creating files in build directory: >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build" >> >> dispatcher_include_template.sh >> >> dispatcher_head.sh >> >> setpaths.sh >> >> setpaths.csh >> >> setpaths_all.sh >> >> setpaths_all.csh >> >> setpaths_debug.sh >> >> unsetpaths.sh >> >> setpaths_debug.csh >> >> unsetpaths.csh >> >> SConstruct >> >> Makefile >> >> run_tests.csh >> >> Processing: >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/libtbx/command_line" >> >> Processing: >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx/command_line" >> >> Processing: >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/fable/command_line" >> >> Processing: >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx/command_line" >> >> Processing: >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx/command_line" >> >> Processing: >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx/command_line" >> >> Processing: >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx/command_line" >> >> Processing: >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx/command_line" >> >> Processing: >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx/libtbx_refresh.py" >> >> Processing: >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx/libtbx_refresh.py" >> >> Generating C++ header files in: >> >> >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/scitbx/array_family" >> >> Generating C++ files in: >> >> >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/scitbx/array_family/boost_python" >> >> Using fable to convert scitbx/lbfgs.f >> >> Processing: >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx/libtbx_refresh.py" >> >> Generating C++ files in: >> >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/cctbx/eltbx" >> >> Generating C++ files in: >> >> >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/cctbx/boost_python" >> >> Processing: >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx/libtbx_refresh.py" >> >> Generating C++ files in: >> >> >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/smtbx/boost_python" >> >> Processing: >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx/libtbx_refresh.py" >> >> Using fable to convert iotbx/pdb/hybrid_36_f.f >> >> Writing: iotbx/pdb/hybrid_36_fem.cpp >> >> Processing: >> "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx/libtbx_refresh.py" >> >> Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/exe_dev" >> >> Regenerating module files in >> /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base >> >> /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/pango not present, >> could not regenerate pango files >> >> /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/gtk-2.0 not >> present, could not regenerate gdk-pixbuf.loaders >> >> /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/fonts not present, >> could not rebuild fonts >> >> generating index.theme file >> >> Done. >> >> >> >> *Bootstrap success: build* >> >> *++++++++++ MolProbity configure.sh finished.* >> >> >> >> >> >> >> >> [tm375568@uptus060-3 MolProbity]$ ./setup.sh >> >> ++++++++++ creating directories ... >> >> ++++++++++ setting permisions ... >> >> *Couldn't get a file descriptor referring to the console **à I assume >> this can be ignored. * >> >> [tm375568@uptus060-3 MolProbity]$ >> >> >> >> Best Regards, >> >> Charitha Shetty >> >> >> >> *From:* Christopher Williams <christopher.sci.williams(a)gmail.com> >> *Sent:* Monday, August 12, 2019 3:34 PM >> *To:* Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com> >> *Cc:* Nigel Moriarty (nwmoriarty(a)lbl.gov) <nwmoriarty(a)lbl.gov>; >> cctbxbb(a)phenix-online.org; Robert Nolte <robert.t.nolte(a)gsk.com> >> *Subject:* Re: Molprobity / CCTBX incompatibility >> >> >> >> *EXTERNAL* >> >> Hmm. It looks like Reduce and/or Probe has failed to install correctly. >> Most likely an early call to Reduce has resulted in an empty file, which is >> then passed into other programs, resulting in error messages. >> >> >> >> The configure script ran a build process. Do you know if that process >> finished successfully or if it ended with errors? If the build exited >> early, it may have never reached the part where Reduce gets compiled. Some >> dependencies have changed, and I have been having trouble with my own >> builds lately. >> >> >> >> It is also possible that there was just a network hiccup that prevented >> something from downloading correctly, and a second attempt will work. >> >> >> >> I am working on a new configure/install script for more consistent >> handling of dependencies. Hopefully it will be ready in about a day. >> >> >> >> Good luck, >> >> -Christopher Williams >> >> ---Richardson Lab, Duke University >> >> >> >> >> >> >> >> >> >> >> >> *GSK monitors email communications sent to and from GSK in order to >> protect GSK, our employees, customers, suppliers and business partners, >> from cyber threats and loss of GSK Information. GSK monitoring is conducted >> with appropriate confidentiality controls and in accordance with local laws >> and after appropriate consultation.* >> >> *GSK monitors email communications sent to and from GSK in order to >> protect GSK, our employees, customers, suppliers and business partners, >> from cyber threats and loss of GSK Information. GSK monitoring is conducted >> with appropriate confidentiality controls and in accordance with local laws >> and after appropriate consultation.* >> >> *GSK monitors email communications sent to and from GSK in order to >> protect GSK, our employees, customers, suppliers and business partners, >> from cyber threats and loss of GSK Information. GSK monitoring is conducted >> with appropriate confidentiality controls and in accordance with local laws >> and after appropriate consultation.* >> >> *GSK monitors email communications sent to and from GSK in order to >> protect GSK, our employees, customers, suppliers and business partners, >> from cyber threats and loss of GSK Information. GSK monitoring is conducted >> with appropriate confidentiality controls and in accordance with local laws >> and after appropriate consultation.* >> >> *GSK monitors email communications sent to and from GSK in order to >> protect GSK, our employees, customers, suppliers and business partners, >> from cyber threats and loss of GSK Information. GSK monitoring is conducted >> with appropriate confidentiality controls and in accordance with local laws >> and after appropriate consultation.* >> >> *GSK monitors email communications sent to and from GSK in order to >> protect GSK, our employees, customers, suppliers and business partners, >> from cyber threats and loss of GSK Information. GSK monitoring is conducted >> with appropriate confidentiality controls and in accordance with local laws >> and after appropriate consultation.* >> >

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Berkeley Server Downtime (8/16 - 8/18)
by Billy Poon 18 Aug '19

18 Aug '19

Dear all, On Friday, August 16, our servers will be shut down starting at 4:00 pm Pacific for scheduled maintenance in our building. We expect that the servers will be available by 10:00 am Pacific on Sunday (8/18) at the latest. This will affect, - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience. -- 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

1 1

Disruptive and counterproductive comments
by Graeme.Winter＠Diamond.ac.uk 17 Aug '19

17 Aug '19

Deliberately starting a new thread My thinking was that this was feedback on why users find it hard getting started on cctbx. I had assumed, incorrectly as it turns out, that on the developer list a wider discussion was appropriate. This was not meant as criticism, rather direct feedback from talking to potential users at diamond. However I sense that it was not welcome so I’ll keep my thoughts to myself. I’m obviously aware of the work Billy and co are doing to help the situation with conda, but I’m not aware of the longer term intentions for this. Anyhow, sorry for interfering Best wishes Graeme -- 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

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Re: [cctbxbb] CCTBX documentation questionnaire
by ben.williams＠diamond.ac.uk 16 Aug '19

16 Aug '19

Dear Dorothee, Is there a reason for only allowing a single choice of library in the questionnaire? I've wanted to use several components from across the CCTBX project and would like my response to reflect that. I'm sure there are probably others in the same boat. Many thanks, Ben — Ben Williams Post-doctoral research associate Scientific Software Diamond Light Source On 15 Aug 2019 20:05, Dorothee Liebschner <dcliebschner(a)lbl.gov> wrote: Hi everyone, During this year's ECM computing school, it came up that the CCTBX does not have a lot of documentation. This seems to be a major reason why people don't use it, even if they would like to employ the libraries. We would like to find out which parts of the CCTBX are the most interesting for users. We certainly cannot provide extensive documentation for the entire toolbox, but we can see what we can do once we know the main areas of interest. So if you were in the situation of wanting to use the CCTBX but decided to stay away from it because the documentation was non-existent or obscure, please let us know by filling out the questionnaire below (it's anonymous): questionnaire CCTBX documentation<https://forms.gle/9RawJFfHyEvhCVVP7> Best wishes, Dorothee -- Project 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/> -- 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

2 1

cctbx azure pipelines skipping tests if clutter
by richard.gildea＠diamond.ac.uk 14 Aug '19

14 Aug '19

Hi, I noticed that the cctbx azure pipelines run libtbx.find_clutter as part of the Python "syntax" jobs, and if they find any "clutter", then the pipeline immediately fails and doesn't run any further tests (e.g. https://dev.azure.com/cctbx/cctbx_project/_build/results?buildId=374). This raises the following questions: 1) Why skip running tests just because "clutter" has been found? 2) Why run libtbx.find_clutter as part of the "syntax" job, as strictly speaking trailing whitespaces, unused imports etc, aren't syntax issues? 3) If finding clutter is so important, why not add an optional pre-commit hook to help prevent "clutter" ever being committed in the first place? 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 -- 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

3 4

Booststrap fails: zlib.h missing on Mojave with Xcode 10.3
by Luc Bourhis 13 Aug '19

13 Aug '19

Hi, I am trying to setup a Python 3 cctbx. I did python bootstrap.py --git-ssh --python3 --builder cctbxlite But it fails at the installation of OpenSSL. Clang version is "Apple LLVM version 10.0.1 (clang-1001.0.46.4)”. I attached the OpenSSL install log but I don’t see any error in it. And the advice to run xcode-select is bogus: I have it already setup. Best wishes, Luc Installing OpenSSL... log file is /Users/luc/Developer/cctbx/base_tmp/OpenSSL_install_log getting package openssl-1.0.2r.tar.gz... downloading from https://gitcdn.link/repo/dials/dependencies/master/openssl-1.0.2r.tar.gz : 5223 kB installing openssl-1.0.2r.tar.gz... package openssl took 219.5s to install -------------------------------------------------------------------------------- zlib.h missing -- try running 'xcode-select --install' first Process failed with return code 1

3 6

Clipper updates for C++11
by Billy Poon 12 Aug '19

12 Aug '19

Hi everyone, As part of making CCTBX-based software compile with C++11, it looks like we need to update our checkout of clipper to the latest version. http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper.html As a side note, is this a feature that is widely used? If not, we can disable the downloading of the clipper source files. Also, in addition to this post on the bulletin board, I have started an issue on Github (https://github.com/cctbx/cctbx_project/issues/379). Feel free to comment on any of these forums. -- 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

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Re: [cctbxbb] Molprobity / CCTBX incompatibility
by Nigel Moriarty 12 Aug '19

12 Aug '19

But maybe the installation of cctbx has molprobity.reduce and not phenix.reduce so if that is the case we can change the script to look for molprobity.reduce instead of phenix.reduce. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov On Mon, Aug 12, 2019 at 2:58 PM Robert Nolte <robert.t.nolte(a)gsk.com> wrote: > According to the log file when I just tried to run it, it is phenix.reduce > that it can’t find. > > Bob > > > > > > *From:* Nigel Moriarty <nwmoriarty(a)lbl.gov> > *Sent:* Monday, August 12, 2019 5:55 PM > *To:* Robert Nolte <robert.t.nolte(a)gsk.com> > *Cc:* Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com>; > Christopher Williams <christopher.sci.williams(a)gmail.com>; > cctbxbb(a)phenix-online.org > *Subject:* Re: Molprobity / CCTBX incompatibility > > > > *EXTERNAL* > > I'm just trying to find out if, at the command line, whether it is > phenix.reduce or molprobity.reduce. Charitha just needs to type one or the > other to see what happens. > > > Cheers > > > > Nigel > > > > --- > > Nigel W. Moriarty > Building 33R0349, Molecular Biophysics and Integrated Bioimaging > > Lawrence Berkeley National Laboratory > Berkeley, CA 94720-8235 > Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov > Fax : 510-486-5909 Web : CCI.LBL.gov > > > > > > On Mon, Aug 12, 2019 at 2:44 PM Robert Nolte <robert.t.nolte(a)gsk.com> > wrote: > > Nigel, > > Currently it is not running. This was working from the scratch > install last week. I am not sure what is going on now. > > Bob > > > > > > *From:* Nigel Moriarty <nwmoriarty(a)lbl.gov> > *Sent:* Monday, August 12, 2019 4:52 PM > *To:* Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com> > *Cc:* Christopher Williams <christopher.sci.williams(a)gmail.com>; > cctbxbb(a)phenix-online.org; Robert Nolte <robert.t.nolte(a)gsk.com> > *Subject:* Re: Molprobity / CCTBX incompatibility > > > > *EXTERNAL* > > Does molprobity.reduce run? > > > Cheers > > > > Nigel > > > > --- > > Nigel W. Moriarty > Building 33R0349, Molecular Biophysics and Integrated Bioimaging > > Lawrence Berkeley National Laboratory > Berkeley, CA 94720-8235 > Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov > Fax : 510-486-5909 Web : CCI.LBL.gov > > > > > > On Mon, Aug 12, 2019 at 1:14 PM Charitha Belluru Shetty < > charitha-belluru.b.shetty(a)gsk.com> wrote: > > Hi Nigel, > > > > I hit the send button too soon..Ignore my previous email 😊 > > > > -bash-4.2$ source setpaths.sh > > -bash-4.2$ > > -bash-4.2$ env |grep -i reduce > > -bash-4.2$ > > > > So the “setpath.sh” has the below contents… > > > > $ cat /hpc/apps/current/molprobity/v4.4.app/MolProbity/build/setpaths.sh > > # THIS IS AN AUTOMATICALLY GENERATED FILE. > > # DO NOT EDIT! CHANGES WILL BE LOST. > > ocwd="`pwd`" > > if [ -n "$LIBTBX_BUILD_RELOCATION_HINT" ]; then > > cd "$LIBTBX_BUILD_RELOCATION_HINT" > > LIBTBX_BUILD_RELOCATION_HINT= > > export LIBTBX_BUILD_RELOCATION_HINT > > elif [ -n "$BASH_SOURCE" ]; then > > LIBTBX_BUILD=`dirname "$BASH_SOURCE[0]"` > > cd "$LIBTBX_BUILD" > > else > > cd "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build" > > fi > > LIBTBX_BUILD=`pwd -P` > > export LIBTBX_BUILD > > LIBTBX_OPATH="$PATH" > > export LIBTBX_OPATH > > PATH="$LIBTBX_BUILD/bin:$PATH" > > export PATH > > cd "$ocwd" > > ocwd= > > alias libtbx.setpaths_all=". \"$LIBTBX_BUILD/setpaths_all.sh\"" > > alias libtbx.unsetpaths=". \"$LIBTBX_BUILD/unsetpaths.sh\"" > > if [ -n "$LIBTBX_OPATH" ]; then > > LIBTBX_TMPVAL="$LIBTBX_OPATH" > > else > > LIBTBX_TMPVAL= > > fi > > export LIBTBX_TMPVAL > > PATH=`libtbx.path_utility prepend LIBTBX_TMPVAL "$LIBTBX_BUILD/bin" < > /dev/null` > > export PATH > > if [ "$PATH" = "L_I_B_T_B_X_E_M_P_T_Y" ]; then unset PATH; fi > > LIBTBX_TMPVAL= > > LIBTBX_OPATH= > > LIBTBX_BUILD= > > > > > > Best Regards, > > Charitha Shetty > > > > *From:* Nigel Moriarty <nwmoriarty(a)lbl.gov> > *Sent:* Monday, August 12, 2019 4:08 PM > *To:* Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com> > *Cc:* Christopher Williams <christopher.sci.williams(a)gmail.com>; > cctbxbb(a)phenix-online.org; Robert Nolte <robert.t.nolte(a)gsk.com> > *Subject:* Re: Molprobity / CCTBX incompatibility > > > > *EXTERNAL* > > Once you source the setpaths.sh file in the build directory do you have > phenix.reduce or molprobity.reduce? > > Cheers > > > > Nigel > > > > --- > > Nigel W. Moriarty > Building 33R0349, Molecular Biophysics and Integrated Bioimaging > > Lawrence Berkeley National Laboratory > Berkeley, CA 94720-8235 > Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov > Fax : 510-486-5909 Web : CCI.LBL.gov > > > > > > On Mon, Aug 12, 2019 at 12:43 PM Charitha Belluru Shetty < > charitha-belluru.b.shetty(a)gsk.com> wrote: > > Hi Christopher/ Nigel, > > > > Thank you for your quick reply. > > > > The build process was completed without any error. Pasting few of the > lines from it… > > > > > > ===== Running in build: rebuild rotarama > > Processing data files in > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/chem_data/rotarama_data": > > rota8000-cys.data -> rota8000-cys.pickle: converting ... done. > > rota8000-asp.data -> rota8000-asp.pickle: converting ... done. > > rota8000-ser.data -> rota8000-ser.pickle: converting ... done. > > rota8000-gln.data -> rota8000-gln.pickle: converting ... done. > > rota8000-ile.data -> rota8000-ile.pickle: converting ... done. > > rota8000-pro.data -> rota8000-pro.pickle: converting ... done. > > rota8000-lys.data -> rota8000-lys.pickle: converting ... done. > > rota8000-thr.data -> rota8000-thr.pickle: converting ... done. > > rota8000-phetyr.data -> rota8000-phetyr.pickle: converting ... done. > > rota8000-glu.data -> rota8000-glu.pickle: converting ... done. > > rota8000-met.data -> rota8000-met.pickle: converting ... done. > > rota8000-his.data -> rota8000-his.pickle: converting ... done. > > rota8000-leu.data -> rota8000-leu.pickle: converting ... done. > > rota8000-arg.data -> rota8000-arg.pickle: converting ... done. > > rota8000-trp.data -> rota8000-trp.pickle: converting ... done. > > rota8000-asn.data -> rota8000-asn.pickle: converting ... done. > > rota8000-phetyr.data -> rota8000-phetyr.pickle: already up to date. > > rota8000-val.data -> rota8000-val.pickle: converting ... done. > > Processing data files in > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/chem_data/rotarama_data": > > rama8000-ileval-nopreP.data -> rama8000-ileval-nopreP.pickle: converting > ... done. > > rama8000-gly-sym.data -> rama8000-gly-sym.pickle: converting ... done. > > rama8000-cispro.data -> rama8000-cispro.pickle: converting ... done. > > rama8000-general-noGPIVpreP.data -> rama8000-general-noGPIVpreP.pickle: > converting ... done. > > rama8000-transpro.data -> rama8000-transpro.pickle: converting ... done. > > rama8000-prepro-noGP.data -> rama8000-prepro-noGP.pickle: converting ... > done. > > u+s,u,s: 10.06 9.83 0.23 > > ===== Running in .: libtbx.refresh > > Python: 2.7.16 > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/bin/python2.7" > > Compiler: default > > Build mode: release > > Warning level: 0 > > Precompiled Headers: False > > Static libraries: False > > Static exe: False > > Scan Boost headers: False > > Write full flex_fwd.h files: False > > Build Boost.Python extensions: True > > Define BOOST_PYTHON_NO_PY_SIGNATURES: False > > Define BOOST_PYTHON_BOOL_INT_STRICT: True > > Enable OpenMP if possible: False > > Boost threads enabled: True > > Enable CUDA: False > > Use conda: False > > Use opt_resources if available: False > > Use environment flags: False > > Enable C++11: False > > Python3 migration warning policy: None > > command_version_suffix: None > > Relocatable paths anchored at: > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/build > > Top-down list of all modules involved: > > mmtbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx" > > iotbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx" > > ccp4io+adaptbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/ccp4io" > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/ccp4io_adaptbx" > > smtbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx" > > ucif > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/ucif" > > cctbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx" > > scitbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx" > > fable > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/fable" > > omptbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/omptbx" > > boost+adaptbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/boost" > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx" > > tbxx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/tbxx" > > chiltbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/chiltbx" > > libtbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/libtbx" > > Creating files in build directory: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build" > > dispatcher_include_template.sh > > dispatcher_head.sh > > setpaths.sh > > setpaths.csh > > setpaths_all.sh > > setpaths_all.csh > > setpaths_debug.sh > > unsetpaths.sh > > setpaths_debug.csh > > unsetpaths.csh > > SConstruct > > Makefile > > run_tests.csh > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/libtbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/fable/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx/libtbx_refresh.py" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx/libtbx_refresh.py" > > Generating C++ header files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/scitbx/array_family" > > Generating C++ files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/scitbx/array_family/boost_python" > > Using fable to convert scitbx/lbfgs.f > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx/libtbx_refresh.py" > > Generating C++ files in: > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/cctbx/eltbx" > > Generating C++ files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/cctbx/boost_python" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx/libtbx_refresh.py" > > Generating C++ files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/smtbx/boost_python" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx/libtbx_refresh.py" > > Using fable to convert iotbx/pdb/hybrid_36_f.f > > Writing: iotbx/pdb/hybrid_36_fem.cpp > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx/libtbx_refresh.py" > > Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/exe_dev" > > Regenerating module files in > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base > > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/pango not present, > could not regenerate pango files > > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/gtk-2.0 not > present, could not regenerate gdk-pixbuf.loaders > > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/fonts not present, > could not rebuild fonts > > generating index.theme file > > Done. > > > > *Bootstrap success: build* > > *++++++++++ MolProbity configure.sh finished.* > > > > > > > > [tm375568@uptus060-3 MolProbity]$ ./setup.sh > > ++++++++++ creating directories ... > > ++++++++++ setting permisions ... > > *Couldn't get a file descriptor referring to the console **à I assume > this can be ignored. * > > [tm375568@uptus060-3 MolProbity]$ > > > > Best Regards, > > Charitha Shetty > > > > *From:* Christopher Williams <christopher.sci.williams(a)gmail.com> > *Sent:* Monday, August 12, 2019 3:34 PM > *To:* Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com> > *Cc:* Nigel Moriarty (nwmoriarty(a)lbl.gov) <nwmoriarty(a)lbl.gov>; > cctbxbb(a)phenix-online.org; Robert Nolte <robert.t.nolte(a)gsk.com> > *Subject:* Re: Molprobity / CCTBX incompatibility > > > > *EXTERNAL* > > Hmm. It looks like Reduce and/or Probe has failed to install correctly. > Most likely an early call to Reduce has resulted in an empty file, which is > then passed into other programs, resulting in error messages. > > > > The configure script ran a build process. Do you know if that process > finished successfully or if it ended with errors? If the build exited > early, it may have never reached the part where Reduce gets compiled. Some > dependencies have changed, and I have been having trouble with my own > builds lately. > > > > It is also possible that there was just a network hiccup that prevented > something from downloading correctly, and a second attempt will work. > > > > I am working on a new configure/install script for more consistent > handling of dependencies. Hopefully it will be ready in about a day. > > > > Good luck, > > -Christopher Williams > > ---Richardson Lab, Duke University > > > > > > > > > > > > *GSK monitors email communications sent to and from GSK in order to > protect GSK, our employees, customers, suppliers and business partners, > from cyber threats and loss of GSK Information. GSK monitoring is conducted > with appropriate confidentiality controls and in accordance with local laws > and after appropriate consultation.* > > *GSK monitors email communications sent to and from GSK in order to > protect GSK, our employees, customers, suppliers and business partners, > from cyber threats and loss of GSK Information. GSK monitoring is conducted > with appropriate confidentiality controls and in accordance with local laws > and after appropriate consultation.* > > *GSK monitors email communications sent to and from GSK in order to > protect GSK, our employees, customers, suppliers and business partners, > from cyber threats and loss of GSK Information. GSK monitoring is conducted > with appropriate confidentiality controls and in accordance with local laws > and after appropriate consultation.* > > *GSK monitors email communications sent to and from GSK in order to > protect GSK, our employees, customers, suppliers and business partners, > from cyber threats and loss of GSK Information. GSK monitoring is conducted > with appropriate confidentiality controls and in accordance with local laws > and after appropriate consultation.* >

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Re: [cctbxbb] Molprobity / CCTBX incompatibility
by Nigel Moriarty 12 Aug '19

12 Aug '19

I'm just trying to find out if, at the command line, whether it is phenix.reduce or molprobity.reduce. Charitha just needs to type one or the other to see what happens. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov On Mon, Aug 12, 2019 at 2:44 PM Robert Nolte <robert.t.nolte(a)gsk.com> wrote: > Nigel, > > Currently it is not running. This was working from the scratch > install last week. I am not sure what is going on now. > > Bob > > > > > > *From:* Nigel Moriarty <nwmoriarty(a)lbl.gov> > *Sent:* Monday, August 12, 2019 4:52 PM > *To:* Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com> > *Cc:* Christopher Williams <christopher.sci.williams(a)gmail.com>; > cctbxbb(a)phenix-online.org; Robert Nolte <robert.t.nolte(a)gsk.com> > *Subject:* Re: Molprobity / CCTBX incompatibility > > > > *EXTERNAL* > > Does molprobity.reduce run? > > > Cheers > > > > Nigel > > > > --- > > Nigel W. Moriarty > Building 33R0349, Molecular Biophysics and Integrated Bioimaging > > Lawrence Berkeley National Laboratory > Berkeley, CA 94720-8235 > Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov > Fax : 510-486-5909 Web : CCI.LBL.gov > > > > > > On Mon, Aug 12, 2019 at 1:14 PM Charitha Belluru Shetty < > charitha-belluru.b.shetty(a)gsk.com> wrote: > > Hi Nigel, > > > > I hit the send button too soon..Ignore my previous email 😊 > > > > -bash-4.2$ source setpaths.sh > > -bash-4.2$ > > -bash-4.2$ env |grep -i reduce > > -bash-4.2$ > > > > So the “setpath.sh” has the below contents… > > > > $ cat /hpc/apps/current/molprobity/v4.4.app/MolProbity/build/setpaths.sh > > # THIS IS AN AUTOMATICALLY GENERATED FILE. > > # DO NOT EDIT! CHANGES WILL BE LOST. > > ocwd="`pwd`" > > if [ -n "$LIBTBX_BUILD_RELOCATION_HINT" ]; then > > cd "$LIBTBX_BUILD_RELOCATION_HINT" > > LIBTBX_BUILD_RELOCATION_HINT= > > export LIBTBX_BUILD_RELOCATION_HINT > > elif [ -n "$BASH_SOURCE" ]; then > > LIBTBX_BUILD=`dirname "$BASH_SOURCE[0]"` > > cd "$LIBTBX_BUILD" > > else > > cd "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build" > > fi > > LIBTBX_BUILD=`pwd -P` > > export LIBTBX_BUILD > > LIBTBX_OPATH="$PATH" > > export LIBTBX_OPATH > > PATH="$LIBTBX_BUILD/bin:$PATH" > > export PATH > > cd "$ocwd" > > ocwd= > > alias libtbx.setpaths_all=". \"$LIBTBX_BUILD/setpaths_all.sh\"" > > alias libtbx.unsetpaths=". \"$LIBTBX_BUILD/unsetpaths.sh\"" > > if [ -n "$LIBTBX_OPATH" ]; then > > LIBTBX_TMPVAL="$LIBTBX_OPATH" > > else > > LIBTBX_TMPVAL= > > fi > > export LIBTBX_TMPVAL > > PATH=`libtbx.path_utility prepend LIBTBX_TMPVAL "$LIBTBX_BUILD/bin" < > /dev/null` > > export PATH > > if [ "$PATH" = "L_I_B_T_B_X_E_M_P_T_Y" ]; then unset PATH; fi > > LIBTBX_TMPVAL= > > LIBTBX_OPATH= > > LIBTBX_BUILD= > > > > > > Best Regards, > > Charitha Shetty > > > > *From:* Nigel Moriarty <nwmoriarty(a)lbl.gov> > *Sent:* Monday, August 12, 2019 4:08 PM > *To:* Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com> > *Cc:* Christopher Williams <christopher.sci.williams(a)gmail.com>; > cctbxbb(a)phenix-online.org; Robert Nolte <robert.t.nolte(a)gsk.com> > *Subject:* Re: Molprobity / CCTBX incompatibility > > > > *EXTERNAL* > > Once you source the setpaths.sh file in the build directory do you have > phenix.reduce or molprobity.reduce? > > Cheers > > > > Nigel > > > > --- > > Nigel W. Moriarty > Building 33R0349, Molecular Biophysics and Integrated Bioimaging > > Lawrence Berkeley National Laboratory > Berkeley, CA 94720-8235 > Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov > Fax : 510-486-5909 Web : CCI.LBL.gov > > > > > > On Mon, Aug 12, 2019 at 12:43 PM Charitha Belluru Shetty < > charitha-belluru.b.shetty(a)gsk.com> wrote: > > Hi Christopher/ Nigel, > > > > Thank you for your quick reply. > > > > The build process was completed without any error. Pasting few of the > lines from it… > > > > > > ===== Running in build: rebuild rotarama > > Processing data files in > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/chem_data/rotarama_data": > > rota8000-cys.data -> rota8000-cys.pickle: converting ... done. > > rota8000-asp.data -> rota8000-asp.pickle: converting ... done. > > rota8000-ser.data -> rota8000-ser.pickle: converting ... done. > > rota8000-gln.data -> rota8000-gln.pickle: converting ... done. > > rota8000-ile.data -> rota8000-ile.pickle: converting ... done. > > rota8000-pro.data -> rota8000-pro.pickle: converting ... done. > > rota8000-lys.data -> rota8000-lys.pickle: converting ... done. > > rota8000-thr.data -> rota8000-thr.pickle: converting ... done. > > rota8000-phetyr.data -> rota8000-phetyr.pickle: converting ... done. > > rota8000-glu.data -> rota8000-glu.pickle: converting ... done. > > rota8000-met.data -> rota8000-met.pickle: converting ... done. > > rota8000-his.data -> rota8000-his.pickle: converting ... done. > > rota8000-leu.data -> rota8000-leu.pickle: converting ... done. > > rota8000-arg.data -> rota8000-arg.pickle: converting ... done. > > rota8000-trp.data -> rota8000-trp.pickle: converting ... done. > > rota8000-asn.data -> rota8000-asn.pickle: converting ... done. > > rota8000-phetyr.data -> rota8000-phetyr.pickle: already up to date. > > rota8000-val.data -> rota8000-val.pickle: converting ... done. > > Processing data files in > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/chem_data/rotarama_data": > > rama8000-ileval-nopreP.data -> rama8000-ileval-nopreP.pickle: converting > ... done. > > rama8000-gly-sym.data -> rama8000-gly-sym.pickle: converting ... done. > > rama8000-cispro.data -> rama8000-cispro.pickle: converting ... done. > > rama8000-general-noGPIVpreP.data -> rama8000-general-noGPIVpreP.pickle: > converting ... done. > > rama8000-transpro.data -> rama8000-transpro.pickle: converting ... done. > > rama8000-prepro-noGP.data -> rama8000-prepro-noGP.pickle: converting ... > done. > > u+s,u,s: 10.06 9.83 0.23 > > ===== Running in .: libtbx.refresh > > Python: 2.7.16 > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/bin/python2.7" > > Compiler: default > > Build mode: release > > Warning level: 0 > > Precompiled Headers: False > > Static libraries: False > > Static exe: False > > Scan Boost headers: False > > Write full flex_fwd.h files: False > > Build Boost.Python extensions: True > > Define BOOST_PYTHON_NO_PY_SIGNATURES: False > > Define BOOST_PYTHON_BOOL_INT_STRICT: True > > Enable OpenMP if possible: False > > Boost threads enabled: True > > Enable CUDA: False > > Use conda: False > > Use opt_resources if available: False > > Use environment flags: False > > Enable C++11: False > > Python3 migration warning policy: None > > command_version_suffix: None > > Relocatable paths anchored at: > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/build > > Top-down list of all modules involved: > > mmtbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx" > > iotbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx" > > ccp4io+adaptbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/ccp4io" > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/ccp4io_adaptbx" > > smtbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx" > > ucif > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/ucif" > > cctbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx" > > scitbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx" > > fable > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/fable" > > omptbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/omptbx" > > boost+adaptbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/boost" > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx" > > tbxx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/tbxx" > > chiltbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/chiltbx" > > libtbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/libtbx" > > Creating files in build directory: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build" > > dispatcher_include_template.sh > > dispatcher_head.sh > > setpaths.sh > > setpaths.csh > > setpaths_all.sh > > setpaths_all.csh > > setpaths_debug.sh > > unsetpaths.sh > > setpaths_debug.csh > > unsetpaths.csh > > SConstruct > > Makefile > > run_tests.csh > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/libtbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/fable/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx/libtbx_refresh.py" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx/libtbx_refresh.py" > > Generating C++ header files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/scitbx/array_family" > > Generating C++ files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/scitbx/array_family/boost_python" > > Using fable to convert scitbx/lbfgs.f > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx/libtbx_refresh.py" > > Generating C++ files in: > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/cctbx/eltbx" > > Generating C++ files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/cctbx/boost_python" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx/libtbx_refresh.py" > > Generating C++ files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/smtbx/boost_python" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx/libtbx_refresh.py" > > Using fable to convert iotbx/pdb/hybrid_36_f.f > > Writing: iotbx/pdb/hybrid_36_fem.cpp > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx/libtbx_refresh.py" > > Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/exe_dev" > > Regenerating module files in > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base > > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/pango not present, > could not regenerate pango files > > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/gtk-2.0 not > present, could not regenerate gdk-pixbuf.loaders > > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/fonts not present, > could not rebuild fonts > > generating index.theme file > > Done. > > > > *Bootstrap success: build* > > *++++++++++ MolProbity configure.sh finished.* > > > > > > > > [tm375568@uptus060-3 MolProbity]$ ./setup.sh > > ++++++++++ creating directories ... > > ++++++++++ setting permisions ... > > *Couldn't get a file descriptor referring to the console **à I assume > this can be ignored. * > > [tm375568@uptus060-3 MolProbity]$ > > > > Best Regards, > > Charitha Shetty > > > > *From:* Christopher Williams <christopher.sci.williams(a)gmail.com> > *Sent:* Monday, August 12, 2019 3:34 PM > *To:* Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com> > *Cc:* Nigel Moriarty (nwmoriarty(a)lbl.gov) <nwmoriarty(a)lbl.gov>; > cctbxbb(a)phenix-online.org; Robert Nolte <robert.t.nolte(a)gsk.com> > *Subject:* Re: Molprobity / CCTBX incompatibility > > > > *EXTERNAL* > > Hmm. It looks like Reduce and/or Probe has failed to install correctly. > Most likely an early call to Reduce has resulted in an empty file, which is > then passed into other programs, resulting in error messages. > > > > The configure script ran a build process. Do you know if that process > finished successfully or if it ended with errors? If the build exited > early, it may have never reached the part where Reduce gets compiled. Some > dependencies have changed, and I have been having trouble with my own > builds lately. > > > > It is also possible that there was just a network hiccup that prevented > something from downloading correctly, and a second attempt will work. > > > > I am working on a new configure/install script for more consistent > handling of dependencies. Hopefully it will be ready in about a day. > > > > Good luck, > > -Christopher Williams > > ---Richardson Lab, Duke University > > > > > > > > > > > > *GSK monitors email communications sent to and from GSK in order to > protect GSK, our employees, customers, suppliers and business partners, > from cyber threats and loss of GSK Information. GSK monitoring is conducted > with appropriate confidentiality controls and in accordance with local laws > and after appropriate consultation.* > > *GSK monitors email communications sent to and from GSK in order to > protect GSK, our employees, customers, suppliers and business partners, > from cyber threats and loss of GSK Information. GSK monitoring is conducted > with appropriate confidentiality controls and in accordance with local laws > and after appropriate consultation.* > > *GSK monitors email communications sent to and from GSK in order to > protect GSK, our employees, customers, suppliers and business partners, > from cyber threats and loss of GSK Information. GSK monitoring is conducted > with appropriate confidentiality controls and in accordance with local laws > and after appropriate consultation.* >

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Re: [cctbxbb] Molprobity / CCTBX incompatibility
by Nigel Moriarty 12 Aug '19

12 Aug '19

Does molprobity.reduce run? Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov On Mon, Aug 12, 2019 at 1:14 PM Charitha Belluru Shetty < charitha-belluru.b.shetty(a)gsk.com> wrote: > Hi Nigel, > > > > I hit the send button too soon..Ignore my previous email 😊 > > > > -bash-4.2$ source setpaths.sh > > -bash-4.2$ > > -bash-4.2$ env |grep -i reduce > > -bash-4.2$ > > > > So the “setpath.sh” has the below contents… > > > > $ cat /hpc/apps/current/molprobity/v4.4.app/MolProbity/build/setpaths.sh > > # THIS IS AN AUTOMATICALLY GENERATED FILE. > > # DO NOT EDIT! CHANGES WILL BE LOST. > > ocwd="`pwd`" > > if [ -n "$LIBTBX_BUILD_RELOCATION_HINT" ]; then > > cd "$LIBTBX_BUILD_RELOCATION_HINT" > > LIBTBX_BUILD_RELOCATION_HINT= > > export LIBTBX_BUILD_RELOCATION_HINT > > elif [ -n "$BASH_SOURCE" ]; then > > LIBTBX_BUILD=`dirname "$BASH_SOURCE[0]"` > > cd "$LIBTBX_BUILD" > > else > > cd "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build" > > fi > > LIBTBX_BUILD=`pwd -P` > > export LIBTBX_BUILD > > LIBTBX_OPATH="$PATH" > > export LIBTBX_OPATH > > PATH="$LIBTBX_BUILD/bin:$PATH" > > export PATH > > cd "$ocwd" > > ocwd= > > alias libtbx.setpaths_all=". \"$LIBTBX_BUILD/setpaths_all.sh\"" > > alias libtbx.unsetpaths=". \"$LIBTBX_BUILD/unsetpaths.sh\"" > > if [ -n "$LIBTBX_OPATH" ]; then > > LIBTBX_TMPVAL="$LIBTBX_OPATH" > > else > > LIBTBX_TMPVAL= > > fi > > export LIBTBX_TMPVAL > > PATH=`libtbx.path_utility prepend LIBTBX_TMPVAL "$LIBTBX_BUILD/bin" < > /dev/null` > > export PATH > > if [ "$PATH" = "L_I_B_T_B_X_E_M_P_T_Y" ]; then unset PATH; fi > > LIBTBX_TMPVAL= > > LIBTBX_OPATH= > > LIBTBX_BUILD= > > > > > > Best Regards, > > Charitha Shetty > > > > *From:* Nigel Moriarty <nwmoriarty(a)lbl.gov> > *Sent:* Monday, August 12, 2019 4:08 PM > *To:* Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com> > *Cc:* Christopher Williams <christopher.sci.williams(a)gmail.com>; > cctbxbb(a)phenix-online.org; Robert Nolte <robert.t.nolte(a)gsk.com> > *Subject:* Re: Molprobity / CCTBX incompatibility > > > > *EXTERNAL* > > Once you source the setpaths.sh file in the build directory do you have > phenix.reduce or molprobity.reduce? > > Cheers > > > > Nigel > > > > --- > > Nigel W. Moriarty > Building 33R0349, Molecular Biophysics and Integrated Bioimaging > > Lawrence Berkeley National Laboratory > Berkeley, CA 94720-8235 > Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov > Fax : 510-486-5909 Web : CCI.LBL.gov > > > > > > On Mon, Aug 12, 2019 at 12:43 PM Charitha Belluru Shetty < > charitha-belluru.b.shetty(a)gsk.com> wrote: > > Hi Christopher/ Nigel, > > > > Thank you for your quick reply. > > > > The build process was completed without any error. Pasting few of the > lines from it… > > > > > > ===== Running in build: rebuild rotarama > > Processing data files in > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/chem_data/rotarama_data": > > rota8000-cys.data -> rota8000-cys.pickle: converting ... done. > > rota8000-asp.data -> rota8000-asp.pickle: converting ... done. > > rota8000-ser.data -> rota8000-ser.pickle: converting ... done. > > rota8000-gln.data -> rota8000-gln.pickle: converting ... done. > > rota8000-ile.data -> rota8000-ile.pickle: converting ... done. > > rota8000-pro.data -> rota8000-pro.pickle: converting ... done. > > rota8000-lys.data -> rota8000-lys.pickle: converting ... done. > > rota8000-thr.data -> rota8000-thr.pickle: converting ... done. > > rota8000-phetyr.data -> rota8000-phetyr.pickle: converting ... done. > > rota8000-glu.data -> rota8000-glu.pickle: converting ... done. > > rota8000-met.data -> rota8000-met.pickle: converting ... done. > > rota8000-his.data -> rota8000-his.pickle: converting ... done. > > rota8000-leu.data -> rota8000-leu.pickle: converting ... done. > > rota8000-arg.data -> rota8000-arg.pickle: converting ... done. > > rota8000-trp.data -> rota8000-trp.pickle: converting ... done. > > rota8000-asn.data -> rota8000-asn.pickle: converting ... done. > > rota8000-phetyr.data -> rota8000-phetyr.pickle: already up to date. > > rota8000-val.data -> rota8000-val.pickle: converting ... done. > > Processing data files in > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/chem_data/rotarama_data": > > rama8000-ileval-nopreP.data -> rama8000-ileval-nopreP.pickle: converting > ... done. > > rama8000-gly-sym.data -> rama8000-gly-sym.pickle: converting ... done. > > rama8000-cispro.data -> rama8000-cispro.pickle: converting ... done. > > rama8000-general-noGPIVpreP.data -> rama8000-general-noGPIVpreP.pickle: > converting ... done. > > rama8000-transpro.data -> rama8000-transpro.pickle: converting ... done. > > rama8000-prepro-noGP.data -> rama8000-prepro-noGP.pickle: converting ... > done. > > u+s,u,s: 10.06 9.83 0.23 > > ===== Running in .: libtbx.refresh > > Python: 2.7.16 > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/bin/python2.7" > > Compiler: default > > Build mode: release > > Warning level: 0 > > Precompiled Headers: False > > Static libraries: False > > Static exe: False > > Scan Boost headers: False > > Write full flex_fwd.h files: False > > Build Boost.Python extensions: True > > Define BOOST_PYTHON_NO_PY_SIGNATURES: False > > Define BOOST_PYTHON_BOOL_INT_STRICT: True > > Enable OpenMP if possible: False > > Boost threads enabled: True > > Enable CUDA: False > > Use conda: False > > Use opt_resources if available: False > > Use environment flags: False > > Enable C++11: False > > Python3 migration warning policy: None > > command_version_suffix: None > > Relocatable paths anchored at: > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/build > > Top-down list of all modules involved: > > mmtbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx" > > iotbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx" > > ccp4io+adaptbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/ccp4io" > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/ccp4io_adaptbx" > > smtbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx" > > ucif > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/ucif" > > cctbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx" > > scitbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx" > > fable > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/fable" > > omptbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/omptbx" > > boost+adaptbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/boost" > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx" > > tbxx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/tbxx" > > chiltbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/chiltbx" > > libtbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/libtbx" > > Creating files in build directory: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build" > > dispatcher_include_template.sh > > dispatcher_head.sh > > setpaths.sh > > setpaths.csh > > setpaths_all.sh > > setpaths_all.csh > > setpaths_debug.sh > > unsetpaths.sh > > setpaths_debug.csh > > unsetpaths.csh > > SConstruct > > Makefile > > run_tests.csh > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/libtbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/fable/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx/libtbx_refresh.py" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx/libtbx_refresh.py" > > Generating C++ header files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/scitbx/array_family" > > Generating C++ files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/scitbx/array_family/boost_python" > > Using fable to convert scitbx/lbfgs.f > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx/libtbx_refresh.py" > > Generating C++ files in: > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/cctbx/eltbx" > > Generating C++ files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/cctbx/boost_python" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx/libtbx_refresh.py" > > Generating C++ files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/smtbx/boost_python" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx/libtbx_refresh.py" > > Using fable to convert iotbx/pdb/hybrid_36_f.f > > Writing: iotbx/pdb/hybrid_36_fem.cpp > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx/libtbx_refresh.py" > > Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/exe_dev" > > Regenerating module files in > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base > > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/pango not present, > could not regenerate pango files > > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/gtk-2.0 not > present, could not regenerate gdk-pixbuf.loaders > > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/fonts not present, > could not rebuild fonts > > generating index.theme file > > Done. > > > > *Bootstrap success: build* > > *++++++++++ MolProbity configure.sh finished.* > > > > > > > > [tm375568@uptus060-3 MolProbity]$ ./setup.sh > > ++++++++++ creating directories ... > > ++++++++++ setting permisions ... > > *Couldn't get a file descriptor referring to the console **à I assume > this can be ignored. * > > [tm375568@uptus060-3 MolProbity]$ > > > > Best Regards, > > Charitha Shetty > > > > *From:* Christopher Williams <christopher.sci.williams(a)gmail.com> > *Sent:* Monday, August 12, 2019 3:34 PM > *To:* Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com> > *Cc:* Nigel Moriarty (nwmoriarty(a)lbl.gov) <nwmoriarty(a)lbl.gov>; > cctbxbb(a)phenix-online.org; Robert Nolte <robert.t.nolte(a)gsk.com> > *Subject:* Re: Molprobity / CCTBX incompatibility > > > > *EXTERNAL* > > Hmm. It looks like Reduce and/or Probe has failed to install correctly. > Most likely an early call to Reduce has resulted in an empty file, which is > then passed into other programs, resulting in error messages. > > > > The configure script ran a build process. Do you know if that process > finished successfully or if it ended with errors? If the build exited > early, it may have never reached the part where Reduce gets compiled. Some > dependencies have changed, and I have been having trouble with my own > builds lately. > > > > It is also possible that there was just a network hiccup that prevented > something from downloading correctly, and a second attempt will work. > > > > I am working on a new configure/install script for more consistent > handling of dependencies. Hopefully it will be ready in about a day. > > > > Good luck, > > -Christopher Williams > > ---Richardson Lab, Duke University > > > > > > > > > > > > *GSK monitors email communications sent to and from GSK in order to > protect GSK, our employees, customers, suppliers and business partners, > from cyber threats and loss of GSK Information. GSK monitoring is conducted > with appropriate confidentiality controls and in accordance with local laws > and after appropriate consultation.* > > *GSK monitors email communications sent to and from GSK in order to > protect GSK, our employees, customers, suppliers and business partners, > from cyber threats and loss of GSK Information. GSK monitoring is conducted > with appropriate confidentiality controls and in accordance with local laws > and after appropriate consultation.* >

1 0

Re: [cctbxbb] Molprobity / CCTBX incompatibility
by Nigel Moriarty 12 Aug '19

12 Aug '19

Once you source the setpaths.sh file in the build directory do you have phenix.reduce or molprobity.reduce? Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov On Mon, Aug 12, 2019 at 12:43 PM Charitha Belluru Shetty < charitha-belluru.b.shetty(a)gsk.com> wrote: > Hi Christopher/ Nigel, > > > > Thank you for your quick reply. > > > > The build process was completed without any error. Pasting few of the > lines from it… > > > > > > ===== Running in build: rebuild rotarama > > Processing data files in > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/chem_data/rotarama_data": > > rota8000-cys.data -> rota8000-cys.pickle: converting ... done. > > rota8000-asp.data -> rota8000-asp.pickle: converting ... done. > > rota8000-ser.data -> rota8000-ser.pickle: converting ... done. > > rota8000-gln.data -> rota8000-gln.pickle: converting ... done. > > rota8000-ile.data -> rota8000-ile.pickle: converting ... done. > > rota8000-pro.data -> rota8000-pro.pickle: converting ... done. > > rota8000-lys.data -> rota8000-lys.pickle: converting ... done. > > rota8000-thr.data -> rota8000-thr.pickle: converting ... done. > > rota8000-phetyr.data -> rota8000-phetyr.pickle: converting ... done. > > rota8000-glu.data -> rota8000-glu.pickle: converting ... done. > > rota8000-met.data -> rota8000-met.pickle: converting ... done. > > rota8000-his.data -> rota8000-his.pickle: converting ... done. > > rota8000-leu.data -> rota8000-leu.pickle: converting ... done. > > rota8000-arg.data -> rota8000-arg.pickle: converting ... done. > > rota8000-trp.data -> rota8000-trp.pickle: converting ... done. > > rota8000-asn.data -> rota8000-asn.pickle: converting ... done. > > rota8000-phetyr.data -> rota8000-phetyr.pickle: already up to date. > > rota8000-val.data -> rota8000-val.pickle: converting ... done. > > Processing data files in > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/chem_data/rotarama_data": > > rama8000-ileval-nopreP.data -> rama8000-ileval-nopreP.pickle: converting > ... done. > > rama8000-gly-sym.data -> rama8000-gly-sym.pickle: converting ... done. > > rama8000-cispro.data -> rama8000-cispro.pickle: converting ... done. > > rama8000-general-noGPIVpreP.data -> rama8000-general-noGPIVpreP.pickle: > converting ... done. > > rama8000-transpro.data -> rama8000-transpro.pickle: converting ... done. > > rama8000-prepro-noGP.data -> rama8000-prepro-noGP.pickle: converting ... > done. > > u+s,u,s: 10.06 9.83 0.23 > > ===== Running in .: libtbx.refresh > > Python: 2.7.16 > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/bin/python2.7" > > Compiler: default > > Build mode: release > > Warning level: 0 > > Precompiled Headers: False > > Static libraries: False > > Static exe: False > > Scan Boost headers: False > > Write full flex_fwd.h files: False > > Build Boost.Python extensions: True > > Define BOOST_PYTHON_NO_PY_SIGNATURES: False > > Define BOOST_PYTHON_BOOL_INT_STRICT: True > > Enable OpenMP if possible: False > > Boost threads enabled: True > > Enable CUDA: False > > Use conda: False > > Use opt_resources if available: False > > Use environment flags: False > > Enable C++11: False > > Python3 migration warning policy: None > > command_version_suffix: None > > Relocatable paths anchored at: > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/build > > Top-down list of all modules involved: > > mmtbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx" > > iotbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx" > > ccp4io+adaptbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/ccp4io" > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/ccp4io_adaptbx" > > smtbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx" > > ucif > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/ucif" > > cctbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx" > > scitbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx" > > fable > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/fable" > > omptbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/omptbx" > > boost+adaptbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/boost" > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx" > > tbxx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/tbxx" > > chiltbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/chiltbx" > > libtbx > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/libtbx" > > Creating files in build directory: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build" > > dispatcher_include_template.sh > > dispatcher_head.sh > > setpaths.sh > > setpaths.csh > > setpaths_all.sh > > setpaths_all.csh > > setpaths_debug.sh > > unsetpaths.sh > > setpaths_debug.csh > > unsetpaths.csh > > SConstruct > > Makefile > > run_tests.csh > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/libtbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/fable/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx/command_line" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/boost_adaptbx/libtbx_refresh.py" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/scitbx/libtbx_refresh.py" > > Generating C++ header files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/scitbx/array_family" > > Generating C++ files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/scitbx/array_family/boost_python" > > Using fable to convert scitbx/lbfgs.f > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/cctbx/libtbx_refresh.py" > > Generating C++ files in: > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/cctbx/eltbx" > > Generating C++ files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/cctbx/boost_python" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/smtbx/libtbx_refresh.py" > > Generating C++ files in: > > > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/include/smtbx/boost_python" > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/iotbx/libtbx_refresh.py" > > Using fable to convert iotbx/pdb/hybrid_36_f.f > > Writing: iotbx/pdb/hybrid_36_fem.cpp > > Processing: > "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/modules/cctbx_project/mmtbx/libtbx_refresh.py" > > Processing: "/hpc/apps/2018/molprobity/v4.4.app/MolProbity/build/exe_dev" > > Regenerating module files in > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base > > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/pango not present, > could not regenerate pango files > > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/gtk-2.0 not > present, could not regenerate gdk-pixbuf.loaders > > /hpc/apps/2018/molprobity/v4.4.app/MolProbity/base/etc/fonts not present, > could not rebuild fonts > > generating index.theme file > > Done. > > > > *Bootstrap success: build* > > *++++++++++ MolProbity configure.sh finished.* > > > > > > > > [tm375568@uptus060-3 MolProbity]$ ./setup.sh > > ++++++++++ creating directories ... > > ++++++++++ setting permisions ... > > *Couldn't get a file descriptor referring to the console **à** I assume > this can be ignored.* > > [tm375568@uptus060-3 MolProbity]$ > > > > Best Regards, > > Charitha Shetty > > > > *From:* Christopher Williams <christopher.sci.williams(a)gmail.com> > *Sent:* Monday, August 12, 2019 3:34 PM > *To:* Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com> > *Cc:* Nigel Moriarty (nwmoriarty(a)lbl.gov) <nwmoriarty(a)lbl.gov>; > cctbxbb(a)phenix-online.org; Robert Nolte <robert.t.nolte(a)gsk.com> > *Subject:* Re: Molprobity / CCTBX incompatibility > > > > *EXTERNAL* > > Hmm. It looks like Reduce and/or Probe has failed to install correctly. > Most likely an early call to Reduce has resulted in an empty file, which is > then passed into other programs, resulting in error messages. > > > > The configure script ran a build process. Do you know if that process > finished successfully or if it ended with errors? If the build exited > early, it may have never reached the part where Reduce gets compiled. Some > dependencies have changed, and I have been having trouble with my own > builds lately. > > > > It is also possible that there was just a network hiccup that prevented > something from downloading correctly, and a second attempt will work. > > > > I am working on a new configure/install script for more consistent > handling of dependencies. Hopefully it will be ready in about a day. > > > > Good luck, > > -Christopher Williams > > ---Richardson Lab, Duke University > > > > > > > > > > > > *GSK monitors email communications sent to and from GSK in order to > protect GSK, our employees, customers, suppliers and business partners, > from cyber threats and loss of GSK Information. GSK monitoring is conducted > with appropriate confidentiality controls and in accordance with local laws > and after appropriate consultation.* >

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