February 2016 - cctbxbb - phenix-online.org

Boost Python 1.56
by Luc Bourhis 14 Apr '17

14 Apr '17

Hi, I have improvements to the smtbx on their way to be committed which require Boost version 1.56. This is related to Boost.Threads, whose support I re-activated a few months ago on Nick’s request. I need the function boost::thread::physical_concurrency which returns the number of physical cores on the machine, as opposed to virtual cores when hyperthreading is enabled (which it is by default on any Intel machine). That function is not available in Boost 1.55 which is the version currently used in the nightly tests: it appeared in 1.56. So, would it be possible to move to Boost 1.56? Otherwise, I will need to backport that function. Not too difficult but not thrilling. Best wishes, Luc

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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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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

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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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mon_lib dependency
by Roger Martin 01 Feb '16

01 Feb '16

Hi, looking at the prebuilts(http://cci.lbl.gov/cctbx_build/dev-565/cctbx-installer-dev-565-in… for CentOS I see the dependency for mon_lib in verify_mon_lib_data.py. Is mon_lib available stand alone or comes in the full ccp4 package only? Where do most of you get a copy of mon_lib?

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