August 2017 - cctbxbb - phenix-online.org

Compiling CCTBX with newer GCC on Mac
by Lance Westerhoff 04 Oct '17

04 Oct '17

Hello All- How does one introduce an alternate gcc compiler for CCTBX on Mac? I must be missing it in the documentation. I don’t want to use the old one in /usr/bin (and instead I want to you my newer one in /opt/gcc). I’ve tried all of the standard methods used by other build systems (change the $PATH, set $CXX and $CC, etc) but to no avail. These environment variables seem to be disregarded. We do use this compiler for building CCTBX on linux without too much trouble, so I think the support should be there. Specifically: mac-build64:build jenkins$ env | grep CXX CXX=/opt/gcc/current/bin/g++ mac-build64:build jenkins$ env | grep CC CC=/opt/gcc/current/bin/gcc mac-build64:build jenkins$ which gcc /opt/gcc/current/bin/gcc mac-build64:build jenkins$ g++ -v Using built-in specs. COLLECT_GCC=g++ COLLECT_LTO_WRAPPER=/opt/gcc/gcc-6.3.0-08092017/libexec/gcc/x86_64-apple-darwin11.4.2/6.3.0/lto-wrapper Target: x86_64-apple-darwin11.4.2 Configured with: ../gcc-6.3.0/configure --prefix=/opt/gcc/gcc-6.3.0-08092017 --enable-languages=c,c++,fortran,objc --with-gmp=/opt/gcc/gcc-6.3.0-08092017 --with-mpfr=/opt/gcc/gcc-6.3.0-08092017 --with-mpc=/opt/gcc/gcc-6.3.0-08092017 --enable-libgomp --disable-multilib Thread model: posix gcc version 6.3.0 (GCC) mac-build64:build jenkins$ /opt/python/current/bin/python ../modules/cctbx_project/libtbx/configure.py cctbx Python: 2.7.9 "/opt/python/current/bin/python" Compiler: default .... This script is only applicable to Linux - exiting. Done. mac-build64:build jenkins$ make ./bin/libtbx.scons -j "`./bin/libtbx.show_number_of_processors`" scons: Reading SConscript files ... On MacOS, using clang 4.2.0 Xcode 4.6.3 Build version 4H1503 ... Thanks for your help! -Lance ____________________ Lance M. Westerhoff, Ph.D. President and General Manager QuantumBio Inc. WWW: http://www.quantumbioinc.com Email: lance(a)quantumbioinc.com

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Should we enable boost threads in bootstrap?
by Graeme.Winter＠diamond.ac.uk 28 Sep '17

28 Sep '17

Afternoon all, Should we do this? Any opinions? Could be useful for threads in a semi-portable way... Thanks & 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

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rna3p error
by Haiguang Liu 31 Aug '17

31 Aug '17

Dear All, I recently run into an error while processing DNA molecules using pdb_interpreter. The error message is as the following: File "/Users/hgliu/test/cctbx/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 5419, in __init__ restraints_loading_flags=restraints_loading_flags) File "/Users/hgliu/test/cctbx/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 3221, in __init__ log=log, File "/Users/hgliu/test/cctbx/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 2507, in __init__ m_j=mm, File "/Users/hgliu/test/cctbx/modules/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 1693, in get_lib_link return mon_lib_srv.link_link_id_dict["rna3p"] KeyError: 'rna3p' After searching through the threads, I found the same error has been reported, but no solution posted. Any suggestion is appreciated. Best, haiguang

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Berkeley servers are back in service
by Billy Poon 03 Aug '17

03 Aug '17

Hi everybody, The servers at Berkeley are now available. Please let us know of any issues. 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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Emergency shutdown
by Nigel Moriarty 02 Aug '17

02 Aug '17

Folks Phenix servers are shutting down due to a grass fire in the area. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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Changing boost versions
by Nicholas Devenish 01 Aug '17

01 Aug '17

Hi All, Graeme's thread reminded me to ask about something I've been struggling with; is there a built-in/easy way to specify a different installation of boost to use? The build seems to construct lib boost_python manually, for some reason, so I don't know how easy it is to disentangle. Thanks, Nick

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