[cctbxbb] Compiling CCTBX with newer GCC on Mac

Fri Aug 18 02:08:06 PDT 2017

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>
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
> Email:    lance at quantumbioinc.com
>
> Phone:   814-235-6908 <(814)%20235-6908>
> Fax:        814-235-6909 <(814)%20235-6909>
>
>
> This message and any attachments are solely for the intended recipient and
> should be considered confidential. If you are not the intended recipient,
> please immediately and permanently delete.
>
> On Aug 16, 2017, at 6:42 PM, Billy Poon <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
> Fax: (510) 486-5909
> Web: https://phenix-online.org
>
> On Wed, Aug 16, 2017 at 2:49 PM, Lance Westerhoff <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
>> Email:    lance at quantumbioinc.com
>>
>>
>>
>>
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>> cctbxbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/cctbxbb
>>
>
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