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Re: [cctbxbb] [Cctbx-cvs] SF.net SVN: cctbx:[25333] trunk/libtbx/env_config.py
by markus.gerstel＠diamond.ac.uk 09 Sep '16

09 Sep '16

Hi, I just spent some time tracking software crashes to this change. Is setting the default to en_US really appropriate and what we want? In particular it affects the output of downstream, external software we run from within python. What is the unicode issue you hint at in the commit message? -Markus Dr Markus Gerstel MBCS Postdoctoral Research Associate Tel: +44 1235 778698 Diamond Light Source Ltd. Diamond House Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE -----Original Message----- From: bkpoon(a)users.sourceforge.net [mailto:[email protected]] Sent: 07 September 2016 00:54 To: cctbx-cvs(a)lists.sourceforge.net Subject: [Cctbx-cvs] SF.net SVN: cctbx:[25333] trunk/libtbx/env_config.py Revision: 25333 http://sourceforge.net/p/cctbx/code/25333 Author: bkpoon Date: 2016-09-06 23:54:29 +0000 (Tue, 06 Sep 2016) Log Message: ----------- Unicode support: set LC_ALL in dispatchers to the one in the user's environment (if available, and supports UTF-8), otherwise use the default setting of en_US.UTF-8; fixes unicode issue with python in Linux (e.g. os.path functions do not work correctly with unicode if LC_ALL=C Modified Paths: -------------- trunk/libtbx/env_config.py Modified: trunk/libtbx/env_config.py =================================================================== --- trunk/libtbx/env_config.py 2016-09-06 21:15:34 UTC (rev 25332) +++ trunk/libtbx/env_config.py 2016-09-06 23:54:29 UTC (rev 25333) @@ -945,6 +945,15 @@ def write_bin_sh_dispatcher(self, source_file, target_file, source_is_python_exe=False): + + # determine LC_ALL from environment (Python UTF-8 compatibility in Linux) + LC_ALL = os.environ.get('LC_ALL') # user setting + if (LC_ALL is not None): + if ( ('UTF-8' not in LC_ALL) and ('utf8' not in LC_ALL) ): + LC_ALL = None + if (LC_ALL is None): + LC_ALL = 'en_US.UTF-8' # default + f = target_file.open("w") if (source_file is not None): print >> f, '#! /bin/sh' @@ -975,7 +984,7 @@ print >> f, '#' print >> f, _SHELLREALPATH_CODE print >> f, 'unset PYTHONHOME' - print >> f, 'LC_ALL=C' + print >> f, 'LC_ALL=' + LC_ALL print >> f, 'export LC_ALL' print >> f, 'LIBTBX_BUILD="$(shellrealpath "$0" && cd "$(dirname "$RESULT")/.." && pwd)"' print >> f, 'export LIBTBX_BUILD' This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. ------------------------------------------------------------------------------ _______________________________________________ Cctbx-cvs mailing list Cctbx-cvs(a)lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cctbx-cvs -- 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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Inserting F000 into reflection (mtg) file
by Nicholas Pearce 22 Aug '16

22 Aug '16

Hi Everyone, I’ve been looking through the cctbx/phenix scripts and although there’s a script for estimating F000 (phenix.f000), I can’t find any way of inserting it into an mtz file to make it accessible for easy map generation. Is this implemented anywhere/what do people use as the best way of doing this? If the insertion of F000 into an mtz file has been purposefully avoided, I presume it's done because we don't want the possibility of someone refining a model where F000 is used in refinement. Unless there’s another reason? Thanks, Nick

2 1

Git
by Graeme.Winter＠diamond.ac.uk 01 Aug '16

01 Aug '16

Folks, Can we revisit the idea of moving to git for cctbx? Thanks Graeme -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Structure Factor for 000
by Gareth.Nisbet＠diamond.ac.uk 28 Jul '16

28 Jul '16

Is it possible to get the structure_factors function to give the structure factor for the 000 reflection? I appreciate this might be a slightly odd question. Gareth -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Berkeley Server Downtime (24 hours, 7/22 - 7/23)
by Billy Poon 20 Jul '16

20 Jul '16

Dear all, On Friday, July 22, our servers will be shut down starting at 5:00 pm Pacific for scheduled maintenance in our building. We expect that the servers will be available the next day (7/23) by 5:00 pm Pacific at the latest. This will affect, - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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Re: [cctbxbb] Git
by R. D. Oeffner 02 Jul '16

02 Jul '16

How often is this git repo of cctbx copied from the svn repo of cctbx? Rob -----Original Message----- From: cctbxbb-request(a)phenix-online.org Sent: Friday, July 1, 2016 8:00 PM To: cctbxbb(a)phenix-online.org Subject: cctbxbb Digest, Vol 88, Issue 1 Send cctbxbb mailing list submissions to cctbxbb(a)phenix-online.org To subscribe or unsubscribe via the World Wide Web, visit http://phenix-online.org/mailman/listinfo/cctbxbb or, via email, send a message with subject or body 'help' to cctbxbb-request(a)phenix-online.org You can reach the person managing the list at cctbxbb-owner(a)phenix-online.org When replying, please edit your Subject line so it is more specific than "Re: Contents of cctbxbb digest..." Today's Topics: 1. Re: Git (markus.gerstel(a)diamond.ac.uk) ---------------------------------------------------------------------- Message: 1 Date: Fri, 1 Jul 2016 12:34:56 +0000 From: <markus.gerstel(a)diamond.ac.uk> To: <cctbxbb(a)phenix-online.org> Subject: Re: [cctbxbb] Git Message-ID: <415F7F573406BB498256C68158D45674666211BB@exchmbx01> Content-Type: text/plain; charset="utf-8" Hello everyone, Following up the earlier discussion, do have we reached a consensus? Also, I think timeframe has not been discussed, but I assume this will boil down to ?after phenix release? anyway. In the meantime I have contacted (nearly) all cctbx developers and obtained their github user-IDs - alongside some enthusiastic* feedback. I will mass-invite you all soonishly to a cctbx organisation with a preliminary git copy of the svn history to play with. Best wishes -Markus Markus Gerstel MBCS Postdoctoral Research Associate Tel: +44 1235 778698 Diamond Light Source Ltd. Diamond House Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE * The best comment I received was ?What?s CCTBX?? ? and that was talking to the correct person :) (name withheld) -- 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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Installation failure after package updates
by markus.gerstel＠diamond.ac.uk 27 Jun '16

27 Jun '16

Following the latest package updates we are now observing installer failures. In particular the configure step appears to fail with a missing libffi.so.6 Any ideas how to rectify this, or if this error can be ignored safely? -Markus Running with --verbose: ========================================================================== DIALS Installation version: dev20160610 machine type: intel-linux-2.6-x86_64 OS version: 2.6.32-573.18.1.el6.x86_64 destination: /dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610 # of processors: 24 ========================================================================= Configuring DIALS components... /dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/build ['/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/base/bin/python', '/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/libtbx/configure.py', '--current_working_directory', '/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/build', 'dials', 'xia2', 'iota', 'prime'] : Python: 2.7.8 "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/base/bin/python" : Compiler: default : Build mode: release : Warning level: 0 : Precompiled Headers: False : Static libraries: False : Static exe: False : Scan Boost headers: False : Write full flex_fwd.h files: False : Build Boost.Python extensions: True : Define BOOST_PYTHON_NO_PY_SIGNATURES: False : Define BOOST_PYTHON_BOOL_INT_STRICT: True : Enable OpenMP if possible: False : Boost threads enabled: False : Enable CUDA: False : Use opt_resources if available: False : Use environment flags: False : Enable C++11: False : Force true division: True : command_version_suffix: None : Relocatable paths anchored at: /dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/build : Top-down list of all modules involved: : prime "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/prime" : iota "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/iota" : xia2 "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/xia2" : mmtbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/mmtbx" : dials "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/dials" : xfel "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/xfel" : cma_es "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/cma_es" : gltbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/gltbx" : crys3d "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/crys3d" : rstbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/rstbx" : spotfinder "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/spotfinder" : annlib+adaptbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/annlib" : "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/annlib_adaptbx" : dxtbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/dxtbx" : iotbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/iotbx" : cbflib+adaptbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cbflib" : "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/cbflib_adaptbx" : ccp4io+adaptbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/ccp4io" : "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/ccp4io_adaptbx" : smtbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/smtbx" : ucif "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/ucif" : cctbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/cctbx" : chiltbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/chiltbx" : scitbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/scitbx" : fable "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/fable" : omptbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/omptbx" : boost+adaptbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/boost" : "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/boost_adaptbx" : tbxx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/tbxx" : libtbx "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/libtbx" : Creating files in build directory: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/build" : dispatcher_include_template.sh : dispatcher_head.sh : setpaths.sh : setpaths.csh : setpaths_all.sh : setpaths_all.csh : setpaths_debug.sh : unsetpaths.sh : setpaths_debug.csh : unsetpaths.csh : SConstruct : Makefile : run_tests.csh : Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/libtbx/command_line" : Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/boost_adaptbx/command_line" : Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/fable/command_line" : Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/scitbx/command_line" : Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/cctbx/command_line" : Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/smtbx/command_line" : Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/cbflib_adaptbx/command_line" : Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/iotbx/command_line" : Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/dxtbx/command_line" : Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/spotfinder/command_line" : Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/rstbx/command_line" : Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/crys3d/command_line" : Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/gltbx/command_line" : Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/xfel/command_line" : Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/xfel/ui/command_line" : Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/dials/command_line" : Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/mmtbx/command_line" : Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/xia2/command_line" : Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/iota/command_line" : Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/prime/command_line" : Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/boost_adaptbx/libtbx_refresh.py" : Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/scitbx/libtbx_refresh.py" : Generating C++ header files in: : "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/build/include/scitbx/array_family" : Generating C++ files in: : "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/build/include/scitbx/array_family/boost_python" : Using fable to convert scitbx/lbfgs.f : Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/cctbx/libtbx_refresh.py" : Generating C++ files in: : "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/build/cctbx/eltbx" : Generating C++ files in: : "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/build/include/cctbx/boost_python" : Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/smtbx/libtbx_refresh.py" : Generating C++ files in: : "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/build/include/smtbx/boost_python" : Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/cbflib_adaptbx/libtbx_refresh.py" : Copying to lib: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cbflib/pycbf/pycbf.py" : Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/iotbx/libtbx_refresh.py" : Using fable to convert iotbx/pdb/hybrid_36_f.f : Writing: iotbx/pdb/hybrid_36_fem.cpp : Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/annlib_adaptbx/libtbx_refresh.py" : Generating C++ files for self-inclusive approximate nearest neighbor : Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/crys3d/libtbx_refresh.py" : Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/gltbx/libtbx_refresh.py" : Generating C++ files in: : "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/build/gltbx" : Info: Re-using existing font cpp files. : Hint: Remove gltbx/FONTS_UCS_DONE_FLAG_FILE : to force generation of new font files. : Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/xfel/libtbx_refresh.py" : Creating cxi_user directory : Creating cxi_user/__init__.py : Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/dials/libtbx_refresh.py" : DIALS 1.dev.360-ge6510c8 : Identifying autocompletable commands: dials.analyse_background dials.combine_found_spots dials.find_spots dials.index dials.integrate dials.reciprocal_lattice_viewer dials.refine dials.reindex dials.rl_png : Installing autocompletion script into: setpaths_all.sh setpaths_debug.sh setpaths.sh : Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/mmtbx/libtbx_refresh.py" : Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/xia2/libtbx_refresh.py" : XIA2 0.4.0.381-g9b3a992 : Processing: "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/build/exe_dev" : Regenerating module files in /dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/base : /dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/base/etc/pango not present, could not regenerate pango files : generating gtk.immodules file : /dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/base/bin/gtk-query-immodules-2.0: error while loading shared libraries: libffi.so.6: cannot open shared object file: No such file or directory : Traceback (most recent call last): : File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/libtbx/configure.py", line 22, in <module> : if not run(): : File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/libtbx/configure.py", line 17, in run : libtbx.env_config.cold_start(sys.argv) : File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/libtbx/env_config.py", line 2264, in cold_start : env.refresh() : File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/libtbx/env_config.py", line 1537, in refresh : regenerate_module_files.run(libtbx.env.under_base('.'), only_if_needed=True) : File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/libtbx/auto_build/regenerate_module_files.py", line 154, in run : fix_gtk(base_dir, out) : File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/libtbx/auto_build/regenerate_module_files.py", line 72, in fix_gtk : log=out) : File "/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/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 '/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/base/bin/gtk-query-immodules-2.0 /dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/base/lib/gtk-2.0/2.10.0/immodules/*.so> /dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/base/etc/gtk-2.0/gtk.immodules' failed with exit code 127 Traceback (most recent call last): File "./bin/install.py", line 97, in <module> installer(sys.argv[1:]).install() File "/scratch/jenkins_slave/workspace/dials_install_dls_module/dials-installer-dev/lib/libtbx/auto_build/install_distribution.py", line 197, in install self.install_from_binary() File "/scratch/jenkins_slave/workspace/dials_install_dls_module/dials-installer-dev/lib/libtbx/auto_build/install_distribution.py", line 318, in install_from_binary self.reconfigure(log=log) File "/scratch/jenkins_slave/workspace/dials_install_dls_module/dials-installer-dev/lib/libtbx/auto_build/install_distribution.py", line 484, in reconfigure call(args=args, log=log, verbose=self.options.verbose) File "/scratch/jenkins_slave/workspace/dials_install_dls_module/dials-installer-dev/lib/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 '/dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/base/bin/python /dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/modules/cctbx_project/libtbx/configure.py --current_working_directory /dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20160610/build dials xia2 iota prime' failed with exit code 1 Markus Gerstel MBCS Postdoctoral Research Associate Tel: +44 1235 778698 Diamond Light Source Ltd. Diamond House Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

2 6

Re: [cctbxbb] error
by markus.gerstel＠diamond.ac.uk 23 Jun '16

23 Jun '16

Hi James, CCing cctbxbb for further support I can reproduce at least similar errors with both DIALS 1.2.5 and current nightly builds. I think this may be a matplotlib 1.3.1 problem. A minimal reproducer is: $ dials.python > import matplotlib.pyplot as plt > plt.imshow([[1]]) Gtk-Message... > (press ctrl+D) Segmentation fault When compiled on the same machine I do not get the Gtk-Messages, but I do get the segmentation fault. Markus Gerstel MBCS Postdoctoral Research Associate Tel: +44 1235 778698 Diamond Light Source Ltd. Diamond House Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE From: Parkhurst, James (DLSLtd,RAL,LSCI) Sent: 21 June 2016 16:58 To: Gerstel, Markus (DLSLtd,RAL,LSCI) Subject: FW: error Hi Markus, I've been getting my summer student to do the cctbx_introduction tutorials in dials_scratch. He's using a version of dials downloaded from the website and when he runs the introduction script he gets errors about gdk-pixbuf giving paths to /scratch/jenkins_slave/workspace/. This seems like there is a jenkins path being set in the distributed installers. Would you have any idea how I can fix this? I'm downloading the linux installer of DIALS now so I can test this myself. Thanks, James ________________________________ [sse87232@ws188 cctbx_introduction_1]$ dials.python cctbx_introduction_1_test.py ximg2701_00001.cbf (cctbx_introduction_1_test.py:6243): GdkPixbuf-WARNING **: Cannot open pixbuf loader module file '/scratch/jenkins_slave/workspace/dials_release_build/compilationtarget/native/label/dials-ws133/build_dials/base/etc/gtk-2.0/gdk-pixbuf.loaders': No such file or directory (cctbx_introduction_1_test.py:6243): GdkPixbuf-WARNING **: Cannot open pixbuf loader module file '/scratch/jenkins_slave/workspace/dials_release_build/compilationtarget/native/label/dials-ws133/build_dials/base/etc/gtk-2.0/gdk-pixbuf.loaders': No such file or directory (cctbx_introduction_1_test.py:6243): GdkPixbuf-WARNING **: Cannot open pixbuf loader module file '/scratch/jenkins_slave/workspace/dials_release_build/compilationtarget/native/label/dials-ws133/build_dials/base/etc/gtk-2.0/gdk-pixbuf.loaders': No such file or directory (cctbx_introduction_1_test.py:6243): GdkPixbuf-WARNING **: Cannot open pixbuf loader module file '/scratch/jenkins_slave/workspace/dials_release_build/compilationtarget/native/label/dials-ws133/build_dials/base/etc/gtk-2.0/gdk-pixbuf.loaders': No such file or directory (cctbx_introduction_1_test.py:6243): GdkPixbuf-WARNING **: Cannot open pixbuf loader module file '/scratch/jenkins_slave/workspace/dials_release_build/compilationtarget/native/label/dials-ws133/build_dials/base/etc/gtk-2.0/gdk-pixbuf.loaders': No such file or directory (cctbx_introduction_1_test.py:6243): GdkPixbuf-WARNING **: Cannot open pixbuf loader module file '/scratch/jenkins_slave/workspace/dials_release_build/compilationtarget/native/label/dials-ws133/build_dials/base/etc/gtk-2.0/gdk-pixbuf.loaders': No such file or directory (cctbx_introduction_1_test.py:6243): GdkPixbuf-WARNING **: Cannot open pixbuf loader module file '/scratch/jenkins_slave/workspace/dials_release_build/compilationtarget/native/label/dials-ws133/build_dials/base/etc/gtk-2.0/gdk-pixbuf.loaders': No such file or directory Segmentation fault (core dumped) [sse87232@ws188 cctbx_introduction_1]$ which dials.python /dls/science/users/sse87232/dials/dials-v1-2-4/build/bin/dials.python -- 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

4 6

past contributors
by markus.gerstel＠diamond.ac.uk 16 Jun '16

16 Jun '16

I have now contacted everyone who ever contributed to cctbx in the past to get name/email details in preparation for an svn->git conversion. Everyone except these three: Erik McKee (emckee) Vishal Verma (vermav) ydr (y0udar) Anyone know how to get into contact with them? -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 1

Not wishing to raise this again but...
by Graeme.Winter＠diamond.ac.uk 16 Jun '16

16 Jun '16

... is there any enthusiasm out there for moving cctbx to git? The more I work with git the more I wish this existed properly for cctbx. I've raised this a bunch of times and always it is "not right now" however "a good idea" - this'll be the last time I ask... Could we move to git, please? I note the bootstrap script for Windows now has a git dependency even! Am happy to help if I can with anything though I think it should be pretty simple... was for DIALS & xia2 :) 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

8 23

Not wishing to raise this again but...
by R.D. Oeffner 15 Jun '16

15 Jun '16

Personally I think moving the cctbx to git is a great idea as it would make it easier and safer when developing and testing new features. Given so many teams are using the cctbx this seems like a compelling reason for it to be moved. We had a chat a while ago with Berkeley about this but I've forgotten what the consensus was. Rob > > Message: 1 > Date: Tue, 14 Jun 2016 12:10:03 +0000 > From: <Graeme.Winter(a)diamond.ac.uk> > To: <cctbxbb(a)phenix-online.org> > Subject: Re: [cctbxbb] Not wishing to raise this again but... > Message-ID: <13999B6FC038EB44B067771E3CFBD091BC327D8E@exchmbx03> > Content-Type: text/plain; charset="us-ascii" > > Hi All, > > This sounds like it is heading in a pragmatic direction - I would find > it very helpful to gauge feeling for or against this. To make this > simple I have attempted (starting from a completely ignorant position) > to put together one of those online survey things: > > https://www.surveymonkey.co.uk/r/GXPY5JW > > If you could pick an option that would be great, explaining why would > be even better, or hitting reply-all to this thread would also work > (as has previously done so) I'll collate answers over the next few > days & feed back when we have (say) 10-20 or a few days have passed > >> From experience with moving xia2 & DIALS it was surprisingly >> straightforward (an opinion) > > Thanks & cheerio Graeme > > -----Original Message----- > From: cctbxbb-bounces(a)phenix-online.org > [mailto:[email protected]] On Behalf Of > markus.gerstel(a)diamond.ac.uk > Sent: 14 June 2016 12:18 > To: cctbxbb(a)phenix-online.org > Subject: Re: [cctbxbb] Not wishing to raise this again but... > > Hi Pavel, > > I volunteered to do this some time ago, just like for DIALS, and would > still be happy to do this. > We can do the move slowly, so allow users (developers) with a git > repository while development still happens in SVN for say a couple of > weeks, and I would be happy to run the git support for that time and > for the aftermath of the move. > > Best wishes > -Markus > > -----Original Message----- > From: cctbxbb-bounces(a)phenix-online.org > [mailto:[email protected]] On Behalf Of Pavel Afonine > Sent: 14 June 2016 12:11 > To: cctbx mailing list > Subject: Re: [cctbxbb] Not wishing to raise this again but... > > Hey there! > > Well I guess I say something even though I don't have much to say > really. I've been contributing to CCTBX for the past 13 years, so I > feel like this conversation is not too irrelevant to me to say the > least. > > I don't have strong opinion about staying with svn vs moving to git. I > routinely contribute to CCTBX (which is SVN-based) and I routinely > contribute to my other activity - Q|R (Quantum Refinement, which is > hosted by GitHub). I'm comfortable with both environments as I'm using > only the minimal functionality of both: check in, check out, diff.. > period. I'm not interested in branching/etc sophistication; this is > just because the way I structure my workflow.. > > My current understanding is that moving CCTBX to use git boils down to: > - actually someone doing it; AND > - taking good proper responsible care of the aftermath (if any). > > So far no-one volunteered to embrace this challenge, as far as I know. > > In summary I think we should move to git, at least to follow the > vector of progress. > > All the best, > Pavel >

3 2

bootstrap.py build on Ubuntu
by David Waterman 14 Jun '16

14 Jun '16

Hi folks I recently tried building cctbx+dials on Ubuntu 15.04 following the instructions here: http://dials.github.io/documentation/installation_developer.html This failed during installation of pango-1.16.1. Looking at pango_install_log, I see the command that failed was as follows: gcc -DHAVE_CONFIG_H -I. -I. -I../.. -DSYSCONFDIR=\"/home/fcx32934/sw/dials_bootstrap_test/base/etc\" -DLIBDIR=\"/home/fcx32934/sw/dials_bootstrap_test/base/lib\" -DG_DISABLE_CAST_CHECKS -I../.. -DG_DISABLE_DEPRECATED -I/home/fcx32934/sw/dials_bootstrap_test/base/include -I/home/fcx32934/sw/dials_bootstrap_test/base/include/freetype2 -g -O2 -Wall -MT fribidi.lo -MD -MP -MF .deps/fribidi.Tpo -c fribidi.c -fPIC -DPIC -o .libs/fribidi.o In file included from fribidi.h:31:0, from fribidi.c:28: fribidi_config.h:1:18: fatal error: glib.h: No such file or directory The file glib.h appears to be in base/include/glib-2.0/, however this directory was not explicitly included in the command above, only its parent. This suggests a configuration failure in pango to me. Taking a look at base_tmp/pango-1.16.1/config.log, I see what look like the relevant lines: configure:22227: checking for GLIB configure:22235: $PKG_CONFIG --exists --print-errors "$GLIB_MODULES" configure:22238: $? = 0 configure:22253: $PKG_CONFIG --exists --print-errors "$GLIB_MODULES" configure:22256: $? = 0 configure:22304: result: yes but this doesn't tell me very much. Does anyone have any suggestions as to how I might proceed? Many thanks -- David

3 10

Nightly test server down?
by Luc Bourhis 14 Jun '16

14 Jun '16

Hi, http://cci-vm-6.lbl.gov:8010/waterfall does not answer anymore from where I stand (Paris). Best wishes, Luc

3 2

flex.histogram: add weights?
by Graeme.Winter＠diamond.ac.uk 14 Jun '16

14 Jun '16

Hi Folks I would like to be able to compute a weighted flex histogram i.e. instead of adding 1 for every element in array add weight[i] for array[i] instead (ie. generalized) Has anyone done this already? Don't want to break anything, will require the histogram itself being non-integral... 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

Project Scientist positions for computational methods
by Nicholas Sauter 13 Jun '16

13 Jun '16

Two Project Scientist positions are available in my group in the *Molecular Biophysics and Integrated Bioimaging* <http://biosciences.lbl.gov/divisions/mbib/> (MBIB) Division at Lawrence Berkeley National Lab. *Bioimaging Project Scientist* Position Summary: We have an exciting opportunity for a Bioimaging Project Scientist who will apply neuromorphic computing techniques to structural biology problems in X-ray diffraction, CryoEM, and CryoET. This will be a cross-disciplinary effort between MBIB and the Computational Research (CRD) Division at Lawrence Berkeley National Laboratory. The research group will include investigators Nick Sauter (X-ray Crystallography), Karen Davies (CryoEM/ET), and Chao Yang (Scalable Solvers). Specific Responsibilities: - Investigate how to apply deep learning algorithms to specific data processing and data interpretation problems in structural biology. - Implement convolutional neural network (CNN) code on neuromorphic computing hardware such as the IBM TrueNorth chip. Example problems include the identification of positive diffraction events in X-ray free-electron laser diffraction, conformational classification in CryoEM single particle reconstruction, and the identification of 3D sections for CryoET subtomogram averaging. - Use tools such as MatConvNet, CAFFE, THEANO or TensorFlow to construct and train CNNs that can be used to optimally classify experimental data. Required Qualifications: - Research experience in Structural Biology, with expertise in allied fields such as Bioinformatics, Mathematics, Computer Science, or Engineering (Ph.D. + 3 years or equivalent) - Strong background in image analysis and machine learning, including neural networks. - Working knowledge of image classification and/or other image processing techniques. - Proficient programming skills in MATLAB and/or Python. - Working knowledge of performance optimization for scientific codes. *Algorithm Developer Project Scientist* Position Summary: We are seeking an algorithm developer for the increasingly complex analysis of large diffraction datasets in structural biology. Current projects utilize XFEL crystallography and spectroscopy to investigate the photosynthetic mechanism of water splitting and to probe other metalloenzyme reactions. We also wish to test whether diffuse scattering can reveal correlated atomic motions in crystals. Many problems remain to be solved, including the details of how to optimally merge datasets from thousands of crystals. Our software development projects (including packages such as DIALS <http://dials.lbl.gov/> and cctbx.xfel <http://cci.lbl.gov/xfel>) have been highlighted in several high-impact publications listed HERE <http://biosciences.lbl.gov/profiles/nicholas-sauter>. Specific Responsibilities: - Continue work on the DIALS data integration suite. - Test new algorithms for optimally characterizing and merging data from serial crystallography experiments. - Analyze anomalous scattering from metalloenzymes using XFEL diffraction. - Investigate whether diffuse scattering can reveal correlated atomic motions in crystals. Required Qualifications: - Expertise in one or more computational techniques including, but not limited to, ray tracing to test underlying physical models of the diffraction, Bayesian approaches for refining model parameters, macromolecular modeling and refinement, neural networks for interpreting image features, as well as signal processing and denoising methods. - Extensive data analysis experience in crystallography or from more general bioimaging backgrounds are welcome. - We particularly encourage strong mathematical intuition and a track record of bringing new ideas and tools to fruition, as evidenced through written publication and clear presentation. Candidates should send an expression of interest, CV, and list of three references to Nick Sauter, nksauter(a)lbl.gov*. *Further details are posted at https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=82554. Nicholas K. Sauter, Ph. D. Computer Staff Scientist, Molecular Biophysics and Integrated Bioimaging Division Lawrence Berkeley National Laboratory 1 Cyclotron Rd., Bldg. 33R0345 Berkeley, CA 94720

1 0

Not wishing to raise this again but...
by R. D. Oeffner 13 Jun '16

13 Jun '16

Switching to git for the cctbx would be very liberating for developing and testing code I believe. If bisecting git hash values seems cumbersome one can always tag each commit with the number of previous commits made to the branch used for the build. These numbers are sequential and obviously straightforward to use for bisecting. We do this currently for the phaser git repo: https://git.csx.cam.ac.uk/x/cimr-phaser/phaser.git Rob Date: Mon, 13 Jun 2016 21:24:58 +0000 From: <richard.gildea(a)diamond.ac.uk> To: <cctbxbb(a)phenix-online.org> Subject: Re: [cctbxbb] Not wishing to raise this again but... Message-ID: <1BB183A24316FD4DA62A5F8B952D4291CC715321@exchmbx03> Content-Type: text/plain; charset="windows-1252" At least according to Google Trends, svn has been on a downward trend since about 2009/10, whereas git is still firmly on an upward trend (and overtook svn in popularity long ago): <https://www.google.co.uk/trends/explore#q=git%20commit%2C%20svn%20commit&cm…> https://www.google.co.uk/trends/explore#q=git%20commit%2C%20svn%20commit&cm… <https://www.google.co.uk/trends/explore#q=git%20commit%2C%20svn%20commit&cm…><https://www.google.co.uk/trends/explore#q=git%20commit%2C%20svn%20commit&cm…><https://www.google.co.uk/trends/explore#q=git%20commit%2C%20svn%20commit&cm…> [cid:162fa876-cc25-6335-73af-714b0957d71e] I think that avoiding a move to git is simply delaying the inevitable (and if the cctbx didn't ever move with the times then we'd still be stuck with CVS). In my opinion, the potential benefits to using git far outweigh the (slightly) added complexity. <https://www.google.co.uk/trends/explore#q=git%20commit%2C%20svn%20commit&cm…><https://www.google.co.uk/trends/explore#q=git%20commit%2C%20svn%20commit&cm…>Cheers, Richard ________________________________ From: cctbxbb-bounces(a)phenix-online.org [cctbxbb-bounces(a)phenix-online.org] on behalf of Nicholas Sauter [nksauter(a)lbl.gov] Sent: 13 June 2016 22:05 To: cctbx mailing list Subject: Re: [cctbxbb] Not wishing to raise this again but... I'd vote against the switch to git. Simple things, like svn update [remote directory] seem too complicated. As for slightly involved tasks like code bisection to locate the past commit that broke the test, well....I've never been able to figure this one out so I am pretty lost trying to debug DIALS. I do not wish to make things difficult for the maintenance of cctbx.xfel. Nick Nicholas K. Sauter, Ph. D. Computer Staff Scientist, Molecular Biophysics and Integrated Bioimaging Division Lawrence Berkeley National Laboratory 1 Cyclotron Rd., Bldg. 33R0345 Berkeley, CA 94720 (510) 486-5713 On Mon, Jun 13, 2016 at 8:52 AM, Luc Bourhis <luc_j_bourhis(a)mac.com<mailto:[email protected]>> wrote: On 13 Jun 2016, at 17:09, Graeme.Winter(a)Diamond.ac.uk<mailto:[email protected]> wrote: ? is there any enthusiasm out there for moving cctbx to git? The more I work with git the more I wish this existed properly for cctbx. I?ve raised this a bunch of times and always it is ?not right now? however ?a good idea? ? this?ll be the last time I ask? Could we move to git, please? I note the bootstrap script for Windows now has a git dependency even! +1 ? and time to share some thoughts! It would be great if we could get the cctbx up and running by just cloning, configuring and building without needing to download anything else. That could be done by adding SCons, Boost, and ccp4io as submodules in the cctbx repository. And I reckon ccp4io_adaptbx should be added as a subtree since it is developed by the same people as the cctbx. Just an idea to think about as I haven?t not worked out the details at all. Best wishes, Luc _______________________________________________ cctbxbb mailing list cctbxbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/cctbxbb -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

1 0

XQuartz 2.7.9 issue for OS X
by Billy Poon 11 Jun '16

11 Jun '16

Hi all, There seems to be an issue with XQuartz 2.7.9 on OS X when trying to render an OpenGL window (e.g. Coot, PyMOL, Phenix GLViewer) over SSH using X forwarding (i.e. ssh -Y). You will get an error that looks like X Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 150 (GLX) Minor opcode of failed request: 3 (X_GLXCreateContext) It seems like indirect rendering of a GLX context does not work properly on 2.7.9. Downgrading to XQuartz 2.7.8 works for me. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

1 0

Who is using bootstrap.py on Windows?
by Robert Oeffner 10 Jun '16

10 Jun '16

Hi all, I would like to know if there are teams other than Phenix and Dials-west in Berkeley doing regular builds on Windows using cctbx_project/libtbx/auto_build/bootstrap.py. I plan to make some simplifications of this script using the ssh client that is part of Git for Windows rather than the one found in the PuTTY suite which we use currently. Many thanks, Robert

2 1

Berkeley Server Downtime (6/3/2016)
by Billy Poon 01 Jun '16

01 Jun '16

Dear all, On Friday, June 3, our servers will be shutdown starting at 6:30 am Pacific for scheduled maintenance in our building (7 - 8 am). This will affect, - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) We expect that the servers will be available by 8:30 am Pacific at the latest. Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

1 0

The curious incident of the test at install time
by R. D. Oeffner 13 May '16

13 May '16

Hi Markus, Those changes were made by me and Oleg. I just tested a fresh installation of phenix-dev-2407-intel-linux-2.6-centos5 which is built with cctbx_project revision 24442. The test of cctbx_project/cctbx/regression/tst_grm_pickling.py passed without problems. I'm not aware of why this test is failing on dials after installation. Since the test is to do with the phenix restraints manager perhaps this test is not critical to dials. Perhaps the phenix restraints manager code together with this test should be moved into the phenix repository but that is not my call. Rob -----Original Message----- From: cctbxbb-request(a)phenix-online.org Sent: Friday, May 13, 2016 20:00 To: cctbxbb(a)phenix-online.org Subject: cctbxbb Digest, Vol 86, Issue 7 Message: 2 Date: Fri, 13 May 2016 09:47:18 +0000 From: <markus.gerstel(a)diamond.ac.uk> To: <cctbxbb(a)phenix-online.org> Subject: [cctbxbb] The curious incident of the test at install time Message-ID: <415F7F573406BB498256C68158D45674612998A2(a)EXCHMBX01.fed.cclrc.ac.uk> Content-Type: text/plain; charset=iso-8859-1 Hi everyone, we have observed the test cctbx_project/cctbx/regression/tst_grm_pickling.py to be failing, however only on an installation installed from the installer. It appears to run successfully on our bootstrapped developer build. I presume that the test requires some external data that we do not distribute? The relevant change occurred between r24437 and r24441, and is almost certainly r24439, which enabled the failing bit of the test. Stacktrace below. -Markus $ libtbx.python /dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/cctbx/regression/tst_grm_pickling.py Time pickling/unpickling: 0.0187, 0.0097 Traceback (most recent call last): File "/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/cctbx/regression/tst_grm_pickling.py", line 198, in <module> exercise_all(sys.argv[1:]) File "/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/cctbx/regression/tst_grm_pickling.py", line 195, in exercise_all test_nucleic_acid(mon_lib_srv, ener_lib) File "/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/cctbx/regression/tst_grm_pickling.py", line 177, in test_nucleic_acid log=null_out()) File "/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 5455, in run log=log) File "/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 5005, in __init__ restraints_loading_flags=restraints_loading_flags, File "/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 2956, in __init__ log=log, File "/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 2343, in __init__ m_j=mm) File "/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 1568, in get_lib_link return mon_lib_srv.link_link_id_dict["rna3p"] KeyError: 'rna3p' -- 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 ------------------------------ Message: 3 Date: Fri, 13 May 2016 09:50:03 +0000 From: <Graeme.Winter(a)diamond.ac.uk> To: <cctbxbb(a)phenix-online.org> Subject: Re: [cctbxbb] The curious incident of the test at install time Message-ID: <13999B6FC038EB44B067771E3CFBD091BC2E3E7A(a)EXCHMBX03.fed.cclrc.ac.uk> Content-Type: text/plain; charset="us-ascii" Markus I got this error this morning in the regular update / compile shuffle and it's on my to-nag list, also feel like I have seen this before... Cheerio G -----Original Message----- From: cctbxbb-bounces(a)phenix-online.org [mailto:[email protected]] On Behalf Of markus.gerstel(a)diamond.ac.uk Sent: 13 May 2016 10:47 To: cctbxbb(a)phenix-online.org Subject: [cctbxbb] The curious incident of the test at install time Hi everyone, we have observed the test cctbx_project/cctbx/regression/tst_grm_pickling.py to be failing, however only on an installation installed from the installer. It appears to run successfully on our bootstrapped developer build. I presume that the test requires some external data that we do not distribute? The relevant change occurred between r24437 and r24441, and is almost certainly r24439, which enabled the failing bit of the test. Stacktrace below. -Markus $ libtbx.python /dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/cctbx/regression/tst_grm_pickling.py Time pickling/unpickling: 0.0187, 0.0097 Traceback (most recent call last): File "/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/cctbx/regression/tst_grm_pickling.py", line 198, in <module> exercise_all(sys.argv[1:]) File "/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/cctbx/regression/tst_grm_pickling.py", line 195, in exercise_all test_nucleic_acid(mon_lib_srv, ener_lib) File "/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/cctbx/regression/tst_grm_pickling.py", line 177, in test_nucleic_acid log=null_out()) File "/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 5455, in run log=log) File "/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 5005, in __init__ restraints_loading_flags=restraints_loading_flags, File "/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 2956, in __init__ log=log, File "/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 2343, in __init__ m_j=mm) File "/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 1568, in get_lib_link return mon_lib_srv.link_link_id_dict["rna3p"] KeyError: 'rna3p' -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom _______________________________________________ cctbxbb mailing list cctbxbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/cctbxbb ------------------------------ _______________________________________________ cctbxbb mailing list cctbxbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/cctbxbb End of cctbxbb Digest, Vol 86, Issue 7 **************************************

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The curious incident of the test at install time
by markus.gerstel＠diamond.ac.uk 13 May '16

13 May '16

Hi everyone, we have observed the test cctbx_project/cctbx/regression/tst_grm_pickling.py to be failing, however only on an installation installed from the installer. It appears to run successfully on our bootstrapped developer build. I presume that the test requires some external data that we do not distribute? The relevant change occurred between r24437 and r24441, and is almost certainly r24439, which enabled the failing bit of the test. Stacktrace below. -Markus $ libtbx.python /dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/cctbx/regression/tst_grm_pickling.py Time pickling/unpickling: 0.0187, 0.0097 Traceback (most recent call last): File "/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/cctbx/regression/tst_grm_pickling.py", line 198, in <module> exercise_all(sys.argv[1:]) File "/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/cctbx/regression/tst_grm_pickling.py", line 195, in exercise_all test_nucleic_acid(mon_lib_srv, ener_lib) File "/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/cctbx/regression/tst_grm_pickling.py", line 177, in test_nucleic_acid log=null_out()) File "/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 5455, in run log=log) File "/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 5005, in __init__ restraints_loading_flags=restraints_loading_flags, File "/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 2956, in __init__ log=log, File "/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 2343, in __init__ m_j=mm) File "/dls/science/groups/scisoft/DIALS/CD/nightly/dials-dev20160513/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 1568, in get_lib_link return mon_lib_srv.link_link_id_dict["rna3p"] KeyError: 'rna3p' -- 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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easy_mp stack traces
by Graeme.Winter＠diamond.ac.uk 13 May '16

13 May '16

Dear Gabor, some time back Markus added the capability to retain stack traces through easy_mp execution. These were reverted which now means that by default the stack traces are lost :( I don't have a clear understanding what the exact design of the newly built scheduling/stacktrace system is, perhaps you could explain this since we’re in the dark here. We are however pretty certain that the corner cases that lead to you modifying the code do not apply to us with DIALS or xia2. Could you please advise how we can now enable the stacktrace to be preserved globally, in all cases, and for all dials.*/xia2.* programs? Just today this has come up twice, and is a support issue for us, see e.g. https://github.com/dials/dials/issues/139 where we are simply flying blind. Thanks in advance and best wishes, Graeme & xia2 / DIALS team -- 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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Installation with distutils?
by Luc Bourhis 09 May '16

09 May '16

Hi fellow cctbx developers, unless I am missing something, nobody has written a “setup.py” to install the cctbx with distutils in Python standard site-packages? If so, I am planning to contribute one as this would make it easier for us at Bruker. I am just asking in case I would duplicate existing work. Best wishes, Luc

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problem when using Python to convert from numpy array to flex.int array
by Jun Aishima 04 May '16

04 May '16

I have used the bootstrap method to build cctbx with my own Python (in a virtual environment). I setup my virtual environment, then source $CCTBX/build/setpaths.sh (bash). I am currently trying to turn a detector image (uint16) read in with fabio, which results in a numpy ndarray, and then turn that into a scitbx flex array. Since I've had problems doing this in my system, I've written a little script that reproduces the problem: ********** import fabio file=fabio.open('testcrystal_1_001.img') # adsc detector image file.data[0] from scitbx.array_family import flex flex.int(file.data[3071]) # this is a 3072x3072 image. For some reason, row 0 causes no problems. ********** At the end of this email is the stack trace I get. Has anybody had similar issues? I first saw this when I was trying to convert the entire image into a flex array, but now I've seen it with only one row [3071], while still working for [0:1500], so it doesn't seem like a simple memory issue. Any help would be appreciated. Jun Aishima ********** show_stack(1): <stdin>(1) <module> libc backtrace (23 frames, most recent call last): /home/aishimaj/spotter/bin/python() [0x414199] /lib64/libc.so.6(__libc_start_main+0xfd) [0x366d21ed5d] /home/aishimaj/spotter/bin/python(Py_Main+0xb22) [0x4150b2] /home/aishimaj/spotter/bin/python(PyRun_AnyFileExFlags+0x6b) [0x4ce82b] /home/aishimaj/spotter/bin/python(PyRun_InteractiveLoopFlags+0x4e) [0x4ce01e] /home/aishimaj/spotter/bin/python(PyRun_InteractiveOneFlags+0x1ff) [0x4cdd9f] /home/aishimaj/spotter/bin/python(PyEval_EvalCode+0x32) [0x4ad362] /home/aishimaj/spotter/bin/python(PyEval_EvalCodeEx+0x877) [0x4ad257] /home/aishimaj/spotter/bin/python(PyEval_EvalFrameEx+0x6a0b) [0x4aa8bb] /home/aishimaj/spotter/bin/python(PyObject_Call+0x47) [0x419ba7] /home/aishimaj/spotter/bin/python() [0x46df9f] /home/aishimaj/spotter/bin/python() [0x47623f] /home/aishimaj/spotter/bin/python(PyObject_Call+0x47) [0x419ba7] /home/aishimaj/spotter/bin/python() [0x42296f] /home/aishimaj/spotter/bin/python(PyObject_Call+0x47) [0x419ba7] /beamline/phenix/bootstrap/build/lib/libboost_python.so(+0x2d088) [0x7f5561101088] /beamline/phenix/bootstrap/build/lib/libboost_python.so(boost::python::handle_exception_impl(boost::function0<void>)+0x43) [0x7f5561112013] /beamline/phenix/bootstrap/build/lib/libboost_python.so(+0x2fe08) [0x7f5561103e08] /beamline/phenix/bootstrap/build/lib/libboost_python.so(boost::python::objects::function::call(_object*, _object*) const+0xef) [0x7f55611031ff] /beamline/phenix/bootstrap/build/lib/scitbx_array_family_flex_ext.so(boost::python::objects::signature_py_function_impl<boost::python::detail::caller<scitbx::af::versa<int, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > >* (*)(boost::python::numeric::array const&), boost::python::detail::constructor_policy<boost::python::default_call_policies>, boost::mpl::vector2<scitbx::af::versa<int, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > >*, boost::python::numeric::array const&> >, boost::mpl::v_item<void, boost::mpl::v_item<boost::python::api::object, boost::mpl::v_mask<boost::mpl::vector2<scitbx::af::versa<int, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > >*, boost::python::numeric::array const&>, 1>, 1>, 1> >::operator()(_object*, _object*)+0x52) [0x7f555ed68452] /beamline/phenix/bootstrap/build/lib/scitbx_array_family_flex_ext.so(scitbx::af::boost_python::flex_int_from_numpy_array(boost::python::numeric::array const&)+0x29) [0x7f555f039f79] /beamline/phenix/bootstrap/build/lib/scitbx_array_family_flex_ext.so(scitbx::af::versa<int, scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > > scitbx::af::boost_python::versa_flex_from_numpy_array<int>(boost::python::numeric::array const&)+0x1c87) [0x7f555f0415c7] /lib64/libc.so.6() [0x366d2326a0] Segmentation fault (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. Jun Aishima | Post Doc - MX | Australian Synchrotron p: (03) 8540 4114 | f: (03) 8540 4200 jun.aishima(a)synchrotron.org.au<mailto:[email protected]> | www.synchrotron.org.au 800 Blackburn Road, Clayton, Victoria 3168

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Algorithm developer postdoc opening at Berkeley National Lab
by Nicholas Sauter 28 Apr '16

28 Apr '16

Berkeley Lab's Molecular Biophysics and Integrated Bioimaging Division <http://biosciences.lbl.gov/divisions/mbib/> is looking for a Computational Biologist Postdoctoral Fellow to work in the Sauter group. We are seeking an algorithm developer for the increasingly complex analysis of large diffraction datasets in structural biology. Current projects utilize XFEL crystallography and spectroscopy to investigate the photosynthetic mechanism of water splitting and to probe other metalloenzyme reactions. We also wish to test whether diffuse scattering can reveal correlated atomic motions in crystals. Many problems remain to be solved, including the details of how to optimally merge datasets from thousands of crystals. Our software development projects (including packages such as DIALS <http://dials.lbl.gov> and cctbx.xfel <http://cci.lbl.gov/xfel>) have been highlighted in several high-impact publications listed HERE <http://biosciences.lbl.gov/profiles/nicholas-sauter>. Candidates should have expertise in one or more computational techniques including, but not limited to, ray tracing to test underlying physical models of the diffraction, Bayesian approaches for refining model parameters, macromolecular modeling and refinement, neural networks for interpreting image features, as well as signal processing and denoising methods. Extensive data analysis experience in crystallography or from more general bioimaging backgrounds are welcome. We particularly encourage strong mathematical intuition and a track record of bringing new ideas and tools to fruition, as evidenced through written publication and clear presentation. Candidates should send an expression of interest, CV, and list of three references to *Nick Sauter, nksauter(a)lbl.gov <nksauter(a)lbl.gov>.* Further details are posted at https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=82354. Nicholas K. Sauter, Ph. D. Computer Staff Scientist, Molecular Biophysics and Integrated Bioimaging Division Lawrence Berkeley National Laboratory 1 Cyclotron Rd., Bldg. 33R0345 Berkeley, CA 94720

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