[cctbxbb] Compiling CCTBX with newer GCC on Mac
Lance Westerhoff
lance at quantumbioinc.com
Fri Aug 18 09:24:39 PDT 2017
Hi Gabor-
Actually, the whole reason we chose to build CCTBX on Mac was to get a library which can take C++11 strings, etc. (since we shifted to C++11 years ago - hence the requirement that we rebuild CCTBX using gcc6.x)
I can’t [yet] speak for the Mac version of CCTBX, but the Linux version - at least for the functions we use - have been working great for some time. I guess we shall see if that carries forward with the Mac version. I think we should know within hours.
For a test and to help you debug, even though we can’t use the library w/o C++11, I’m glad to try it and send you the results. How does one pass a compiler flag into the CCTBX build system? (the default for gcc-6.3 is to build with C++11 so indeed I will need to pass in -std=c++98 in order to complete the test)
-Lance
> On Aug 18, 2017, at 5:08 AM, Gabor Bunkoczi <gabor.bunkoczi at googlemail.com> wrote:
>
> 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 <lance at quantumbioinc.com <mailto:lance at quantumbioinc.com>> 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<long unsigned int, boost::property<boost::edge_weight_t, boost::python::api::object> >::stored_edge_property(const boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, boost::python::api::object> >&)’
> { ::new(static_cast<void*>(__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<long unsigned int, boost::property<boost::edge_weight_t, boost::python::api::object> >::stored_edge_property(const boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, boost::python::api::object> >&)’ is implicitly declared as deleted because ‘boost::detail::stored_edge_property<long unsigned int, boost::property<boost::edge_weight_t, boost::python::api::object> >’ 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.
>
> WWW: http://www.quantumbioinc.com <http://www.quantumbioinc.com/>
> Email: lance at quantumbioinc.com <mailto:lance at quantumbioinc.com>
>
> Phone: 814-235-6908 <tel:(814)%20235-6908>
> Fax: 814-235-6909 <tel:(814)%20235-6909>
>
>
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>
>> On Aug 16, 2017, at 6:42 PM, Billy Poon <BKPoon at lbl.gov <mailto:BKPoon at lbl.gov>> 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 <tel:(510)%20486-5709>
>> Fax: (510) 486-5909 <tel:(510)%20486-5909>
>> Web: https://phenix-online.org <https://phenix-online.org/>
>> On Wed, Aug 16, 2017 at 2:49 PM, Lance Westerhoff <lance at quantumbioinc.com <mailto:lance at quantumbioinc.com>> 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 <http://www.quantumbioinc.com/>
>> Email: lance at quantumbioinc.com <mailto:lance at quantumbioinc.com>
>>
>>
>>
>>
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