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.

./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

On Aug 16, 2017, at 6:42 PM, Billy Poon <[email protected]> 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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