- cctbxbb - phenix-online.org

Building cctbx bundles without phenix.* dispatcher scripts
by Graeme.Winter＠diamond.ac.uk 02 Jul '15

02 Jul '15

Hi Folks Following on from various conversations going on here about programs in the default dials bundle which necessarily includes cctbx & lots of useful utilities in there, the question was asked why it includes bits of Phenix. In real life it does not include bits of phenix - they are bits of e.g. mmtbx which have dispatcher scripts which ask to be called phenix.xyz for example, as they are *also* used in phenix. Is there a way we can set the dispatcher prefix at the time of running libtbx.configure? That way you could have phenix.xyz or cctbx.xyz in other situations… then in the dials bundles we could make it clear that there are no bits of Phenix in there. Many thanks in advance, 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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bootstrap external dependencies
by markus.gerstel＠diamond.ac.uk 16 Jun '15

16 Jun '15

Good morning, last night we ran into a problem with some of the remaining external dependencies in the bootstrap script base install step. The sphinx package will currently download 11 files during its installation (list below). As with all other downloads I would like to be able to download these files beforehand and then pass them to our build systems directly, so that the subsequent builds are no longer dependant on network connectivity or pypi server reliability. I would like to propose a python-extra package for the bootstrap script, that checks the existence of a base_tmp/python_extra directory, and, if found, would install all python packages in that folder. This would be an easy facility to automatically build extra python packages (at DLS we already add a few extra packages, such as junit-xml, so this would actually simplify our build process), and would not affect any other bootstrap users. Alternatively, since the dependencies are fixed as they come from the Sphinx archive on the cci servers, we could package them up as well and put static build instructions into build_sphinx() in install_base_packages.py. Thoughts? -Markus The packages are: https://pypi.python.org/packages/source/J/Jinja2/Jinja2-2.7.3.tar.gz#md5=b9… https://pypi.python.org/packages/source/d/docutils/docutils-0.12.tar.gz#md5… https://pypi.python.org/packages/source/P/Pygments/Pygments-2.0.2.tar.gz#md… https://pypi.python.org/packages/source/M/MarkupSafe/MarkupSafe-0.23.tar.gz… https://pypi.python.org/packages/source/n/nose/nose-1.3.7.tar.gz#md5=4d3ad0… https://pypi.python.org/packages/source/p/pyparsing/pyparsing-2.0.3.tar.gz#… https://pypi.python.org/packages/source/t/tornado/tornado-4.2.tar.gz#md5=c5… https://pypi.python.org/packages/source/p/python-dateutil/python-dateutil-2… https://pypi.python.org/packages/source/c/certifi/certifi-2015.04.28.tar.gz… https://pypi.python.org/packages/source/b/backports.ssl_match_hostname/back… https://pypi.python.org/packages/source/s/six/six-1.9.0.tar.gz#md5=476881ef… -- 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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Race condition in bootstrap python installation
by markus.gerstel＠diamond.ac.uk 27 May '15

27 May '15

We have recently seen intermittent build failures with the bootstrap base installation at Diamond. These all occurred during the compilation of python and were usually of the form : gcc -pthread -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Wl,-rpath=\$ORIGIN/../lib Parser/acceler.o Parser/grammar1.o Parser/listnode.o Parser/node.o Parser/parser.o Parser/parsetok.o Parser/bitset.o Parser/metagrammar.o Parser/firstsets.o Parser/grammar.o Parser/pgen.o Objects/obmalloc.o Python/mysnprintf.o Python/pyctype.o Parser/tokenizer_pgen.o Parser/printgrammar.o Parser/pgenmain.o -lpthread -ldl -lutil -o Parser/pgen : Parser/node.o: file not recognized: File truncated : collect2: ld returned 1 exit status : make[1]: *** [Parser/pgen] Error 1 : make[1]: Leaving directory `/scratch/jenkins_slave/workspace/dials_bootstrap_platforms/compilationtarget/native/label/dials-ws154/build_dials/base_tmp/Python-2.7.8_cci' : make: *** [Include/graminit.h] Error 2 : make: *** Waiting for unfinished jobs.... Traceback (most recent call last): File "modules/cctbx_project/libtbx/auto_build/install_base_packages.py", line 1194, in <module> installer(args=sys.argv, log=sys.stdout) File "modules/cctbx_project/libtbx/auto_build/install_base_packages.py", line 184, in __init__ self.build_dependencies(packages=packages) File "modules/cctbx_project/libtbx/auto_build/install_base_packages.py", line 571, in build_dependencies getattr(self, 'build_%s'%i)() File "modules/cctbx_project/libtbx/auto_build/install_base_packages.py", line 622, in build_python self.call('make -j %s install'%(self.nproc), log=log, cwd=python_dir) File "modules/cctbx_project/libtbx/auto_build/install_base_packages.py", line 264, in call return call(args, log=log, verbose=self.verbose, **kwargs) File "/scratch/jenkins_slave/workspace/dials_bootstrap_platforms/compilationtarget/native/label/dials-ws154/build_dials/modules/cctbx_project/libtbx/auto_build/installer_utils.py", line 81, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) RuntimeError: Call to 'make -j 4 install' failed with exit code 2 Other indicated errors are /usr/bin/ld: final link failed: File truncated or /usr/bin/ld: can not read symbols: File truncated I suspect that these errors are manifestations of a race condition in the python build process, which the bootstrap script now by default runs with a -j 4 parallel make. To test this we are now using --nproc=1 for the base installation step. We haven't seen these build failures since. I suggest we set the python compilation to never run with parallel make. Any other ideas? -Markus -- 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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Native python unittests for the libtbx testing framework
by markus.gerstel＠diamond.ac.uk 19 May '15

19 May '15

Dear cctbx developers and users, For a side-project of mine I experimented with native python unit tests (some information available on https://docs.python.org/2/library/unittest.html if you are not familiar with it). The python unittest framework has a couple of advantages over the libtbx testing world. I found that the two most immediate advantages are: Automated test discovery. There is no need to keep a complete list of test files in another python file, which is what we currently do in run_tests.py. Multiple test functions per python test file. At the moment we can run multiple tests via command line parameters to the python test files. This of course means that you need to keep a list of '(test file, parameter)' tuples in run_tests.py, and you need some boilerplate dispatcher in your test file. This can lead to two situations: you may have a number of tests with numeric parameters, and no one knows what the parameters stand for. One example of this can be found in DIALS, where tst_index.py is run with numeric parameters 1 to 4 and 7 to 15, but not 5 and 6. The alternative situation is that you end up with a massive test file, that tests the entire class under test, but figuring out what specifically went wrong is probably more time consuming than necessary. In contrast in Python unittests any function in the file that is named test_* will be identified and run as a separate test. I find that this automatically leads to smaller and thus more readable tests. I understand that libtbx has been developed before Python unittest was around, that there is a substantial amount of code around that relies on current libtbx behaviour, and that there is no pressing need to change anything. However I would like to be able to take advantage of the tools that are out there, so I wrote a function that uses Python unittest for test discovery, and can be placed in run_tests.py. With this function you can then use regular Python unittests and run them with either through libtbx, with the python unittest tools, or directly. In each case you end up with the test results reported in the way you would expect. What I would like to do is integrate this logic in libtbx directly, so that we can use it for all cctbx modules. Since it does not modify libtbx default behaviour and only becomes active after a change in the run_tests.py of the relevant module it should be fully backwards compatible with virtually no downsides. What do you think? -Markus run_tests.py previously: (..) tst_list = ( "$D/test/algorithms/profile_model/nave/tst_model.py", ) (..) run_tests.py new: (..) tst_list = ( "$D/test/algorithms/profile_model/nave/tst_model.py", ) + discover_unittests("dlstbx") (..) discover_unittests function: def discover_unittests(module, pattern='tst_*.py'): try: import inspect import os import sys import unittest except: return tuple([]) dist_dir = libtbx.env.dist_path(module) found_tests = unittest.defaultTestLoader.discover(dist_dir, pattern=pattern) def recursive_TestSuite_to_list(suite): list = [] for t in suite: if isinstance(t, unittest.TestSuite): list.extend(recursive_TestSuite_to_list(t)) elif isinstance(t, unittest.TestCase): module = t.__class__.__module__ if module == 'unittest.loader': # This indicates a loading error. # Regenerate file name and try to run file directly. path = t._testMethodName.replace('.', os.path.sep) list.append("$D/%s.py" % path) else: module = inspect.getsourcefile(sys.modules[module]) function = "%s.%s" % (t.__class__.__name__, t._testMethodName) list.append([module, function]) else: raise Exception("Unknown test object (%s)" % t) return list test_list = recursive_TestSuite_to_list(found_tests) return tuple(test_list) -- 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] Native python unittests for the libtbx testing framework
by Jan Marten Simons 19 May '15

19 May '15

Am Freitag 15 Mai 2015 18:07:33 schrieb Pavel Afonine: > Hi Markus, > > lucky you, I wish I have time for side projects! > > I've been working on cctbx (and writing tests!) for the past 12 years > and can't name any problem using "libtbx testing world". Most tests are > written this way. Why I am not so keen to use an alternative? > - why introduce inconsistency for no obvious clear pressing reasons; > - I have no spare time to learn and get used to an alternative > framework (again, for no obvious clear pressing reason); > - some rare developers (mostly postdocs that come and go) used > Python test framework in the past on the code that I work too and that I > have to maintain when people are gone. I find it is an irritating > overhead for me dealing with these tests, so typically I bother to > re-write them to use libtbx tools. Hi Pavel, those are sound and valid reasons from your point of view. But please also consider this alternative view: Coming from other python projects people are likely to have experience with the python unit test framework. As cctbx is using its own testing functionality people might be put off from writing tests or at least have to overcome this additional barrier on entry. I'm a strong supporter of sticking/moving to standards like PEP0008 [1] or pip/whl* based installs as conforming to those helps people to quickly find their way into the code. * wouldn't it be great if one could simply tell people this: "To install cctbx simply type 'pip install cctbx' in your terminal."? [1] https://www.python.org/dev/peps/pep-0008/ With regards, Dipl. Phys. Jan M. Simons Institute of Crystallography RWTH Aachen University

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Re: [cctbxbb] Fw: Build constraints in SConscript?
by Graeme.Winter＠diamond.ac.uk 15 May '15

15 May '15

Nigel If you export the environment variable I sent before before kicking off a build you should make fully portable binaries. We've been doing this in dials for a while. Best wishes Graeme On 15 May 2015 18:00, Nigel Moriarty <nwmoriarty(a)lbl.gov> wrote: Greame Did you try replacing 10.8 in the SConscript file with 10.7? Please do so and let me know if this works. I was working on getting the mechanism to be OS specific on the buildbot and bootstrap when Rob solved the problem independently. If you don't tell me if changing 10.8 to 10.7 works I will do something to get it working here and we can worry about your 2011 vintage OS next week. Cheers Nigel --- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division 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<http://CCI.LBL.gov> On Fri, May 15, 2015 at 2:31 AM, <Graeme.Winter(a)diamond.ac.uk<mailto:[email protected]>> wrote: Dear Rob Given that the tests are currently not working right anyway, and there are no build / deployment tests for testing builds on an older version of OS X than they are compiled on, this is an easy problem to get in to. It's also a collaborative project where we're all working hard on making things work. This will happen from time to time. I had thought the same environment variable based mechanism for the builds was already in place for PHENIX - am surprised it is not! So, no worries. Perhaps I came across more grumpy than I meant to below. Occurs to me it would be very handy to have one email address for all cctbx related developers where (someone) could ask (something like this) and get an answer perhaps suggesting a more optimum solution? Thoughts anyone? (lots of mail lists in send: list!) Thanks & best wishes Graeme -----Original Message----- From: R.D. Oeffner [mailto:[email protected]<mailto:[email protected]>] Sent: 15 May 2015 10:26 To: Winter, Graeme (DLSLtd,RAL,LSCI); cctbxbb(a)phenix-online.org<mailto:[email protected]>; dials-support(a)lists.sourceforge.net<mailto:[email protected]>; dials-dev(a)cci.lbl.gov<mailto:[email protected]>; Nigel W Moriarty Subject: Re: Fw: Build constraints in SConscript? Dear Graeme, I'm sorry for the trouble my change caused and the time taken to identify it. Ironically we had the same issue as you with Phenix not installing on anything lower than OSX 10.9. As nothing appeared to be specified in our build system to that effect my change was a quick fix to address the problem. It was genuinely well intended. Nigel, I defer to you for implementing the minimum OSX platform for Phenix builds. Rob > FROM: Graeme.Winter(a)Diamond.ac.uk<mailto:[email protected]> > SENT: Friday, May 15, 2015 9:09 AM > TO: Graeme.Winter(a)Diamond.ac.uk<mailto:[email protected]> ; cctbxbb(a)phenix-online.org<mailto:[email protected]> ; > robert(a)oeffner.net<mailto:[email protected]> > CC: dials-support(a)lists.sourceforge.net<mailto:[email protected]> ; dials-dev(a)cci.lbl.gov<mailto:[email protected]> > SUBJECT: RE: Build constraints in SConscript? > > [gw56@ws133 libtbx]$ svn commit -m "Reverting with extreme prejudice > hard coded 10.8 requirement, build no longer works on 10.7 and > earlier; please use ENV VAR method to achieve this kind of constraint; > reverted revision=22202" SConscript > > Sending SConscript > > Transmitting file data . > > Committed revision 22223. > > Please use MACOSX_DEPLOYMENT_TARGET=(version) locally for your > personal requirement, export this before kicking off bootstrap.py > > Best wishes Graeme > > ==================== DIFFS FOLLOW ==================== > > Revision: 22223 > http://sourceforge.net/p/cctbx/code/22223 [1] > Author: graeme_winter > Date: 2015-05-15 08:06:10 +0000 (Fri, 15 May 2015) > Log Message: > ----------- > Reverting with extreme prejudice hard coded 10.8 requirement, build no > longer works on 10.7 and earlier; please use ENV VAR method to achieve > this kind of constraint; reverted revision=22202 > > Modified Paths: > -------------- > trunk/libtbx/SConscript > > Modified: trunk/libtbx/SConscript > =================================================================== > --- trunk/libtbx/SConscript 2015-05-15 02:13:42 UTC (rev 22222) > +++ trunk/libtbx/SConscript 2015-05-15 08:06:10 UTC (rev 22223) > @@ -803,7 +803,7 @@ > env_etc.static_libraries = 1 > env_etc.static_bpl = 0 > > - link_flags = ["-w", "-mmacosx-version-min=10.8"] # suppress > "source/lib does not exist" warning > + link_flags = ["-w"] # suppress "source/lib does not exist" warning > if libtbx.env.build_options.force_32bit: > if (env_etc.gcc_version and env_etc.gcc_version >= 40201) or > env_etc.clang_version: > link_flags.extend(["-arch", "i386"]) > @@ -811,8 +811,7 @@ > env_etc.c_link = "cc" > env_etc.ccflags_base = [ > "-fPIC", > - "-fno-strict-aliasing", > - "-mmacosx-version-min=10.8"] > + "-fno-strict-aliasing"] > if env_etc.clang_version: > setup_clang_warning(env_etc, libtbx.env.build_options.warning_level) > else: > @@ -828,7 +827,7 @@ > env_etc.ccflags_base.extend(["-no-cpp-precomp"]) > if (env_etc.gcc_version < 40201): > env_etc.ccflags_base.append("-Wno-long-double") > - env_etc.cxxflags_base = ["-mmacosx-version-min=10.8"] > + env_etc.cxxflags_base = [] > if env_etc.clang_version is None and env_etc.gcc_version < 40000: > env_etc.cxxflags_base.append("-fcoalesce-templates") > env_etc.cxxflags_base.append("-DBOOST_ALL_NO_LIB") > @@ -861,11 +860,10 @@ > if env_etc.apple_gcc_builds.gcc < 5646: > # fixed on 10.6 (Snow Leopard) whose Dev Tools start with that build > opts.insert(0, "-gstabs+") > - env_etc.shlinkflags = ["-mmacosx-version-min=10.8"] > + env_etc.shlinkflags = [] > env_etc.shlinkflags_bpl = [ > "-w", # suppress "source/lib does not exist" warning > - "-bundle", "-mmacosx-version-min=10.8", > - "-undefined", "dynamic_lookup"] > + "-bundle", "-undefined", "dynamic_lookup"] > if libtbx.env.build_options.force_32bit: > if (env_etc.gcc_version and env_etc.gcc_version >= 40201) or > env_etc.clang_version: > env_etc.ccflags_base.extend(["-arch", "i386"]) > > FROM: Graeme.Winter(a)diamond.ac.uk<mailto:[email protected]> [mailto:[email protected]<mailto:[email protected]>] > > SENT: 15 May 2015 09:01 > TO: cctbxbb(a)phenix-online.org<mailto:[email protected]>; robert(a)oeffner.net<mailto:[email protected]> > CC: dials-support(a)lists.sourceforge.net<mailto:[email protected]>; dials-dev(a)cci.lbl.gov<mailto:[email protected]> > SUBJECT: Build constraints in SConscript? > > Hi Folks > > A while back we worked on making DIALS work right built on 10.10 but > executed on 10.6 or later – this is very useful as lots of people > have 10.6/7 macs & are not keen to update. This is done by the very > flexible mechanism of exporting an environment variable prior to > compilation > > Then this commit appears > > env_etc.static_bpl = 0 > @@ -802,7 +803,7 @@ > env_etc.static_libraries = 1 > env_etc.static_bpl = 0 > > - link_flags = ["-w"] # suppress "source/lib does not exist" warning > + link_flags = ["-w", "-mmacosx-version-min=10.8"] # suppress > "source/lib does not exist" warning > if libtbx.env.build_options.force_32bit: > if (env_etc.gcc_version and env_etc.gcc_version >= 40201) or > env_etc.clang_version: > link_flags.extend(["-arch", "i386"]) > @@ -810,7 +811,8 @@ > env_etc.c_link = "cc" > env_etc.ccflags_base = [ > "-fPIC", > - "-fno-strict-aliasing"] > + "-fno-strict-aliasing", > + "-mmacosx-version-min=10.8"] > if env_etc.clang_version: > setup_clang_warning(env_etc, libtbx.env.build_options.warning_level) > else: > @@ -826,7 +828,7 @@ > env_etc.ccflags_base.extend(["-no-cpp-precomp"]) > if (env_etc.gcc_version < 40201): > env_etc.ccflags_base.append("-Wno-long-double") > - env_etc.cxxflags_base = [] > + env_etc.cxxflags_base = ["-mmacosx-version-min=10.8"] > if env_etc.clang_version is None and env_etc.gcc_version < 40000: > env_etc.cxxflags_base.append("-fcoalesce-templates") > env_etc.cxxflags_base.append("-DBOOST_ALL_NO_LIB") > @@ -859,10 +861,10 @@ > > to > > Modified Paths: > -------------- > trunk/libtbx/SConscript > > and now our build no longer works on 10.7. This is *REALLY* annoying. > The head of the commit message follows below. > > Please could someone fix this? The environment variable method is > *FAR* better, works for the dependencies and also allows dials to work > on older machines. You broke our build. Before this it worked fine. > > (we can’t automate this test as we are not supposed to deploy out of > support machines on lab network, so this was missed) > > Thanks Graeme > > EFFNER > > to cctbx-cvs > > May 13 > > Revision: 22202 > http://sourceforge.net/p/cctbx/code/22202 [2] > Author: oeffner > Date: 2015-05-13 15:48:24 +0000 (Wed, 13 May 2015) > Log Message: > ----------- > ensure installers can run on MacOSX 10.8 or higher > > -- > > 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 > > No virus found in this message. > Checked by AVG - www.avg.com<http://www.avg.com> [3] > Version: 2015.0.5941 / Virus Database: 4342/9780 - Release Date: > 05/15/15 > > Links: > ------ > [1] http://sourceforge.net/p/cctbx/code/22223 > [2] http://sourceforge.net/p/cctbx/code/22202 > [3] http://www.avg.com -- 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] Fw: Build constraints in SConscript?
by Graeme.Winter＠diamond.ac.uk 15 May '15

15 May '15

Dear Rob Given that the tests are currently not working right anyway, and there are no build / deployment tests for testing builds on an older version of OS X than they are compiled on, this is an easy problem to get in to. It's also a collaborative project where we're all working hard on making things work. This will happen from time to time. I had thought the same environment variable based mechanism for the builds was already in place for PHENIX - am surprised it is not! So, no worries. Perhaps I came across more grumpy than I meant to below. Occurs to me it would be very handy to have one email address for all cctbx related developers where (someone) could ask (something like this) and get an answer perhaps suggesting a more optimum solution? Thoughts anyone? (lots of mail lists in send: list!) Thanks & best wishes Graeme -----Original Message----- From: R.D. Oeffner [mailto:[email protected]] Sent: 15 May 2015 10:26 To: Winter, Graeme (DLSLtd,RAL,LSCI); cctbxbb(a)phenix-online.org; dials-support(a)lists.sourceforge.net; dials-dev(a)cci.lbl.gov; Nigel W Moriarty Subject: Re: Fw: Build constraints in SConscript? Dear Graeme, I'm sorry for the trouble my change caused and the time taken to identify it. Ironically we had the same issue as you with Phenix not installing on anything lower than OSX 10.9. As nothing appeared to be specified in our build system to that effect my change was a quick fix to address the problem. It was genuinely well intended. Nigel, I defer to you for implementing the minimum OSX platform for Phenix builds. Rob > FROM: Graeme.Winter(a)Diamond.ac.uk > SENT: Friday, May 15, 2015 9:09 AM > TO: Graeme.Winter(a)Diamond.ac.uk ; cctbxbb(a)phenix-online.org ; > robert(a)oeffner.net > CC: dials-support(a)lists.sourceforge.net ; dials-dev(a)cci.lbl.gov > SUBJECT: RE: Build constraints in SConscript? > > [gw56@ws133 libtbx]$ svn commit -m "Reverting with extreme prejudice > hard coded 10.8 requirement, build no longer works on 10.7 and > earlier; please use ENV VAR method to achieve this kind of constraint; > reverted revision=22202" SConscript > > Sending SConscript > > Transmitting file data . > > Committed revision 22223. > > Please use MACOSX_DEPLOYMENT_TARGET=(version) locally for your > personal requirement, export this before kicking off bootstrap.py > > Best wishes Graeme > > ==================== DIFFS FOLLOW ==================== > > Revision: 22223 > http://sourceforge.net/p/cctbx/code/22223 [1] > Author: graeme_winter > Date: 2015-05-15 08:06:10 +0000 (Fri, 15 May 2015) > Log Message: > ----------- > Reverting with extreme prejudice hard coded 10.8 requirement, build no > longer works on 10.7 and earlier; please use ENV VAR method to achieve > this kind of constraint; reverted revision=22202 > > Modified Paths: > -------------- > trunk/libtbx/SConscript > > Modified: trunk/libtbx/SConscript > =================================================================== > --- trunk/libtbx/SConscript 2015-05-15 02:13:42 UTC (rev 22222) > +++ trunk/libtbx/SConscript 2015-05-15 08:06:10 UTC (rev 22223) > @@ -803,7 +803,7 @@ > env_etc.static_libraries = 1 > env_etc.static_bpl = 0 > > - link_flags = ["-w", "-mmacosx-version-min=10.8"] # suppress > "source/lib does not exist" warning > + link_flags = ["-w"] # suppress "source/lib does not exist" warning > if libtbx.env.build_options.force_32bit: > if (env_etc.gcc_version and env_etc.gcc_version >= 40201) or > env_etc.clang_version: > link_flags.extend(["-arch", "i386"]) > @@ -811,8 +811,7 @@ > env_etc.c_link = "cc" > env_etc.ccflags_base = [ > "-fPIC", > - "-fno-strict-aliasing", > - "-mmacosx-version-min=10.8"] > + "-fno-strict-aliasing"] > if env_etc.clang_version: > setup_clang_warning(env_etc, libtbx.env.build_options.warning_level) > else: > @@ -828,7 +827,7 @@ > env_etc.ccflags_base.extend(["-no-cpp-precomp"]) > if (env_etc.gcc_version < 40201): > env_etc.ccflags_base.append("-Wno-long-double") > - env_etc.cxxflags_base = ["-mmacosx-version-min=10.8"] > + env_etc.cxxflags_base = [] > if env_etc.clang_version is None and env_etc.gcc_version < 40000: > env_etc.cxxflags_base.append("-fcoalesce-templates") > env_etc.cxxflags_base.append("-DBOOST_ALL_NO_LIB") > @@ -861,11 +860,10 @@ > if env_etc.apple_gcc_builds.gcc < 5646: > # fixed on 10.6 (Snow Leopard) whose Dev Tools start with that build > opts.insert(0, "-gstabs+") > - env_etc.shlinkflags = ["-mmacosx-version-min=10.8"] > + env_etc.shlinkflags = [] > env_etc.shlinkflags_bpl = [ > "-w", # suppress "source/lib does not exist" warning > - "-bundle", "-mmacosx-version-min=10.8", > - "-undefined", "dynamic_lookup"] > + "-bundle", "-undefined", "dynamic_lookup"] > if libtbx.env.build_options.force_32bit: > if (env_etc.gcc_version and env_etc.gcc_version >= 40201) or > env_etc.clang_version: > env_etc.ccflags_base.extend(["-arch", "i386"]) > > FROM: Graeme.Winter(a)diamond.ac.uk [mailto:[email protected]] > > SENT: 15 May 2015 09:01 > TO: cctbxbb(a)phenix-online.org; robert(a)oeffner.net > CC: dials-support(a)lists.sourceforge.net; dials-dev(a)cci.lbl.gov > SUBJECT: Build constraints in SConscript? > > Hi Folks > > A while back we worked on making DIALS work right built on 10.10 but > executed on 10.6 or later – this is very useful as lots of people > have 10.6/7 macs & are not keen to update. This is done by the very > flexible mechanism of exporting an environment variable prior to > compilation > > Then this commit appears > > env_etc.static_bpl = 0 > @@ -802,7 +803,7 @@ > env_etc.static_libraries = 1 > env_etc.static_bpl = 0 > > - link_flags = ["-w"] # suppress "source/lib does not exist" warning > + link_flags = ["-w", "-mmacosx-version-min=10.8"] # suppress > "source/lib does not exist" warning > if libtbx.env.build_options.force_32bit: > if (env_etc.gcc_version and env_etc.gcc_version >= 40201) or > env_etc.clang_version: > link_flags.extend(["-arch", "i386"]) > @@ -810,7 +811,8 @@ > env_etc.c_link = "cc" > env_etc.ccflags_base = [ > "-fPIC", > - "-fno-strict-aliasing"] > + "-fno-strict-aliasing", > + "-mmacosx-version-min=10.8"] > if env_etc.clang_version: > setup_clang_warning(env_etc, libtbx.env.build_options.warning_level) > else: > @@ -826,7 +828,7 @@ > env_etc.ccflags_base.extend(["-no-cpp-precomp"]) > if (env_etc.gcc_version < 40201): > env_etc.ccflags_base.append("-Wno-long-double") > - env_etc.cxxflags_base = [] > + env_etc.cxxflags_base = ["-mmacosx-version-min=10.8"] > if env_etc.clang_version is None and env_etc.gcc_version < 40000: > env_etc.cxxflags_base.append("-fcoalesce-templates") > env_etc.cxxflags_base.append("-DBOOST_ALL_NO_LIB") > @@ -859,10 +861,10 @@ > > to > > Modified Paths: > -------------- > trunk/libtbx/SConscript > > and now our build no longer works on 10.7. This is *REALLY* annoying. > The head of the commit message follows below. > > Please could someone fix this? The environment variable method is > *FAR* better, works for the dependencies and also allows dials to work > on older machines. You broke our build. Before this it worked fine. > > (we can’t automate this test as we are not supposed to deploy out of > support machines on lab network, so this was missed) > > Thanks Graeme > > EFFNER > > to cctbx-cvs > > May 13 > > Revision: 22202 > http://sourceforge.net/p/cctbx/code/22202 [2] > Author: oeffner > Date: 2015-05-13 15:48:24 +0000 (Wed, 13 May 2015) > Log Message: > ----------- > ensure installers can run on MacOSX 10.8 or higher > > -- > > 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 > > No virus found in this message. > Checked by AVG - www.avg.com [3] > Version: 2015.0.5941 / Virus Database: 4342/9780 - Release Date: > 05/15/15 > > Links: > ------ > [1] http://sourceforge.net/p/cctbx/code/22223 > [2] http://sourceforge.net/p/cctbx/code/22202 > [3] http://www.avg.com -- 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 2

Build constraints in SConscript?
by Graeme.Winter＠diamond.ac.uk 15 May '15

15 May '15

Hi Folks A while back we worked on making DIALS work right built on 10.10 but executed on 10.6 or later - this is very useful as lots of people have 10.6/7 macs & are not keen to update. This is done by the very flexible mechanism of exporting an environment variable prior to compilation Then this commit appears env_etc.static_bpl = 0 @@ -802,7 +803,7 @@ env_etc.static_libraries = 1 env_etc.static_bpl = 0 - link_flags = ["-w"] # suppress "source/lib does not exist" warning + link_flags = ["-w", "-mmacosx-version-min=10.8"] # suppress "source/lib does not exist" warning if libtbx.env.build_options.force_32bit: if (env_etc.gcc_version and env_etc.gcc_version >= 40201) or env_etc.clang_version: link_flags.extend(["-arch", "i386"]) @@ -810,7 +811,8 @@ env_etc.c_link = "cc" env_etc.ccflags_base = [ "-fPIC", - "-fno-strict-aliasing"] + "-fno-strict-aliasing", + "-mmacosx-version-min=10.8"] if env_etc.clang_version: setup_clang_warning(env_etc, libtbx.env.build_options.warning_level) else: @@ -826,7 +828,7 @@ env_etc.ccflags_base.extend(["-no-cpp-precomp"]) if (env_etc.gcc_version < 40201): env_etc.ccflags_base.append("-Wno-long-double") - env_etc.cxxflags_base = [] + env_etc.cxxflags_base = ["-mmacosx-version-min=10.8"] if env_etc.clang_version is None and env_etc.gcc_version < 40000: env_etc.cxxflags_base.append("-fcoalesce-templates") env_etc.cxxflags_base.append("-DBOOST_ALL_NO_LIB") @@ -859,10 +861,10 @@ to Modified Paths: -------------- trunk/libtbx/SConscript and now our build no longer works on 10.7. This is *really* annoying. The head of the commit message follows below. Please could someone fix this? The environment variable method is *far* better, works for the dependencies and also allows dials to work on older machines. You broke our build. Before this it worked fine. (we can't automate this test as we are not supposed to deploy out of support machines on lab network, so this was missed) Thanks Graeme effner to cctbx-cvs [https://ssl.gstatic.com/bt/C3341AA7A1A076756462EE2E5CD71C11/2x/ic_expand_sm…] May 13 Revision: 22202 http://sourceforge.net/p/cctbx/code/22202 Author: oeffner Date: 2015-05-13 15:48:24 +0000 (Wed, 13 May 2015) Log Message: ----------- ensure installers can run on MacOSX 10.8 or higher -- 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

1 1

Does cctbx have an easy to access spherical harmonic table?
by Graeme.Winter＠diamond.ac.uk 10 May '15

10 May '15

Hi Folks, Looked and something is used from boost but they don’t appear to be clearly wrapped to Python. in scitbx.math.nss_spherical_harmonics found nearly what I was looking for but it seems to be for some other purpose & not really do what I want (and needs mystery things in constructor….) >>> _sh = sh(2, 1) Traceback (most recent call last): File "<stdin>", line 1, in <module> Boost.Python.ArgumentError: Python argument types in nss_spherical_harmonics.__init__(nss_spherical_harmonics, int, int) did not match C++ signature: __init__(_object*, int l_max, int mangle, scitbx::math::zernike::log_factorial_generator<double> lgf) Any clues would be welcome, else wise most sensible thing seems to be to wrap up to Python the boost spherical harmonic code… 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

3 3

bin data by a Miller index
by Mooers, Blaine H.M. (HSC) 24 Apr '15

24 Apr '15

Dear cctbxbb: I have a simple question. I have a data set with a strong off origin Patterson peak (0,0,0.11). I want to plot the average I/sig per zone l = n. I expect to see enhanced values at l=9n. How do you bin data by the L Miller index in iotbx? Best regards, Blaine Blaine Mooers, Ph.D. Assistant Professor Director of the Laboratory of Biomolecular Structure and Function Department of Biochemistry and Molecular Biology University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center Rm. 466 Shipping address: 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 Letter address: P.O. Box 26901, BRC 466 Oklahoma City, OK 73190 office: (405) 271-8300 lab: (405) 271-8313 fax: (405) 271-3910 e-mail: blaine-mooers(a)ouhsc.edu Faculty webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/… Small Angle Scattering webpage: http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/sma… X-ray lab webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/…

2 1

scitbx test crashing on mac
by markus.gerstel＠diamond.ac.uk 14 Apr '15

14 Apr '15

Good morning, The test scitbx.rigid_body.proto.tst_singular has been failing consistently on our MacOS 10.10 system for a day now. Last known good svn rev. is 21989. It passes on the linux systems. Apologies if this is not the right place to report scitbx problems to. -Markus Stacktrace 11 Python 0x0000000100010d03 PyObject_Call + 99 10 libboost_python.dylib 0x0000000101a0f893 boost::python::objects::function_call(_object*, _object*, _object*) + 83 9 libboost_python.dylib 0x0000000101a147f1 boost::python::handle_exception_impl(boost::function0<void>) + 81 8 libboost_python.dylib 0x0000000101a0fe5a boost::detail::function::void_function_ref_invoker0<boost::python::objects::(anonymous namespace)::bind_return, void>::invoke(boost::detail::function::function_buffer&) + 26 7 libboost_python.dylib 0x0000000101a0db6a boost::python::objects::function::call(_object*, _object*) const + 826 6 scitbx_linalg_ext.so 0x000000010518b521 boost::python::objects::caller_py_function_impl<boost::python::detail::caller<scitbx::af::shared<double> (scitbx::matrix::eigensystem::real_symmetric<double>::*)() const, boost::python::default_call_policies, boost::mpl::vector2<scitbx::af::shared<double>, scitbx::matrix::eigensystem::real_symmetric<double>&> > >::operator()(_object*, _object*) + 65 5 scitbx_linalg_ext.so 0x000000010518b6be _object* boost::python::detail::invoke<boost::python::to_python_value<scitbx::af::shared<double> const&>, scitbx::af::shared<double> (scitbx::matrix::eigensystem::real_symmetric<double>::*)() const, boost::python::arg_from_python<scitbx::matrix::eigensystem::real_symmetric<double>&> >(boost::python::detail::invoke_tag_<false, true>, boost::python::to_python_value<scitbx::af::shared<double> const&> const&, scitbx::af::shared<double> (scitbx::matrix::eigensystem::real_symmetric<double>::*&)() const, boost::python::arg_from_python<scitbx::matrix::eigensystem::real_symmetric<double>&>&) + 46 4 ??? 0x000000010183fc20 0x0 + 4320394272 3 libsystem_platform.dylib 0x00007fff86f16f1a _sigtramp + 26 2 boost_python_meta_ext.so 0x00000001005bdf80 initboost_python_meta_ext + 0 Floating-point error (Python and libc call stacks above) This crash may be due to a problem in any imported Python module, including modules which are not part of the cctbx project. To disable the traps leading to this message, define these environment variables (e.g. assign the value 1): BOOST_ADAPTBX_FPE_DEFAULT BOOST_ADAPTBX_SIGNALS_DEFAULT This will NOT solve the problem, just mask it, but may allow you to proceed in case it is not critical. Standard Error show_stack(1): /Users/dlshudson/jenkins_slave/workspace/cctbx_tests_platforms/label/dials-mac-mini/build_dials/modules/cctbx_project/scitbx/rigid_body/proto/featherstone.py(38) generalized_inverse show_stack(2): /Users/dlshudson/jenkins_slave/workspace/cctbx_tests_platforms/label/dials-mac-mini/build_dials/modules/cctbx_project/scitbx/rigid_body/proto/featherstone.py(373) FDab show_stack(3): /Users/dlshudson/jenkins_slave/workspace/cctbx_tests_platforms/label/dials-mac-mini/build_dials/modules/cctbx_project/scitbx/rigid_body/proto/test_simulation.py(28) energies_and_accelerations_update show_stack(4): /Users/dlshudson/jenkins_slave/workspace/cctbx_tests_platforms/label/dials-mac-mini/build_dials/modules/cctbx_project/scitbx/rigid_body/proto/test_simulation.py(16) __init__ show_stack(5): /Users/dlshudson/jenkins_slave/workspace/cctbx_tests_platforms/label/dials-mac-mini/build_dials/modules/cctbx_project/scitbx/rigid_body/proto/tst_singular.py(72) exercise_six_dof show_stack(6): /Users/dlshudson/jenkins_slave/workspace/cctbx_tests_platforms/label/dials-mac-mini/build_dials/modules/cctbx_project/scitbx/rigid_body/proto/tst_singular.py(146) run show_stack(7): /Users/dlshudson/jenkins_slave/workspace/cctbx_tests_platforms/label/dials-mac-mini/build_dials/modules/cctbx_project/scitbx/rigid_body/proto/tst_singular.py(162) <module> libc backtrace (43 frames, most recent call last): 44 ??? 0x0000000000000003 0x0 + 3 43 Python 0x0000000100000d71 Python + 3441 42 Python 0x0000000100000e58 Python + 3672 41 Python 0x00000001000edd44 Py_Main + 3076 40 Python 0x00000001000d64a7 PyRun_SimpleFileExFlags + 711 39 Python 0x00000001000d6984 PyRun_FileExFlags + 164 38 Python 0x00000001000ad596 PyEval_EvalCode + 54 37 Python 0x00000001000adc22 PyEval_EvalCodeEx + 1666 36 Python 0x00000001000b179f PyEval_EvalFrameEx + 14111 35 Python 0x00000001000b5556 fast_function + 118 34 Python 0x00000001000adc22 PyEval_EvalCodeEx + 1666 33 Python 0x00000001000b179f PyEval_EvalFrameEx + 14111 32 Python 0x00000001000b5556 fast_function + 118 31 Python 0x00000001000adc22 PyEval_EvalCodeEx + 1666 30 Python 0x00000001000b295b PyEval_EvalFrameEx + 18651 29 Python 0x0000000100010d03 PyObject_Call + 99 28 Python 0x0000000100069e23 type_call + 339 27 Python 0x000000010006fccd slot_tp_init + 141 26 Python 0x0000000100010d03 PyObject_Call + 99 25 Python 0x000000010001e207 instancemethod_call + 247 24 Python 0x0000000100010d03 PyObject_Call + 99 23 Python 0x0000000100036a6c function_call + 364 22 Python 0x00000001000adc22 PyEval_EvalCodeEx + 1666 21 Python 0x00000001000b179f PyEval_EvalFrameEx + 14111 20 Python 0x00000001000b5556 fast_function + 118 19 Python 0x00000001000adc22 PyEval_EvalCodeEx + 1666 18 Python 0x00000001000b179f PyEval_EvalFrameEx + 14111 17 Python 0x00000001000b5556 fast_function + 118 16 Python 0x00000001000adc22 PyEval_EvalCodeEx + 1666 15 Python 0x00000001000b179f PyEval_EvalFrameEx + 14111 14 Python 0x00000001000b5556 fast_function + 118 13 Python 0x00000001000adc22 PyEval_EvalCodeEx + 1666 12 Python 0x00000001000b295b PyEval_EvalFrameEx + 18651 11 Python 0x0000000100010d03 PyObject_Call + 99 10 libboost_python.dylib 0x0000000101a0f893 boost::python::objects::function_call(_object*, _object*, _object*) + 83 9 libboost_python.dylib 0x0000000101a147f1 boost::python::handle_exception_impl(boost::function0<void>) + 81 8 libboost_python.dylib 0x0000000101a0fe5a boost::detail::function::void_function_ref_invoker0<boost::python::objects::(anonymous namespace)::bind_return, void>::invoke(boost::detail::function::function_buffer&) + 26 7 libboost_python.dylib 0x0000000101a0db6a boost::python::objects::function::call(_object*, _object*) const + 826 6 scitbx_linalg_ext.so 0x000000010518b521 boost::python::objects::caller_py_function_impl<boost::python::detail::caller<scitbx::af::shared<double> (scitbx::matrix::eigensystem::real_symmetric<double>::*)() const, boost::python::default_call_policies, boost::mpl::vector2<scitbx::af::shared<double>, scitbx::matrix::eigensystem::real_symmetric<double>&> > >::operator()(_object*, _object*) + 65 5 scitbx_linalg_ext.so 0x000000010518b6be _object* boost::python::detail::invoke<boost::python::to_python_value<scitbx::af::shared<double> const&>, scitbx::af::shared<double> (scitbx::matrix::eigensystem::real_symmetric<double>::*)() const, boost::python::arg_from_python<scitbx::matrix::eigensystem::real_symmetric<double>&> >(boost::python::detail::invoke_tag_<false, true>, boost::python::to_python_value<scitbx::af::shared<double> const&> const&, scitbx::af::shared<double> (scitbx::matrix::eigensystem::real_symmetric<double>::*&)() const, boost::python::arg_from_python<scitbx::matrix::eigensystem::real_symmetric<double>&>&) + 46 4 ??? 0x000000010183fc20 0x0 + 4320394272 3 libsystem_platform.dylib 0x00007fff86f16f1a _sigtramp + 26 2 boost_python_meta_ext.so 0x00000001005bdf80 initboost_python_meta_ext + 0 Floating-point error (Python and libc call stacks above) This crash may be due to a problem in any imported Python module, including modules which are not part of the cctbx project. To disable the traps leading to this message, define these environment variables (e.g. assign the value 1): BOOST_ADAPTBX_FPE_DEFAULT BOOST_ADAPTBX_SIGNALS_DEFAULT This will NOT solve the problem, just mask it, but may allow you to proceed in case it is not critical. -- 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

5 9

bootstrap script broken - more rotamer goodness
by markus.gerstel＠diamond.ac.uk 08 Apr '15

08 Apr '15

Hi, We received an error report from a dials user that he could not install dials from source. This appears to be caused by the mmtbx.rebuild_rotarama_cache command run after the compilation, which has been introduced in http://sourceforge.net/p/cctbx/code/21921/ I guess this needs either to be run conditional on the library being installed or be changed to fail gracefully. -Markus -- 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 3

Re: [cctbxbb] [Dials-support] DIALS source tarball
by Graeme.Winter＠diamond.ac.uk 08 Apr '15

08 Apr '15

Sadly this also does not fix anything :o( not sure why this was not flagged when I configured chem_data... libtbx.python "/Users/graeme/svn/cctbx/modules/cctbx_project/cctbx/regression/tst_geometry_restraints_2.py" [FAIL] Time: 6.44 Return code: 1 OKs: 0 Standard error: Traceback (most recent call last): File "/Users/graeme/svn/cctbx/modules/cctbx_project/cctbx/regression/tst_geometry_restraints_2.py", line 866, in <module> exercise_all(sys.argv[1:]) File "/Users/graeme/svn/cctbx/modules/cctbx_project/cctbx/regression/tst_geometry_restraints_2.py", line 862, in exercise_all exercise_na_restraints_output_to_geo(verbose=verbose) File "/Users/graeme/svn/cctbx/modules/cctbx_project/cctbx/regression/tst_geometry_restraints_2.py", line 818, in exercise_na_restraints_output_to_geo log=out2) File "/Users/graeme/svn/cctbx/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 5274, in run nonbonded_distance_threshold=nonbonded_distance_threshold) File "/Users/graeme/svn/cctbx/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 4952, in geometry_restraints_manager ss_manager.initialize(log=self.log) File "/Users/graeme/svn/cctbx/modules/cctbx_project/mmtbx/secondary_structure/__init__.py", line 280, in initialize self.find_automatically(log=log) File "/Users/graeme/svn/cctbx/modules/cctbx_project/mmtbx/secondary_structure/__init__.py", line 313, in find_automatically self.sec_str_from_pdb_file = self.find_sec_str(log=log) File "/Users/graeme/svn/cctbx/modules/cctbx_project/mmtbx/secondary_structure/__init__.py", line 369, in find_sec_str (records, stderr) = run_ksdssp_direct(pdb_str) File "/Users/graeme/svn/cctbx/modules/cctbx_project/mmtbx/secondary_structure/__init__.py", line 728, in run_ksdssp_direct exe_path = get_ksdssp_exe_path() File "/Users/graeme/svn/cctbx/modules/cctbx_project/mmtbx/secondary_structure/__init__.py", line 709, in get_ksdssp_exe_path raise RuntimeError("ksdssp module is not configured") RuntimeError: ksdssp module is not configured On 8 Apr 2015, at 11:02, <richard.gildea(a)diamond.ac.uk<mailto:[email protected]>> <richard.gildea(a)diamond.ac.uk<mailto:[email protected]>> wrote: $ du -h --max-depth=0 chem_data 1.6G chem_data Not sure we really want to include this in the dials builds, just to make one test happy, especially when we have no use for any of the monomer library functionality in dials. Cheers, Richard ________________________________ From: Graeme Winter [graeme.winter(a)gmail.com<mailto:[email protected]>] Sent: 08 April 2015 10:58 To: Gildea, Richard (DLSLtd,RAL,LSCI); Gerstel, Markus (DLSLtd,RAL,LSCI); asbrewster(a)lbl.gov<mailto:[email protected]>; cctbxbb(a)phenix-online.org<mailto:[email protected]> Cc: dials-support(a)lists.sourceforge.net<mailto:[email protected]> Subject: Re: [Dials-support] [cctbxbb] DIALS source tarball can we add this to the dials build through some kind of tarball download which does not need a cci account? Thanks graeme On Wed, Apr 8, 2015 at 10:52 AM <richard.gildea(a)diamond.ac.uk<mailto:[email protected]><mailto:[email protected]>> wrote: Hi Markus, I agree that it would be better if the tests would either work gracefully with CCP4 monomer library, or (possibly better?) only run if chem_data is available. In the latter case, a simple libtbx.env.has_module("chem_data") could be used in the test to check whether chem_data is available. As a workaround, we developers should be able to add the chem_data repository to our sources after which the tests should pick up the correct version of the monomer library: $ svn co svn+ssh://[email protected]/chem_data/trunk<http://[email protected]/chem_data/trunk> chem_data $ libtbx.configure chem_data Cheers, Richard ________________________________________ From: Gerstel, Markus (DLSLtd,RAL,LSCI) Sent: 08 April 2015 09:33 To: Gildea, Richard (DLSLtd,RAL,LSCI); asbrewster(a)lbl.gov<mailto:[email protected]><mailto:[email protected]>; cctbxbb(a)phenix-online.org<mailto:[email protected]><mailto:[email protected]> Cc: dials-support(a)lists.sourceforge.net<mailto:[email protected]><mailto:[email protected]> Subject: RE: [Dials-support] [cctbxbb] DIALS source tarball Hi Richard, I think you've found it. I have unset CLIBD_MON, and now the test skips cleanly. Of course this also means that users should not run cctbx tests on their machines... Is there no central 'mmtbx_skip_test_if_chem_data_db_missing' function, that just goes 'prints "Skip this test"; exit' if the library isn't present? Or a boolean _is_available() function if you prefer. Either would resolve this problem as well as the current untestability of mmtbx. -Markus -----Original Message----- From: Gildea, Richard (DLSLtd,RAL,LSCI) Sent: 08 April 2015 09:15 To: Gerstel, Markus (DLSLtd,RAL,LSCI); asbrewster(a)lbl.gov<mailto:[email protected]><mailto:[email protected]>; cctbxbb(a)phenix-online.org<mailto:[email protected]><mailto:[email protected]> Cc: dials-support(a)lists.sourceforge.net<mailto:[email protected]><mailto:[email protected]> Subject: RE: [Dials-support] [cctbxbb] DIALS source tarball Hi Markus, Presumably the test is looking for a monomer that is present in chem_data but not in the ccp4 monomer library? Could we unset the CLIBD_MON variable for the purposes of testing the dials installers? Cheers, Richard ________________________________________ From: Gerstel, Markus (DLSLtd,RAL,LSCI) Sent: 08 April 2015 09:07 To: Gildea, Richard (DLSLtd,RAL,LSCI); asbrewster(a)lbl.gov<mailto:[email protected]><mailto:[email protected]>; cctbxbb(a)phenix-online.org<mailto:[email protected]><mailto:[email protected]> Cc: dials-support(a)lists.sourceforge.net<mailto:[email protected]><mailto:[email protected]> Subject: RE: [Dials-support] [cctbxbb] DIALS source tarball Hi Richard, Aaron, This is correct, we do not currently run mmtbx tests at all, as up to 107 of them do not fail gracefully, ie. skip properly. The test in question works fine (ie: is skipped because CCP4 is not made available) on our cctbx test system, but breaks in our final dials installer tests (where CCP4 is made available). CLIBD_MON is set to the /lib/data/monomers folder in the shared DLS CCP4 6.5 update 1 installation. Best wishes, Markus -----Original Message----- From: richard.gildea(a)diamond.ac.uk<mailto:[email protected]><mailto:[email protected]> [mailto:[email protected]<mailto:[email protected]>] Sent: 07 April 2015 21:36 To: asbrewster(a)lbl.gov<mailto:[email protected]><mailto:[email protected]>; cctbxbb(a)phenix-online.org<mailto:[email protected]><mailto:[email protected]> Cc: dials-support(a)lists.sourceforge.net<mailto:[email protected]><mailto:[email protected]> Subject: Re: [Dials-support] [cctbxbb] DIALS source tarball Hi Aaron, I'm not sure your fix as I understand it actually helps. The test that was failing was in the cctbx module, not mmtbx, and as far as I am aware we are running libtbx.run_tests_parallel module=cctbx module=dxtbx etc in our nightly builds (and that is what we as developers are running locally on our own development machines). If individual tests (particularly those in the more general modules such as cctbx, iotbx, etc.) rely on external dependencies (such as chem_data) being available, then the individual tests should test for presence of said dependencies and skip gracefully if not available. I have a feeling that we're not even including mmtbx in our nightly build tests (too many fail due to missing dependencies such as chem_data). Cheers, Richard ________________________________ From: Aaron Brewster [asbrewster(a)lbl.gov<mailto:[email protected]><mailto:[email protected]>] Sent: 07 April 2015 20:29 To: cctbx mailing list Cc: Waterman, David (STFC,RAL,SC); Gildea, Richard (DLSLtd,RAL,LSCI); Johan Hattne; <dials-support(a)lists.sourceforge.net<mailto:[email protected]><mailto:[email protected]>> Subject: Re: [cctbxbb] [Dials-support] DIALS source tarball Hi Markus, two points. First, you are correct that the dials builds are not passing tests related to the chem_data folder which includes monomer libraries. This is because chem_data is required by mmtbx but isn't included in the dials build. Partly because we're unsure if pieces of it are proprietary. In the meantime, I've worked with Nigel to change the cctbx_regression.test_nightly to look for the chem_data repository and skip the mmtbx tests if it's not present. mmtbx will still be tested nightly as part of the standalone cctbx and phenix packages. Because of this change, perhaps you could revert your recent changes to cctbx/regression/tst_geometry_restraints_2.py? It isn't necessary to check for chem_data in every sub test as it is tested for at the top level now. Second, the log you provided is not the one on buildbot. Your log indicates you have a CCP4 installation that includes a monomer library that is being picked up by the tests. Is one of the MMTBX_CCP4_MONOMER_LIB, or CLIBD_MON environment variables set on the system in question? Thanks, -Aaron On Tue, Apr 7, 2015 at 6:41 AM, <markus.gerstel(a)diamond.ac.uk<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>> wrote: Cc'ing cctbx folks David Waterman wrote: So maybe once we have a source tarball up at dials.diamond.ac.uk<http://dials.diamond.ac.uk><http://dials.diamond.ac.uk><http://dials.diamond.ac.uk> (..) Speaking of which: our DIALS builds are currently failing at the installer testing stage. This is due to cctbx/regression/tst_geometry_restraints_2.py failing deep in mmtbx territory. So far I could not figure out how to get this running properly. Call: libtbx.python tst_geometry_restraints_2.py Standard Output Skipping exercise_with_zeolite(): input file not available Skipping exercise_with_pdb(): chem_data directory not available Standard Error Traceback (most recent call last): File "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/cctbx/regression/tst_geometry_restraints_2.py", line 866, in <module> exercise_all(sys.argv[1:]) File "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/cctbx/regression/tst_geometry_restraints_2.py", line 862, in exercise_all exercise_na_restraints_output_to_geo(verbose=verbose) File "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/cctbx/regression/tst_geometry_restraints_2.py", line 805, in exercise_na_restraints_output_to_geo log=out1) File "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 5270, in run log=log) File "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 4876, in __init__ restraints_loading_flags=restraints_loading_flags, File "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 2902, in __init__ log=log, File "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 2287, in __init__ m_j=mm) File "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 1513, in get_lib_link return mon_lib_srv.link_link_id_dict["rna3p"] KeyError: 'rna3p' (On a side note: We really should call multiple tests within the same python file separately, instead of running them together within a signle run() method. This file contains 4 tests, but these will result in only a single return value for any upstream processing of the test results, such as Jenkins.) -Markus -- 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 ------------------------------------------------------------------------------ BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF _______________________________________________ DIALS-support mailing list DIALS-support(a)lists.sourceforge.net<mailto:[email protected]><mailto:[email protected]> https://lists.sourceforge.net/lists/listinfo/dials-support

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Re: [cctbxbb] [Dials-support] DIALS source tarball
by markus.gerstel＠diamond.ac.uk 08 Apr '15

08 Apr '15

Hi Richard, I think you've found it. I have unset CLIBD_MON, and now the test skips cleanly. Of course this also means that users should not run cctbx tests on their machines... Is there no central 'mmtbx_skip_test_if_chem_data_db_missing' function, that just goes 'prints "Skip this test"; exit' if the library isn't present? Or a boolean _is_available() function if you prefer. Either would resolve this problem as well as the current untestability of mmtbx. -Markus -----Original Message----- From: Gildea, Richard (DLSLtd,RAL,LSCI) Sent: 08 April 2015 09:15 To: Gerstel, Markus (DLSLtd,RAL,LSCI); asbrewster(a)lbl.gov; cctbxbb(a)phenix-online.org Cc: dials-support(a)lists.sourceforge.net Subject: RE: [Dials-support] [cctbxbb] DIALS source tarball Hi Markus, Presumably the test is looking for a monomer that is present in chem_data but not in the ccp4 monomer library? Could we unset the CLIBD_MON variable for the purposes of testing the dials installers? Cheers, Richard ________________________________________ From: Gerstel, Markus (DLSLtd,RAL,LSCI) Sent: 08 April 2015 09:07 To: Gildea, Richard (DLSLtd,RAL,LSCI); asbrewster(a)lbl.gov; cctbxbb(a)phenix-online.org Cc: dials-support(a)lists.sourceforge.net Subject: RE: [Dials-support] [cctbxbb] DIALS source tarball Hi Richard, Aaron, This is correct, we do not currently run mmtbx tests at all, as up to 107 of them do not fail gracefully, ie. skip properly. The test in question works fine (ie: is skipped because CCP4 is not made available) on our cctbx test system, but breaks in our final dials installer tests (where CCP4 is made available). CLIBD_MON is set to the /lib/data/monomers folder in the shared DLS CCP4 6.5 update 1 installation. Best wishes, Markus -----Original Message----- From: richard.gildea(a)diamond.ac.uk [mailto:[email protected]] Sent: 07 April 2015 21:36 To: asbrewster(a)lbl.gov; cctbxbb(a)phenix-online.org Cc: dials-support(a)lists.sourceforge.net Subject: Re: [Dials-support] [cctbxbb] DIALS source tarball Hi Aaron, I'm not sure your fix as I understand it actually helps. The test that was failing was in the cctbx module, not mmtbx, and as far as I am aware we are running libtbx.run_tests_parallel module=cctbx module=dxtbx etc in our nightly builds (and that is what we as developers are running locally on our own development machines). If individual tests (particularly those in the more general modules such as cctbx, iotbx, etc.) rely on external dependencies (such as chem_data) being available, then the individual tests should test for presence of said dependencies and skip gracefully if not available. I have a feeling that we're not even including mmtbx in our nightly build tests (too many fail due to missing dependencies such as chem_data). Cheers, Richard ________________________________ From: Aaron Brewster [asbrewster(a)lbl.gov] Sent: 07 April 2015 20:29 To: cctbx mailing list Cc: Waterman, David (STFC,RAL,SC); Gildea, Richard (DLSLtd,RAL,LSCI); Johan Hattne; <dials-support(a)lists.sourceforge.net> Subject: Re: [cctbxbb] [Dials-support] DIALS source tarball Hi Markus, two points. First, you are correct that the dials builds are not passing tests related to the chem_data folder which includes monomer libraries. This is because chem_data is required by mmtbx but isn't included in the dials build. Partly because we're unsure if pieces of it are proprietary. In the meantime, I've worked with Nigel to change the cctbx_regression.test_nightly to look for the chem_data repository and skip the mmtbx tests if it's not present. mmtbx will still be tested nightly as part of the standalone cctbx and phenix packages. Because of this change, perhaps you could revert your recent changes to cctbx/regression/tst_geometry_restraints_2.py? It isn't necessary to check for chem_data in every sub test as it is tested for at the top level now. Second, the log you provided is not the one on buildbot. Your log indicates you have a CCP4 installation that includes a monomer library that is being picked up by the tests. Is one of the MMTBX_CCP4_MONOMER_LIB, or CLIBD_MON environment variables set on the system in question? Thanks, -Aaron On Tue, Apr 7, 2015 at 6:41 AM, <markus.gerstel(a)diamond.ac.uk<mailto:[email protected]>> wrote: Cc'ing cctbx folks David Waterman wrote: > So maybe once we have a source tarball up at > dials.diamond.ac.uk<http://dials.diamond.ac.uk> (..) Speaking of which: our DIALS builds are currently failing at the installer testing stage. This is due to cctbx/regression/tst_geometry_restraints_2.py failing deep in mmtbx territory. So far I could not figure out how to get this running properly. Call: libtbx.python tst_geometry_restraints_2.py Standard Output Skipping exercise_with_zeolite(): input file not available Skipping exercise_with_pdb(): chem_data directory not available Standard Error Traceback (most recent call last): File "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/cctbx/regression/tst_geometry_restraints_2.py", line 866, in <module> exercise_all(sys.argv[1:]) File "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/cctbx/regression/tst_geometry_restraints_2.py", line 862, in exercise_all exercise_na_restraints_output_to_geo(verbose=verbose) File "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/cctbx/regression/tst_geometry_restraints_2.py", line 805, in exercise_na_restraints_output_to_geo log=out1) File "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 5270, in run log=log) File "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 4876, in __init__ restraints_loading_flags=restraints_loading_flags, File "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 2902, in __init__ log=log, File "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 2287, in __init__ m_j=mm) File "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 1513, in get_lib_link return mon_lib_srv.link_link_id_dict["rna3p"] KeyError: 'rna3p' (On a side note: We really should call multiple tests within the same python file separately, instead of running them together within a signle run() method. This file contains 4 tests, but these will result in only a single return value for any upstream processing of the test results, such as Jenkins.) -Markus -- 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

1 0

Re: [cctbxbb] [Dials-support] DIALS source tarball
by markus.gerstel＠diamond.ac.uk 08 Apr '15

08 Apr '15

Hi Richard, Aaron, This is correct, we do not currently run mmtbx tests at all, as up to 107 of them do not fail gracefully, ie. skip properly. The test in question works fine (ie: is skipped because CCP4 is not made available) on our cctbx test system, but breaks in our final dials installer tests (where CCP4 is made available). CLIBD_MON is set to the /lib/data/monomers folder in the shared DLS CCP4 6.5 update 1 installation. Best wishes, Markus -----Original Message----- From: richard.gildea(a)diamond.ac.uk [mailto:[email protected]] Sent: 07 April 2015 21:36 To: asbrewster(a)lbl.gov; cctbxbb(a)phenix-online.org Cc: dials-support(a)lists.sourceforge.net Subject: Re: [Dials-support] [cctbxbb] DIALS source tarball Hi Aaron, I'm not sure your fix as I understand it actually helps. The test that was failing was in the cctbx module, not mmtbx, and as far as I am aware we are running libtbx.run_tests_parallel module=cctbx module=dxtbx etc in our nightly builds (and that is what we as developers are running locally on our own development machines). If individual tests (particularly those in the more general modules such as cctbx, iotbx, etc.) rely on external dependencies (such as chem_data) being available, then the individual tests should test for presence of said dependencies and skip gracefully if not available. I have a feeling that we're not even including mmtbx in our nightly build tests (too many fail due to missing dependencies such as chem_data). Cheers, Richard ________________________________ From: Aaron Brewster [asbrewster(a)lbl.gov] Sent: 07 April 2015 20:29 To: cctbx mailing list Cc: Waterman, David (STFC,RAL,SC); Gildea, Richard (DLSLtd,RAL,LSCI); Johan Hattne; <dials-support(a)lists.sourceforge.net> Subject: Re: [cctbxbb] [Dials-support] DIALS source tarball Hi Markus, two points. First, you are correct that the dials builds are not passing tests related to the chem_data folder which includes monomer libraries. This is because chem_data is required by mmtbx but isn't included in the dials build. Partly because we're unsure if pieces of it are proprietary. In the meantime, I've worked with Nigel to change the cctbx_regression.test_nightly to look for the chem_data repository and skip the mmtbx tests if it's not present. mmtbx will still be tested nightly as part of the standalone cctbx and phenix packages. Because of this change, perhaps you could revert your recent changes to cctbx/regression/tst_geometry_restraints_2.py? It isn't necessary to check for chem_data in every sub test as it is tested for at the top level now. Second, the log you provided is not the one on buildbot. Your log indicates you have a CCP4 installation that includes a monomer library that is being picked up by the tests. Is one of the MMTBX_CCP4_MONOMER_LIB, or CLIBD_MON environment variables set on the system in question? Thanks, -Aaron On Tue, Apr 7, 2015 at 6:41 AM, <markus.gerstel(a)diamond.ac.uk<mailto:[email protected]>> wrote: Cc'ing cctbx folks David Waterman wrote: > So maybe once we have a source tarball up at > dials.diamond.ac.uk<http://dials.diamond.ac.uk> (..) Speaking of which: our DIALS builds are currently failing at the installer testing stage. This is due to cctbx/regression/tst_geometry_restraints_2.py failing deep in mmtbx territory. So far I could not figure out how to get this running properly. Call: libtbx.python tst_geometry_restraints_2.py Standard Output Skipping exercise_with_zeolite(): input file not available Skipping exercise_with_pdb(): chem_data directory not available Standard Error Traceback (most recent call last): File "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/cctbx/regression/tst_geometry_restraints_2.py", line 866, in <module> exercise_all(sys.argv[1:]) File "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/cctbx/regression/tst_geometry_restraints_2.py", line 862, in exercise_all exercise_na_restraints_output_to_geo(verbose=verbose) File "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/cctbx/regression/tst_geometry_restraints_2.py", line 805, in exercise_na_restraints_output_to_geo log=out1) File "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 5270, in run log=log) File "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 4876, in __init__ restraints_loading_flags=restraints_loading_flags, File "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 2902, in __init__ log=log, File "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 2287, in __init__ m_j=mm) File "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 1513, in get_lib_link return mon_lib_srv.link_link_id_dict["rna3p"] KeyError: 'rna3p' (On a side note: We really should call multiple tests within the same python file separately, instead of running them together within a signle run() method. This file contains 4 tests, but these will result in only a single return value for any upstream processing of the test results, such as Jenkins.) -Markus -- 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] [Dials-support] DIALS source tarball
by Aaron Brewster 07 Apr '15

07 Apr '15

Hi Richard, At the moment, buildbot for dials runs these three tests: libtbx.import_all_ext cctbx_regression.test_nightly libtbx.run_tests_parallel module=dials nproc=auto verbosity=1 Which doesn't line up exactly with what you described. If you run libtbx.run_tests_parallel module=cctbx module=dxtbx, then you are right that the fix I committed wouldn't be relevant because mmtbx wouldn't be tested. However, since the LBL build bot runs cctbx_regression.test_nightly, my change is needed. After some more discussion, I see that Markus's changes to tst_geometry_restraints_2.py are fine. It looks like there are already sub-tests in there that check for the presence of mmtbx and chem data before running. I think tst_geometry_restraints_2.py was the only test outside of mmtbx that was looking for the monomer libraries. I'm re-running the buildbot dials build now to see if my change to cctbx_regression.test_nightly along with Markus's changes to tst_geometry_restraints_2.py clean up the build. Finally, and perhaps on a different note, should we add dxtbx to cctbx_regression.test_nightly? Right now the list of modules it tests includes libtbx, boost_adaptbx, scitbx, cctbx, iotbx, smtbx, and if chem_data is present, mmtbx. I don't think the build bot is running the dxtbx tests at present. -Aaron On Tue, Apr 7, 2015 at 1:36 PM, <richard.gildea(a)diamond.ac.uk> wrote: > Hi Aaron, > > I'm not sure your fix as I understand it actually helps. The test that was > failing was in the cctbx module, not mmtbx, and as far as I am aware we are > running libtbx.run_tests_parallel module=cctbx module=dxtbx etc in our > nightly builds (and that is what we as developers are running locally on > our own development machines). If individual tests (particularly those in > the more general modules such as cctbx, iotbx, etc.) rely on external > dependencies (such as chem_data) being available, then the individual tests > should test for presence of said dependencies and skip gracefully if not > available. I have a feeling that we're not even including mmtbx in our > nightly build tests (too many fail due to missing dependencies such as > chem_data). > > Cheers, > > Richard > > ________________________________ > From: Aaron Brewster [asbrewster(a)lbl.gov] > Sent: 07 April 2015 20:29 > To: cctbx mailing list > Cc: Waterman, David (STFC,RAL,SC); Gildea, Richard (DLSLtd,RAL,LSCI); > Johan Hattne; <dials-support(a)lists.sourceforge.net> > Subject: Re: [cctbxbb] [Dials-support] DIALS source tarball > > Hi Markus, two points. > > First, you are correct that the dials builds are not passing tests related > to the chem_data folder which includes monomer libraries. This is because > chem_data is required by mmtbx but isn't included in the dials build. > Partly because we're unsure if pieces of it are proprietary. In the > meantime, I've worked with Nigel to change the > cctbx_regression.test_nightly to look for the chem_data repository and skip > the mmtbx tests if it's not present. mmtbx will still be tested nightly as > part of the standalone cctbx and phenix packages. Because of this change, > perhaps you could revert your recent changes to > cctbx/regression/tst_geometry_restraints_2.py? It isn't necessary to check > for chem_data in every sub test as it is tested for at the top level now. > > Second, the log you provided is not the one on buildbot. Your log > indicates you have a CCP4 installation that includes a monomer library that > is being picked up by the tests. Is one of the MMTBX_CCP4_MONOMER_LIB, or > CLIBD_MON environment variables set on the system in question? > > Thanks, > -Aaron > > > > On Tue, Apr 7, 2015 at 6:41 AM, <markus.gerstel(a)diamond.ac.uk<mailto: > markus.gerstel(a)diamond.ac.uk>> wrote: > Cc'ing cctbx folks > > David Waterman wrote: > > So maybe once we have a source tarball up at dials.diamond.ac.uk< > http://dials.diamond.ac.uk> (..) > > Speaking of which: our DIALS builds are currently failing at the installer > testing stage. This is due to cctbx/regression/tst_geometry_restraints_2.py > failing deep in mmtbx territory. > So far I could not figure out how to get this running properly. > > > Call: > > libtbx.python tst_geometry_restraints_2.py > > Standard Output > > Skipping exercise_with_zeolite(): input file not available > Skipping exercise_with_pdb(): chem_data directory not available > > Standard Error > > Traceback (most recent call last): > File > "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/cctbx/regression/tst_geometry_restraints_2.py", > line 866, in <module> > exercise_all(sys.argv[1:]) > File > "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/cctbx/regression/tst_geometry_restraints_2.py", > line 862, in exercise_all > exercise_na_restraints_output_to_geo(verbose=verbose) > File > "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/cctbx/regression/tst_geometry_restraints_2.py", > line 805, in exercise_na_restraints_output_to_geo > log=out1) > File > "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", > line 5270, in run > log=log) > File > "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", > line 4876, in __init__ > restraints_loading_flags=restraints_loading_flags, > File > "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", > line 2902, in __init__ > log=log, > File > "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", > line 2287, in __init__ > m_j=mm) > File > "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", > line 1513, in get_lib_link > return mon_lib_srv.link_link_id_dict["rna3p"] > KeyError: 'rna3p' > > > (On a side note: We really should call multiple tests within the same > python file separately, instead of running them together within a signle > run() method. This file contains 4 tests, but these will result in only a > single return value for any upstream processing of the test results, such > as Jenkins.) > > -Markus > > -- > 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<mailto:[email protected]> > http://phenix-online.org/mailman/listinfo/cctbxbb > >

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Generating crystal copies
by Nicholas Pearce 07 Apr '15

07 Apr '15

Hi Everyone, I'm currently trying to generate crystal contacts/copies. What I want out at the end is a list of symmetry operations to generate the crystallographic copies that form contacts with my input model. I've been using the asu_mappings object, but I'm not sure I'm using the output correctly or if it's the right thing to use. Code snippet used to calculate the mappings: # Extract the xray structure from the reference hierarchy ref_struc = ref_hierarchy.extract_xray_structure(crystal_symmetry=crystal_symmetry) # Extract the mappings that will tell us the adjacent symmetry copies asu_mappings = ref_struc.asu_mappings(buffer_thickness=5) # Symmetry operations for each atom mappings = asu_mappings.mappings() I printed out all of the mappings, as I presumed the vast majority of the them would be the identity, meaning that any non-identity operations would be from atoms in the buffer area I have defined. These non-identity operations would presumably be the ones that would generate the crystal contacts. However, a large number of the atoms only had one mapping, which was not the identity - e.g. asu_mappings.get_rt_mx(x).as_xyz() might give '-x+1/2,-y+1/2,z-1/2' for an atom with only one mapping. The effect of this is that the operations given by this generate symmetry copies that do not contact my input model in real space. I presume this means that asu_mappings is mapping the atoms in my model to some other arbitrary asu, as well as the atoms in the buffer zone around it? Therefore the symmetry operations given are for these mapped atoms? Can anyone help, or suggest an alternative way to generate the crystal contacts? Thanks, Nick

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Re: [cctbxbb] [Dials-support] DIALS source tarball
by markus.gerstel＠diamond.ac.uk 07 Apr '15

07 Apr '15

Cc'ing cctbx folks David Waterman wrote: > So maybe once we have a source tarball up at dials.diamond.ac.uk (..) Speaking of which: our DIALS builds are currently failing at the installer testing stage. This is due to cctbx/regression/tst_geometry_restraints_2.py failing deep in mmtbx territory. So far I could not figure out how to get this running properly. Call: libtbx.python tst_geometry_restraints_2.py Standard Output Skipping exercise_with_zeolite(): input file not available Skipping exercise_with_pdb(): chem_data directory not available Standard Error Traceback (most recent call last): File "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/cctbx/regression/tst_geometry_restraints_2.py", line 866, in <module> exercise_all(sys.argv[1:]) File "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/cctbx/regression/tst_geometry_restraints_2.py", line 862, in exercise_all exercise_na_restraints_output_to_geo(verbose=verbose) File "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/cctbx/regression/tst_geometry_restraints_2.py", line 805, in exercise_na_restraints_output_to_geo log=out1) File "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 5270, in run log=log) File "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 4876, in __init__ restraints_loading_flags=restraints_loading_flags, File "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 2902, in __init__ log=log, File "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 2287, in __init__ m_j=mm) File "/scratch/jenkins_slave/workspace/dials_test_installer/dials-dev/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 1513, in get_lib_link return mon_lib_srv.link_link_id_dict["rna3p"] KeyError: 'rna3p' (On a side note: We really should call multiple tests within the same python file separately, instead of running them together within a signle run() method. This file contains 4 tests, but these will result in only a single return value for any upstream processing of the test results, such as Jenkins.) -Markus -- 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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programmatic access to PDB through cctbx?
by Kaushik Hatti 01 Apr '15

01 Apr '15

Hello, Sorry if this is not relevant to this mailing list. I was wondering if there are any modules available under cctbx to query PDB database programmatically. There was an option to SQL-query PDBe (from here : http://www.ebi.ac.uk/pdbe-as/pdbedatabase/ ). But, this service has been retired since Mar 2015. How else could complex query on PDB possible? An example query could be: list of PDBid with SCOPid="1hba" and (Resolution < 2 and R/Rfree < 15/20) or (Resolution < 3 and R/Rfree < 20/25 ) and Completeness < 95% and structureFactorAvailability="Y" Such a query was possible via above mentioned SQL link. However, I am unable to find any other means now. Thanks in advance, Kaushik Hatti, Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India -- People living deeply have no fear of death - Anais Nin Caution: I am still the dumbest person I have ever known :-)

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dxtbx test failure
by markus.gerstel＠diamond.ac.uk 25 Mar '15

25 Mar '15

Hello everyone, Our last nightly build on RHEL linux x64 failed because the test dxtbx/tests/tst_dxtbx.py , which normally takes roughly 3 seconds to run on the build machine, got stuck for over 5 minutes. All the other tests (cctbx/scitbx/libtbx/iotbx/rstbx and remaining dxtbx) completed successfully. Tests were run via libtbx.run_tests_parallel with nproc=4. As far as I can tell there is no debug output. The libtbx testing suite does not support timeouts like some timeout decorators on python unittest? As far as I can tell tst_dxtbx.py at the moment runs 5 separate tests, so for future debugging it may make sense to split these up. -Markus -- 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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compilation issues
by Dave Lodowski 16 Mar '15

16 Mar '15

Hi, sorry if this is a repeat, but an email sent to the cctbx(a)cci.lbl.gov bounced back to me. We are attempting to install the DIALS package and CCTBX is required for compilation. During compilation of CCTBX, Xrender fails to find the X windows server. OS is Ubuntu LTS 12.04.5 text from console upon failure: Installing Xrender... log file is /home/dave/cctbx/build/base_tmp/Xrender_install_log getting package xrender-0.8.3.tar.gz... downloading from http://cci.lbl.gov/cctbx_dependencies : local copy is current using ./xrender-0.8.3.tar.gz (cached) installing xrender-0.8.3.tar.gz... Traceback (most recent call last): File "../auto_build/install", line 9, in <module> install_base_packages.installer(args=sys.argv, log=sys.stdout) File "../auto_build/install_base_packages.py", line 161, in __init__ self.build_dependencies(packages=packages) File "../auto_build/install_base_packages.py", line 505, in build_dependencies getattr(self, 'build_%s'%i)() File "../auto_build/install_base_packages.py", line 781, in build_render self.build_compiled_package_simple(pkg_name=pkg, pkg_name_label=name) File "../auto_build/install_base_packages.py", line 407, in build_compiled_package_simple log=pkg_log) File "../auto_build/install_base_packages.py", line 392, in configure_and_build self.call("./configure %s" % " ".join(list(config_args)), log=log) File "../auto_build/install_base_packages.py", line 243, in call return call(args, log=log, verbose=self.verbose, **kwargs) File "../auto_build/installer_utils.py", line 71, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) RuntimeError: Call to './configure --prefix="/home/dave/cctbx/build/base"' failed with exit code 1 Log file indicates everything fine till X is required then : checking for X... no configure: error: X is required, but it was either disabled or not found. any suggestions as to how to proceed would be appreciated thanks, --David Lodowski

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test 2
by Nicholas Sauter 05 Mar '15

05 Mar '15

-- Nicholas K. Sauter, Ph. D. Computer Staff Scientist, Physical Biosciences Division Lawrence Berkeley National Laboratory 1 Cyclotron Rd., Bldg. 64R0121 Berkeley, CA 94720-8118 (510) 486-5713

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Atom selections for distance (embarrassingly simple)
by Morten Grøftehauge 18 Feb '15

18 Feb '15

Hi everyone, I'm trying to do some distance extraction of hetero atoms in pdbs. I've got for model in pdb_obj.hierarchy.models(): for chain in model.chains(): for rg in chain.residue_groups(): for ag in rg.atom_groups(): for atom in ag.atoms(): if atom.hetero == True: print atom.distance(atom) Which prints out 0.0 as expected. But I can't figure out how to, say, measure the distance to an atom in the previous residue (if there is a previous residue). I also noticed something weird in this tutorial: http://cctbx.sourceforge.net/sbgrid2008/tutorial.html They truncate a non-standard amino acid to the beta-carbon but this only works because there's an alternate conformation with a standard amino acid (Cys). So it wouldn't work with a seleno-met for instance (I know there's a convert-to-ala function in mmtbx - I said it was weird, not terrible). Anyway, I hope someone can explain the distances thing for me. I'm sure there are multiple ways of doing it (should I just do a selection of "hetatm" and iterate over them and try to get some distanes?). Cheers, Morten

2 1

Partitioning of Grid/Unit Cell
by Nicholas Pearce 15 Feb '15

15 Feb '15

Hi Everyone, I’m trying to partition a grid/space based on smallest distance to atomic sites - as in a voronoi diagram (http://en.wikipedia.org/wiki/Voronoi_diagram <http://en.wikipedia.org/wiki/Voronoi_diagram>). Is there any code in cctbx that could be used to accomplish this? Thanks, Nick Nicholas Pearce, DPhil Student, Structural Genomics Consortium, University of Oxford

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iotbx xray.reconstructed_amplitude and changed SIGF
by Huw Jenkins 12 Feb '15

12 Feb '15

Hi, This is my first post to this list and I hope I can explain my confusion properly. I have been using iotbx to manipulate data stored in mtz files and found that values in columns that should not have been altered by my code are different in the output mtz file. This seems only to occur when the input mtz file contains DANO, SIGDANO columns. When I run the code below F and DANO in input.mtz and output.mtz are the same but SIGF and SIGDANO are different (shown for 5 reflections listed). Is this expected behaviour? Given that in my understanding that code should just read a mtz file, convert the data to a miller array then write the array back out to a new mtz I would expect the values in the input and output to be identical (within rounding error). Thanks, Huw from __future__ import division import sys from iotbx import mtz from iotbx import reflection_file_reader from iotbx import reflection_file_utils def run(args): mtz_file = reflection_file_reader.any_reflection_file("input.mtz") mtz_as_miller_array = mtz_file.as_miller_arrays() f_obs = mtz_as_miller_array[0] mtz_out = f_obs.as_mtz_dataset(column_root_label="F_iotbx") mtz_out.mtz_object().write("output.mtz") if (__name__ == "__main__"): run(sys.argv[1:]) some reflections from input.mtz are: H K L F_ccp4 SIGF_ccp4 DANO_ccp4 SIGDANO_ccp4 ISYM_ccp4 1 2 2 4.90461 2.31536 0 3.27441 0 1 2 3 186.172 1.86381 119.745 3.84862 0 1 2 4 289.31 3.06709 -5.42197 6.46531 0 1 2 5 378.928 2.7118 87.3381 5.56933 0 1 2 6 540.866 4.38513 46.4155 8.8053 0 The same reflections in output.mtz are: H K L F_iotbx SIGF_iotbx DANOF_iotbx SIGDANOF_iotbx ISYMF_iotbx 1 2 2 4.90461 2.00516 0 4.01032 0 1 2 3 186.172 1.8943 119.745 3.7886 0 1 2 4 289.31 3.15096 -5.42197 6.30192 0 1 2 5 378.928 2.74848 87.3381 5.49695 0 1 2 6 540.866 4.3939 46.4155 8.7878 0

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