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.

WWW: http://www.quantumbioinc.com Email: [email protected]

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 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]

_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

Hi Lance, apologies for the late response. I was not aware that C++11 setting is deliberate, in this case my suggestion is clearly not helpful. Could you send me the entire error message from the compiler? It looks like this has been clipped at the outermost stack (perhaps you need to enable more verbose output to get this - for this you can just run directly the command that failed, i.e. "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") Also, can you clarify which versions of CCTBX you are trying to build (with the revision hash), and whether this is a problem on both Linux and Mac. Unfortunately, my knowledge of C++11 is somewhat hazy (to put it in a mild way), and I am unsure whether I will be able to help further, but I am happy to have a good look. To answer your last question, you can try using --use_environment_flags at the configure stage, after setting CXXFLAGS, etc (I have not checked whether this works, but the option exists). BW, Gabor On Fri, Aug 18, 2017 at 5:24 PM, Lance Westerhoff wrote:

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 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 < [email protected]> 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-relea se/workspace/tmp/newbuild-1131/modules/boost/boost/ graph/adjacency_list.hpp:246:0, from /private/var/lib/jenkins-relea se/workspace/tmp/newbuild-1131/modules/cctbx_project/ boost_adaptbx/graph/graph_type.hpp:5, from /private/var/lib/jenkins-relea se/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-rel ease/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: [email protected]

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 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 < [email protected]> 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]

_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

_______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

Hi Lance, I have (admittedly accidentally, because I was not aware of the default in gcc7.2) successfully compiled CCTBX with cxx11 (actually, cxx14, but presumably cxx11 would work as well), and I can confirm that with Boost 1.63 the graph library compiles without an issue. There are minor problems with other source files, but I can provide you with a patch if you need it. Let me know if you need more info. BW, Gabor On Tue, Aug 22, 2017 at 10:28 AM, Gabor Bunkoczi < [email protected]> wrote:

Hi Lance,

this may be relevant, since you are on Boost 1.56

https://stackoverflow.com/questions/25395805/compile- error-with-boost-graph-1-56-0-and-g-4-6-4

(I am on Boost 1.62, but have not tried compiling with c++11.)

BW, Gabor

On Tue, Aug 22, 2017 at 10:21 AM, Gabor Bunkoczi < [email protected]> wrote:

...

Hi Lance,

apologies for the late response. I was not aware that C++11 setting is deliberate, in this case my suggestion is clearly not helpful.

Could you send me the entire error message from the compiler? It looks like this has been clipped at the outermost stack (perhaps you need to enable more verbose output to get this - for this you can just run directly the command that failed, i.e. "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") Also, can you clarify which versions of CCTBX you are trying to build (with the revision hash), and whether this is a problem on both Linux and Mac.

Unfortunately, my knowledge of C++11 is somewhat hazy (to put it in a mild way), and I am unsure whether I will be able to help further, but I am happy to have a good look.

To answer your last question, you can try using --use_environment_flags at the configure stage, after setting CXXFLAGS, etc (I have not checked whether this works, but the option exists).

BW, Gabor

On Fri, Aug 18, 2017 at 5:24 PM, Lance Westerhoff < [email protected]> wrote:

...

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 < [email protected]> 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 < [email protected]> 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-relea se/workspace/tmp/newbuild-1131/modules/boost/boost/graph/adj acency_list.hpp:246:0, from /private/var/lib/jenkins-relea se/workspace/tmp/newbuild-1131/modules/cctbx_project/boost_a daptbx/graph/graph_type.hpp:5, from /private/var/lib/jenkins-relea se/workspace/tmp/newbuild-1131/modules/cctbx_project/boost_a daptbx/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-rel ease/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: [email protected]

Phone: 814-235-6908 <(814)%20235-6908> Fax: 814-235-6909 <(814)%20235-6909>

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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 < [email protected]> 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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