Re: [cctbxbb] Compiling CCTBX with newer GCC on Mac

Hi Lance, presumably the Boost Graph Library is not C++11 compliant, so I would first try to remove the "-std=c++11" flag from your command line (to be safe, you can set it explicitly to -std=c++98). Can you try and let me know whether it works? BTW, I am unsure whether the entire cctbx is c++11 compliant. BW, Gabor On Thu, Aug 17, 2017 at 10:03 PM, Lance Westerhoff wrote:

Hi Billy-

That one worked - thanks!

Now, whether it compiles with the much newer compiler: yes and no. We have two different versions of cctbx on site here. We have been using a version approximating #992 on the Linux side for months. That was our last pull and for our needs, it seems to be working well on linux. That one builds just fine on Mac OS X as well when I perform the following steps. However, when I try to build the much more recent version (#1131), that is when I run into trouble and I I get the following errors. For the most part, because #992 seems to work for Linux for what we need, we should be ok but I wanted to send a report in case this is something you would like to fix. At the moment, we are moving forward. I’ll let you know how things pan out as we actually start to use the Mac CCTBX as hard as we already use the Linux CCTBX.

Thanks for your help!

mac-build64:build jenkins$ which gcc /opt/gcc/current/bin/gcc

mac-build64:build jenkins$ gcc -v Using built-in specs. COLLECT_GCC=gcc 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 iotbx --compiler=gcc --enable-cxx11 Python: 2.7.9 "/opt/python/current/bin/python" Compiler: gcc 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: True Force true division: True command_version_suffix: None .....

mac-build64:build jenkins$ make ./bin/libtbx.scons -j "`./bin/libtbx.show_number_of_processors`" scons: Reading SConscript files ... On MacOS, using gcc 6.3.0Xcode 4.6.3 Build version 4H1503

libtbx.scons: OpenMP is disabled. BOOST_VERSION: 105600 ......

/private/var/lib/jenkins-release/workspace/tmp/ newbuild-1131/modules/cctbx_project/boost_adaptbx/graph/graph_ext.cpp:337:5: required from here /opt/gcc/gcc-6.3.0-08092017/include/c++/6.3.0/bits/stl_construct.h:75:7: error: use of deleted function ‘boost::detail::stored_edge_property >::stored_edge_property(const boost::detail::stored_edge_property >&)’ { ::new(static_cast(__p)) _T1(std::forward<_Args>(__args)...); } ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /private/var/lib/jenkins-release/workspace/tmp/ newbuild-1131/modules/boost/boost/graph/adjacency_list.hpp:246:0, from /private/var/lib/jenkins-release/workspace/tmp/ newbuild-1131/modules/cctbx_project/boost_adaptbx/graph/graph_type.hpp:5, from /private/var/lib/jenkins-release/workspace/tmp/ newbuild-1131/modules/cctbx_project/boost_adaptbx/graph/graph_ext.cpp:1: /private/var/lib/jenkins-release/workspace/tmp/ newbuild-1131/modules/boost/boost/graph/detail/adjacency_list.hpp:290:11: note: ‘boost::detail::stored_edge_property

...

::stored_edge_property(const boost::detail::stored_edge_property >&)’ is implicitly declared as deleted because ‘boost::detail::stored_edge_property >’ declares a move constructor or move assignment operator class stored_edge_property : public stored_edge<Vertex> { ^~~~~~~~~~~~~~~~~~~~ g++ -o boost_adaptbx/graph/maximum_clique_ext.o -c -DBOOST_ALL_NO_LIB -std=c++11 -DBOOST_PYTHON_MAX_BASES=2 -I/private/var/lib/jenkins- release/workspace/tmp/newbuild-1131/modules/boost -fPIC -fno-strict-aliasing -w -DNDEBUG -O3 -ffast-math -I/private/var/lib/jenkins- release/workspace/tmp/newbuild-1131/modules/cctbx_project -I/private/var/lib/jenkins-release/workspace/tmp/newbuild-1131/build/include -I/private/var/lib/jenkins-release/workspace/tmp/newbuild-1131/build/include -I/opt/python/Python-2.7.9-01292015/include/python2.7 /private/var/lib/jenkins-release/workspace/tmp/ newbuild-1131/modules/cctbx_project/boost_adaptbx/graph/ maximum_clique_ext.cpp scons: *** [boost_adaptbx/graph/graph_ext.o] Error 1 scons: building terminated because of errors. usr+sys time: 4.25 seconds wall clock time: 2 minutes 15.94 seconds (135.94 seconds total) make: *** [default] Error 2

-Lance ____________________ Lance M. Westerhoff, Ph.D. President and General Manager QuantumBio Inc.

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On Aug 16, 2017, at 6:42 PM, Billy Poon wrote:

Hi Lance,

Can try adding the "--compiler=gcc" flag to your configure.py command? That should use your custom gcc compiler since it's the first one that's found on your path. When you run "make," you should see a line that looks like "On MacOS, using gcc 4.8.5", but with your version of gcc. The latest gcc that I have tested is 5.4.0 on Ubuntu 16.04, so I do not know if everything will compile with gcc 6.3.0

-- 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

On Wed, Aug 16, 2017 at 2:49 PM, Lance Westerhoff

...

wrote:

...

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: [email protected]

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