January 2016 - cctbxbb - phenix-online.org

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

7 18

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

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?

8 10

FW: Mac builds currently broken on Jenkins
by markus.gerstel＠diamond.ac.uk 29 Jan '16

29 Jan '16

Sorry, this should have gone onto cctbx list. This is running bootstrap.py --builder=dials build on MacOS X, but I don't think it is specific to dials. -Markus From: Gerstel, Markus (DLSLtd,RAL,LSCI) Sent: 22 January 2016 08:51 To: dials-support(a)lists.sourceforge.net Subject: Mac builds currently broken on Jenkins During the build step this happens: (..) /usr/bin/c++ -o annlib_adaptbx/self_include/bd_fix_rad_search.o -c -DBOOST_ALL_NO_LIB -fPIC -fno-strict-aliasing -Wno-c++0x-extensions -Wno-array-bounds -DNDEBUG -O3 -ffast-math -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/build/include -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/boost -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/annlib -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/annlib/src -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/annlib/include -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/annlib_adaptbx/include -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/build/annlib_adaptbx/include annlib_adaptbx/self_include/bd_fix_rad_search.cpp In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/annlib_adaptbx/ann/ann_adaptor.cpp:3: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/annlib_adaptbx/include/annlib_adaptbx/ann_adaptor.h:4: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project/scitbx/array_family/flex_types.h:5: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project/scitbx/array_family/accessors/flex_grid.h:5: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project/scitbx/array_family/small.h:4: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project/scitbx/array_family/small_plain.h:4: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project/scitbx/array_family/tiny.h:4: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project/scitbx/array_family/tiny_plain.h:5: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project/scitbx/array_family/detail/misc.h:4: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project/scitbx/array_family/type_traits.h:29: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/boost/boost/type_traits.hpp:13: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/boost/boost/type_traits/add_const.hpp:16: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/boost/boost/type_traits/detail/type_trait_def.hpp:14: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/boost/boost/type_traits/detail/template_arity_spec.hpp:10: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/boost/boost/mpl/int.hpp:17: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/boost/boost/mpl/int_fwd.hpp:17: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/boost/boost/mpl/aux_/adl_barrier.hpp:17: /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/boost/boost/mpl/aux_/config/adl.hpp:17:10: fatal error: 'boost/mpl/aux_/config/msvc.hpp' file not found #include <boost/mpl/aux_/config/msvc.hpp> ^ /usr/bin/c++ -o annlib_adaptbx/self_include/bd_pr_search.o -c -DBOOST_ALL_NO_LIB -fPIC -fno-strict-aliasing -Wno-c++0x-extensions -Wno-array-bounds -DNDEBUG -O3 -ffast-math -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/build/include -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/boost -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/annlib -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/annlib/src -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/annlib/include -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/annlib_adaptbx/include -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/build/annlib_adaptbx/include annlib_adaptbx/self_include/bd_pr_search.cpp /usr/bin/c++ -o annlib_adaptbx/self_include/bd_search.o -c -DBOOST_ALL_NO_LIB -fPIC -fno-strict-aliasing -Wno-c++0x-extensions -Wno-array-bounds -DNDEBUG -O3 -ffast-math -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/build/include -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/boost -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/annlib -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/annlib/src -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/annlib/include -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/annlib_adaptbx/include -I/Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/build/annlib_adaptbx/include annlib_adaptbx/self_include/bd_search.cpp In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/annlib_adaptbx/ann/boost_python/annlib_ext.cpp:2: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/annlib_adaptbx/include/annlib_adaptbx/ann_adaptor.h:4: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project/scitbx/array_family/flex_types.h:5: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project/scitbx/array_family/accessors/flex_grid.h:5: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project/scitbx/array_family/small.h:4: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project/scitbx/array_family/small_plain.h:4: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project/scitbx/array_family/tiny.h:4: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project/scitbx/array_family/tiny_plain.h:5: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project/scitbx/array_family/detail/misc.h:4: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/cctbx_project/scitbx/array_family/type_traits.h:29: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/boost/boost/type_traits.hpp:13: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/boost/boost/type_traits/add_const.hpp:16: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/boost/boost/type_traits/detail/type_trait_def.hpp:14: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/boost/boost/type_traits/detail/template_arity_spec.hpp:10: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/boost/boost/mpl/int.hpp:17: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/boost/boost/mpl/int_fwd.hpp:17: In file included from /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/boost/boost/mpl/aux_/adl_barrier.hpp:17: /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules/boost/boost/mpl/aux_/config/adl.hpp:17:10: fatal error: 'boost/mpl/aux_/config/msvc.hpp' file not found #include <boost/mpl/aux_/config/msvc.hpp> ^ 1 error generated. scons: *** [annlib_adaptbx/ann/ann_adaptor.o] Error 1 1 error generated. scons: *** [annlib_adaptbx/ann/boost_python/annlib_ext.o] Error 1 scons: building terminated because of errors. usr+sys time: 3.36 seconds, ticks: 13399823, micro-seconds/tick: 0.251 wall clock time: 15.72 seconds Performing actions: build ===== Running in .: deleting dist, tests, tmp removing .pyc files in /Users/dlshudson/jenkins_slave/workspace/dials_package_macosx/build_dials/modules removed 3 files ===== Running in build: run configure.py ===== Running in build: save configure command ===== Running in build: libtbx.scons Process failed with return code 2 Build step 'Execute shell' marked build as failure -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 4

dependency on phenix
by Roger Martin 26 Jan '16

26 Jan '16

Hi, looking through http://sourceforge.net/p/cctbx/code/HEAD/tree/trunk/mmtbx/refinement/minimi… shows at line 61 from phenix.refinement import weight_xray_chem and http://sourceforge.net/p/cctbx/code/HEAD/tree/trunk/mmtbx/refinement/occupa… line 134 Is weight_xray_chem.py code that could move to cctbx? (cctbx_project/mmtbx/refinement/weight_xray_chem.py) Are there other cross dependencies?

2 2

Git (again)
by Graeme.Winter＠diamond.ac.uk 15 Jan '16

15 Jan '16

Hi Folks so, while this is tangential to the discussion of whether or not to move to git, I will observe that our chosen repo supplier appears to be taking some down time again: [gw56@ws133 format]$ svn commit -m "Comment about application of this format" Sending format/FormatSMVRigakuEiger1M.py Transmitting file data .svn: Commit failed (details follow): svn: Can't create directory '/svn/p/cctbx/code/db/transactions/23592-1.txn': Permission denied Over the last year this has not been such a rare occurrence and is always annoying when it does happen. The sourceforge.net website is temporarily in static offline mode. Only a very limited set of project pages are available until the main website returns to service. While this is I agree unrelated to the revision control we elect to use, it should perhaps be part of the same discussion. Meanwhile, all builds for dials will be gone until sf.net is once again live... awesome! Cheerio 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

2 1

Re: [cctbxbb] dials install error
by markus.gerstel＠diamond.ac.uk 13 Jan '16

13 Jan '16

Dear Sid, Unfortunately I don't know what the proper solution to your problem is. We had issues with pango/glibc reported just a few days ago, but I don't know what the outcome to that was. Dear David, Nick, Billy, Following up on the discussion in the thread 'bootstrap.py build on Ubuntu', here is an installer failure on CentOS5 that comes down to pango/libfontconfig/libglib missing some libraries, trace attached. -Markus From: Sidhu, Khushwant (Dr.) [mailto:[email protected]] Sent: 12 January 2016 11:26 To: Gerstel, Markus (DLSLtd,RAL,LSCI) Cc: Sidhu, Khushwant (Dr.) Subject: Re: dials install error Dear Markus, using the --verbose flag, I get the following .... ./install --verbose (snip) : Regenerating module files in /usr/local/dials-dev20160112/base : generating pangorc file at /usr/local/dials-dev20160112/base/etc/pango/pangorc : generating pango.modules file at /usr/local/dials-dev20160112/base/etc/pango/pango.modules : /usr/local/dials-dev20160112/base/bin/pango-querymodules: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by /usr/local/dials-dev20160112/base/lib/libfontconfig.so.1) : /usr/local/dials-dev20160112/base/bin/pango-querymodules: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by /usr/local/dials-dev20160112/base/lib/libglib-2.0.so.0) : Traceback (most recent call last): : File "/usr/local/dials-dev20160112/modules/cctbx_project/libtbx/configure.py", line 22, in <module> : if not run(): : File "/usr/local/dials-dev20160112/modules/cctbx_project/libtbx/configure.py", line 17, in run : libtbx.env_config.cold_start(sys.argv) : File "/usr/local/dials-dev20160112/modules/cctbx_project/libtbx/env_config.py", line 2267, in cold_start : env.refresh() : File "/usr/local/dials-dev20160112/modules/cctbx_project/libtbx/env_config.py", line 1544, in refresh : regenerate_module_files.run(libtbx.env.under_base('.'), only_if_needed=True) : File "/usr/local/dials-dev20160112/modules/cctbx_project/libtbx/auto_build/regenerate_module_files.py", line 153, in run : fix_pango(base_dir, out) : File "/usr/local/dials-dev20160112/modules/cctbx_project/libtbx/auto_build/regenerate_module_files.py", line 59, in fix_pango : call(("%s/bin/pango-querymodules > %s") % (base_dir, pangomodules), log=out) : File "/usr/local/dials-dev20160112/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 '/usr/local/dials-dev20160112/base/bin/pango-querymodules > /usr/local/dials-dev20160112/base/etc/pango/pango.modules' failed with exit code 1 Traceback (most recent call last): File "/usr/local/dials-installer-dev/bin/install.py", line 46, in ? installer(sys.argv[1:]).install() File "/usr/local/dials-installer-dev/lib/libtbx/auto_build/install_distribution.py", line 197, in install self.install_from_binary() File "/usr/local/dials-installer-dev/lib/libtbx/auto_build/install_distribution.py", line 318, in install_from_binary self.reconfigure(log=log) File "/usr/local/dials-installer-dev/lib/libtbx/auto_build/install_distribution.py", line 484, in reconfigure call(args=args, log=log, verbose=self.options.verbose) File "/usr/local/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 '/usr/local/dials-dev20160112/base/bin/python /usr/local/dials-dev20160112/modules/cctbx_project/libtbx/configure.py --current_working_directory /usr/local/dials-dev20160112/build dials xia2' failed with exit code 1 regards Sid -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

3 2

status of mmtbx/phenix.molprobity
by Marcin Wojdyr 04 Jan '16

04 Jan '16

Dear All, we'd like to use mmtbx validation code. Is all the code in mmtbx meant to be open-source, even if the dispatchers have names starting with phenix? In particular I'm thinking about phenix.molprobity. (the names are not a problem, I just want to double check that it's ok if we use it) All the best in 2016, Marcin

2 1