- cctbxbb - phenix-online.org

sequential revision number from git repo
by R.D. Oeffner 05 Apr '16

05 Apr '16

Hi, We are slowly moving phaser svn to git. One issue that we would like to address is if there is a practical way of conveying a linear commit history from the git repo. One approach is to just count the number of revisions that was made to the master branch in the git repo with "git rev-list --count HEAD" and then pretend that number is a revision number. This enables us to tell users "This bug was fixed after revision 6456 of phaser" rather than "This bug was fixed after commit 29b0a1c... of phaser". Is there any pitfalls with this approach? What workarounds do other people using git come up with? Rob -- Robert Oeffner, Ph.D. Research Associate, The Read Group Department of Haematology, Cambridge Institute for Medical Research University of Cambridge Cambridge Biomedical Campus Wellcome Trust/MRC Building Hills Road Cambridge CB2 0XY www.cimr.cam.ac.uk/investigators/read/index.html tel: +44(0)1223 763234 mobile: +44(0)7712 887162

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changes to cctbx we have in ccp4
by Marcin Wojdyr 04 Apr '16

04 Apr '16

Hi All, we have a bunch of changes to cctbx in ccp4. If any of them are of general interest I can push them to svn. They'd need some cleanup before applying, so I'm not attaching any patches for now. - option to use external Boost. It's the same what debian and gentoo distros are doing when packaging cctbx. We change a few lines in the scons scripts and rm cctbx_project/boost/* (but the boost directory itself must be present). We could add an option for it (--use-system-boost ?). - removing -funroll-loops - this option must be a historical leftover. Generally it's better to let compiler decide because unrolling loops may make the program slower as well as faster. I tested it on Phaser a couple years ago. The only noticeable effect of this flag was much bigger binary. - extend --use-environment-flags to handle also CC and CXX. With most of makefiles / build scripts, if the user has multiple compilers installed he selects one with CC=gcc-mp-5 etc. Then if the build script really needs to differentiate between compilers it tries to determine what kind of compiler it is. In cctbx it's the other way around - the --compiler flag tells what kind of compiler it is and the build script guesses executable names. For ccp4 I added in two places in libtbx/SConscript: + if libtbx.env.build_options.use_environment_flags: + if 'CC' in os.environ: cc = os.environ['CC'] + if 'CXX' in os.environ: cxx = os.environ['CXX'] so for _some_ platform/compiler combinations it's possible to use compilers with non-default names. Useful for systems with multiple GCC versions. - probe and reduce are called in mmtbx through phenix wrappers (phenix.probe and phenix.reduce). We prefer to call them directly, but I guess it's not to be changed in cctbx. But after changing the name I also had to remove error checking in mmtbx/validation/clashscore.py that checks return code from phenix.reduce. Reduce itself quite often returns non-zero, it's just that the phenix.reduce wrapper ignores it and always returns 0 (probably not intentionally). - cctbx_project/spotfinder/SConscript - on Windows we have to link dxtbxspotfinder with spotfinder. That's the only such problem when compiling cctbx. OTOH it apparently works for everyone else. I don't know why. It must have something to do with us using MinGW. - A couple of #ifdefs for compiling with MinGW (annlib and gltbx) Marcin

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Berkeley Server Downtime (3/30/2016)
by Billy Poon 30 Mar '16

30 Mar '16

Dear all, On Wednesday, March 30, our servers will be shutdown starting at 7:00 am Pacific for scheduled maintenance in our server room. 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 5 pm 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

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new parallel_map implementation
by Gabor Bunkoczi 29 Mar '16

29 Mar '16

Hi, I have switched over libtbx.easy_mp.parallel_map to use new code that is not susceptible to deadlock when large amounts of data are returned from a worker process. This also means that parameters added to parallel_map to prevent exactly this are no longer necessary (but will be respected), although unlikely to influence performance so much to warrant changing existing code. I have run all tests, but unsure how well this gets tested by regression test, so please let me know if you come across something that is amiss. BW, Gabor

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Troublesome Hall Symbols in CIF
by Luc Bourhis 21 Mar '16

21 Mar '16

Hi, Consider the following two Hall symbols: (1) -C 2y (x,y,-x+z) (2) -I 2y They represent the same setting of the same spacegroup, so in a perfect world the fact that the sgtbx comes with (1) from some list of operators should not matter. Unfortunately, (1) is rejected by CheckCIF right now. Reminder: every single small molecule publication in Acta Cryst. must pass CheckCIF. On the contrary, CheckCIF accepts (2). Yes, I know, this is a bug in CheckCIF. But the IUCR is very slow at fixing bug in that kerberos of a program and we do therefore put our Olex2 users in trouble when they use the smtbx to refine their structure, as opposed to ShelXL, which does output (2). Besides, (2) is clearly more pleasing to the human mind than (1). Thus I reckon there is definitively a case to make a change in the cctbx here. The question is at which level? I don’t think we want to touch the sgtbx. I am of the opinion of patching iotbx.cif. Would that cause any trouble in Phenix and consort? Any remark or suggestion? Best wishes, Luc

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New top-level module: fast_linalg
by Luc Bourhis 07 Mar '16

07 Mar '16

Hi, this is an advanced warning for the introduction of a new top-level module named fast_linalg. In a couple of days, I will push it in one go as 25 commits but don’t be scared, nothing is changed outside the top directory fast_linalg, which also means it is not configured by default. Thus there cannot be any disruption but I thought it would be polite to warn all cctbx developers. The module features the automatic installation and integration of OpenBLAS which I have used to speed up smtbx refinement. I will commit that work later. Best wishes, Luc J. Bourhis

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Dead link for old builds on cctbx_build page
by Luc Bourhis 06 Mar '16

06 Mar '16

Hi, on http://cci.lbl.gov/cctbx_build/, in the phrase “ Old code bundles prior to 2015 may be accessed here.”, the word “here" is a link toward http://cci.lbl.gov/cctbx_legacy_build but this is a dead link. Is this a typo or are those builds truly gone? Best wishes, Luc

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libtbx.easy_mp semantics
by markus.gerstel＠diamond.ac.uk 23 Feb '16

23 Feb '16

Hello everyone, Could someone please explain the libtbx.easy_mp semantics to me? Currently, if you run easy_mp with multiple processes, objects are 'reset' back to their original state, ie. the state of the object in the main thread is retained, changes in the processing threads are dropped. However if you run easy_mp with the number of processes set to 1, object states are modified, because the main thread is the executing thread. How it this supposed to work? For a more detailed test please run $ libtbx.python libtbx/tst_easy_mp_state.py The source code explains the test in more detail. This behaviour currently causes dials.integrate to fail on bzipped input files. Given that this code is used in many places and this particular feature is not obvious, it may explain other anecdotal emergent behaviour, too. -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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FW: Problems with cctbx - Explore symmetry
by robert.mcmeeking＠stfc.ac.uk 19 Feb '16

19 Feb '16

Dear Colleagues I may not have sent my previous message to the most appropriate email address. I now forward including the "phenix-online.org" one. Is there anyone out there who can point me in the right direction? Best Regards Bob From: McMeeking, Robert (STFC,DL,SC) Sent: 13 February 2016 12:18 To: cctbx(a)cci.lbl.gov Cc: McMeeking, Robert (STFC,DL,SC) Subject: Problems with cctbx - Explore symmetry Hello from the UK I am currently experiencing problems with the Explore symmetry web service - http://cci.lbl.gov/cctbx/explore_symmetry.html. When dealing with a particular Hall Symbol there is a cctbx runtime error (Malformed matrix symbol). The symbol in question is: -R 3 2"c It represents a setting for Space Group R -3 c :H (167) I am practically certain this worked fine in the past. I suspect the problem may be related to parsing the double quote symbol. If I replace with a single quote it manages to run OK, but the output information is a non-standard setting for Space Group 165. By way of background: I call the web service from my own CGI script and extract the symmetry operators that I need to display the crystal structure in question. The Hall symbol used is from the Crystallographic Open Database CIF (COD 2100992). I noticed the problem very recently, but because I cache information it is not clear when the problem first appeared. I only need to go through this process when explicit symmetry operators are not present in the CIF in question. I have not, as yet, installed the cctbx system on our server. Inoticed the problem when using our CrystalWorks system to attempt to display entries from the Crystallography365 Project http://cds.dl.ac.uk/cgi-bin/rfm/crystalworks_365?Feb17 Best Regards Bob Dr R.F. McMeeking Honorary Scientist STFC Chemical Database Service at Daresbury

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Updated base dependencies (not Boost)
by Billy Poon 19 Feb '16

19 Feb '16

Hi all, I have a set of new dependencies for base running on a CentOS 6.7 machine. The tests for PHENIX pass, but I'm still testing the GUI. It looks like most of the DIALS tests pass, but there are some that fail due to an updated Python Imaging Library. Testing will take a while longer, but I attached the modified install_base_packages.py and package_defs.py scripts for anyone who wants to try it out. Just use these in place of the ones in cctbx_project/libtbx/auto_build. I'll also clean up the scripts (e.g. remove cruft from the migration to wxPython 3.0.2, refactor some functions) once testing is complete. Aaron and I will be setting up "clean" virtual machine images for CentOS 5, 6, and 7, and Ubuntu 12.04, and 14.04, and eventually Windows 10 and maybe OS X (only Server can be virtualized) for testing the installers. The goal is to simulate what a user would get from a fresh install of an OS and test that our installers work correctly. And after each test, we can revert the virtual machine to an earlier snapshotted state. This should help in debugging some of the recent installation issues. Since our installers include the GUI, the Linux images will have their respective desktop GUIs installed (desktop version instead of server version). We thought about going with minimal server installs, but there are external dependencies, namely X11/Xorg, that we expect the users to have, and installing the desktop GUI would be the easiest way to satisfy any external dependency. Some highlights from the updates, 1) Python Imaging Library has not been updated since 2009. There is an active fork called Pillow that seems to be mostly backwards compatible. I have noticed one change in the API (replace PIL.Image.fromstring with PIL.Image.frombytes), but more testing is needed. 2) The updated version of ReportLab depends on Pillow. 3) GTK2 was not updated to GTK3 since it seems like wxPython only added support for GTK3 in 3.0.2. GTK2 is updated to the latest version. Dependencies for GTK2 (cairo, pango, etc.) are updated. An additional package, HarfBuzz, is needed. 4) libPNG was updated only to 1.5.x, not 1.6.x, because 1.6.x has some stricter checks on the image. Warnings are raised in the GUI. Eventually, this can be upgraded to 1.6.x, but I would need to reprocess all of the PNG icons to remove the offending bits. 5) libFFI was added for the updated version of glib. The updated dependencies have been built on CentOS 5, 6, and 7, and OS X 10.10, but not all the tests have been run yet. The 32-bit version of CentOS 5 is going to require some more work before the updated packages will compile. Let me know if there are any questions or suggestions. Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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