<div dir="ltr"><div>Hi Lance,</div><div><br></div><div>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?</div><div><br></div><div>BTW, I am unsure whether the entire cctbx is c++11 compliant.</div><div><br></div><div>BW, Gabor</div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Aug 17, 2017 at 10:03 PM, Lance Westerhoff <span dir="ltr"><<a href="mailto:lance@quantumbioinc.com" target="_blank">lance@quantumbioinc.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="-ms-word-wrap: break-word;"><div>Hi Billy-</div><div><br></div><div>That one worked - thanks!</div><div><br></div><div>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.</div><div><br></div><div>Thanks for your help!</div><span><div><br></div><div><br></div><div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)">mac-build64:build jenkins$ which gcc</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)">/opt/gcc/current/bin/gcc</div></div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)"><br></div></span><div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)">mac-build64:build jenkins$ gcc -v</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)">Using built-in specs.</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)">COLLECT_GCC=gcc</div><span><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)">COLLECT_LTO_WRAPPER=/opt/gcc/<wbr>gcc-6.3.0-08092017/libexec/<wbr>gcc/x86_64-apple-darwin11.4.2/<wbr>6.3.0/lto-wrapper</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)">Target: x86_64-apple-darwin11.4.2</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)">Configured with: ../gcc-6.3.0/configure --prefix=/opt/gcc/gcc-6.3.0-<wbr>08092017 --enable-languages=c,c++,<wbr>fortran,objc --with-gmp=/opt/gcc/gcc-6.3.0-<wbr>08092017 --with-mpfr=/opt/gcc/gcc-6.3.<wbr>0-08092017 --with-mpc=/opt/gcc/gcc-6.3.0-<wbr>08092017 --enable-libgomp --disable-multilib</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)">Thread model: posix</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)">gcc version 6.3.0 (GCC) </div></span></div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)"><br></div><div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)">mac-build64:build jenkins$ /opt/python/current/bin/python ../modules/cctbx_project/<wbr>libtbx/configure.py cctbx iotbx --compiler=gcc --enable-cxx11</div></div><div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)">Python: 2.7.9 "/opt/python/current/bin/<wbr>python"</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)">Compiler: gcc</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)">Build mode: release</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)">Warning level: 0</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)">Precompiled Headers: False</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)">Static libraries: False</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)">Static exe: False</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)">Scan Boost headers: False</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)">Write full flex_fwd.h files: False</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)">Build Boost.Python extensions: True</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)">Define BOOST_PYTHON_NO_PY_SIGNATURES: False</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)">Define BOOST_PYTHON_BOOL_INT_STRICT: True</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)">Enable OpenMP if possible: False</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)">Boost threads enabled: False</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)">Enable CUDA: False</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)">Use opt_resources if available: False</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)">Use environment flags: False</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)">Enable C++11: True</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)">Force true division: True</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)">command_version_suffix: None</div></div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)">.....</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)"><br></div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)">mac-build64:build jenkins$ make</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)"><span><div style="margin:0px">./bin/libtbx.scons -j "`./bin/libtbx.show_number_of_<wbr>processors`"</div><div style="margin:0px">scons: Reading SConscript files ...</div></span><div style="margin:0px">On MacOS, using gcc 6.3.0Xcode 4.6.3</div><div style="margin:0px">Build version 4H1503</div><div style="margin:0px;min-height:14px"><br></div><div style="margin:0px">libtbx.scons: OpenMP is disabled.</div><div style="margin:0px">BOOST_VERSION: 105600</div><div>......</div><div><br></div><div><div style="margin:0px"><div style="margin:0px">/private/var/lib/jenkins-<wbr>release/workspace/tmp/<wbr>newbuild-1131/modules/cctbx_<wbr>project/boost_adaptbx/graph/<wbr>graph_ext.cpp:337:5: required from here</div><div style="margin:0px">/opt/gcc/gcc-6.3.0-08092017/<wbr>include/c++/6.3.0/bits/stl_<wbr>construct.h:75:7: error: use of deleted function ‘boost::detail::stored_edge_<wbr>property<long unsigned int, boost::property<boost::edge_<wbr>weight_t, boost::python::api::object> >::stored_edge_property(const boost::detail::stored_edge_<wbr>property<long unsigned int, boost::property<boost::edge_<wbr>weight_t, boost::python::api::object> >&)’</div><div style="margin:0px"> { ::new(static_cast<void*>(__p)) _T1(std::forward<_Args>(__<wbr>args)...); }</div><div style="margin:0px"> ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<wbr>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<wbr>~~~~~~</div><div style="margin:0px">In file included from /private/var/lib/jenkins-<wbr>release/workspace/tmp/<wbr>newbuild-1131/modules/boost/<wbr>boost/graph/adjacency_list.<wbr>hpp:246:0,</div><div style="margin:0px"> from /private/var/lib/jenkins-<wbr>release/workspace/tmp/<wbr>newbuild-1131/modules/cctbx_<wbr>project/boost_adaptbx/graph/<wbr>graph_type.hpp:5,</div><div style="margin:0px"> from /private/var/lib/jenkins-<wbr>release/workspace/tmp/<wbr>newbuild-1131/modules/cctbx_<wbr>project/boost_adaptbx/graph/<wbr>graph_ext.cpp:1:</div><div style="margin:0px">/private/var/lib/jenkins-<wbr>release/workspace/tmp/<wbr>newbuild-1131/modules/boost/<wbr>boost/graph/detail/adjacency_<wbr>list.hpp:290:11: note: ‘boost::detail::stored_edge_<wbr>property<long unsigned int, boost::property<boost::edge_<wbr>weight_t, boost::python::api::object> >::stored_edge_property(const boost::detail::stored_edge_<wbr>property<long unsigned int, boost::property<boost::edge_<wbr>weight_t, boost::python::api::object> >&)’ is implicitly declared as deleted because ‘boost::detail::stored_edge_<wbr>property<long unsigned int, boost::property<boost::edge_<wbr>weight_t, boost::python::api::object> >’ declares a move constructor or move assignment operator</div><div style="margin:0px"> class stored_edge_property : public stored_edge<Vertex> {</div><div style="margin:0px"> ^~~~~~~~~~~~~~~~~~~~</div><div style="margin:0px">g++ -o boost_adaptbx/graph/maximum_<wbr>clique_ext.o -c -DBOOST_ALL_NO_LIB -std=c++11 -DBOOST_PYTHON_MAX_BASES=2 -I/private/var/lib/jenkins-<wbr>release/workspace/tmp/<wbr>newbuild-1131/modules/boost -fPIC -fno-strict-aliasing -w -DNDEBUG -O3 -ffast-math -I/private/var/lib/jenkins-<wbr>release/workspace/tmp/<wbr>newbuild-1131/modules/cctbx_<wbr>project -I/private/var/lib/jenkins-<wbr>release/workspace/tmp/<wbr>newbuild-1131/build/include -I/private/var/lib/jenkins-<wbr>release/workspace/tmp/<wbr>newbuild-1131/build/include -I/opt/python/Python-2.7.9-<wbr>01292015/include/python2.7 /private/var/lib/jenkins-<wbr>release/workspace/tmp/<wbr>newbuild-1131/modules/cctbx_<wbr>project/boost_adaptbx/graph/<wbr>maximum_clique_ext.cpp</div><div style="margin:0px">scons: *** [boost_adaptbx/graph/graph_<wbr>ext.o] Error 1</div><div style="margin:0px">scons: building terminated because of errors.</div><div style="margin:0px">usr+sys time: 4.25 seconds</div><div style="margin:0px">wall clock time: 2 minutes 15.94 seconds (135.94 seconds total)</div><div style="margin:0px">make: *** [default] Error 2</div></div></div></div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div>-Lance<br><div><span>
____________________<br>Lance M. Westerhoff, Ph.D.<br>President and General Manager<br>QuantumBio Inc. <br><br>WWW: <a href="http://www.quantumbioinc.com" target="_blank">http://www.quantumbioinc.com</a><br>Email: <a href="mailto:lance@quantumbioinc.com" target="_blank">lance@quantumbioinc.com</a><br><br></span>Phone: <a href="tel:(814)%20235-6908" target="_blank" value="+18142356908">814-235-6908</a><br>Fax: <a href="tel:(814)%20235-6909" target="_blank" value="+18142356909">814-235-6909</a><br><br><br>This message and any attachments are solely for the intended recipient and<br>should be considered confidential. If you are not the intended recipient,<br>please immediately and permanently delete.
</div><div><div class="h5">
<br><div><blockquote type="cite"><div>On Aug 16, 2017, at 6:42 PM, Billy Poon <<a href="mailto:BKPoon@lbl.gov" target="_blank">BKPoon@lbl.gov</a>> wrote:</div><br class="m_-138754997085060984Apple-interchange-newline"><div><div dir="ltr">Hi Lance,<div><br></div><div>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</div></div><div class="gmail_extra"><br clear="all"><div><div class="m_-138754997085060984gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div>--</div><div><span style="font-size:12.8px">Billy K. Poon</span><br></div></div><div>Research Scientist, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory</div><div>1 Cyclotron Road, M/S 33R0345</div><div>Berkeley, CA 94720</div><div>Tel: <a href="tel:(510)%20486-5709" target="_blank" value="+15104865709">(510) 486-5709</a></div><div>Fax: <a href="tel:(510)%20486-5909" target="_blank" value="+15104865909">(510) 486-5909</a></div><div>Web: <a href="https://phenix-online.org/" target="_blank">https://phenix-online.org</a></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Wed, Aug 16, 2017 at 2:49 PM, Lance Westerhoff <span dir="ltr"><<a href="mailto:lance@quantumbioinc.com" target="_blank">lance@quantumbioinc.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left-color:rgb(204,204,204);border-left-width:1px;border-left-style:solid"><br>
Hello All-<br>
<br>
How does one introduce an alternate gcc compiler for CCTBX on Mac? I must be missing it in the documentation.<br>
<br>
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 $CC, etc) but to no avail. These environment variables seem to be disregarded. We do use this compiler for building CCTBX on linux without too much trouble, so I think the support should be there.<br>
<br>
Specifically:<br>
<br>
mac-build64:build jenkins$ env | grep CXX<br>
CXX=/opt/gcc/current/bin/g++<br>
<br>
mac-build64:build jenkins$ env | grep CC<br>
CC=/opt/gcc/current/bin/gcc<br>
<br>
mac-build64:build jenkins$ which gcc<br>
/opt/gcc/current/bin/gcc<br>
<br>
mac-build64:build jenkins$ g++ -v<br>
Using built-in specs.<br>
COLLECT_GCC=g++<br>
COLLECT_LTO_WRAPPER=/opt/gcc/g<wbr>cc-6.3.0-08092017/libexec/gcc/<wbr>x86_64-apple-darwin11.4.2/6.3.<wbr>0/lto-wrapper<br>
Target: x86_64-apple-darwin11.4.2<br>
Configured with: ../gcc-6.3.0/configure --prefix=/opt/gcc/gcc-6.3.0-08<wbr>092017 --enable-languages=c,c++,fortr<wbr>an,objc --with-gmp=/opt/gcc/gcc-6.3.0-<wbr>08092017 --with-mpfr=/opt/gcc/gcc-6.3.0<wbr>-08092017 --with-mpc=/opt/gcc/gcc-6.3.0-<wbr>08092017 --enable-libgomp --disable-multilib<br>
Thread model: posix<br>
gcc version 6.3.0 (GCC)<br>
<br>
mac-build64:build jenkins$ /opt/python/current/bin/python ../modules/cctbx_project/libtb<wbr>x/configure.py cctbx<br>
Python: 2.7.9 "/opt/python/current/bin/pytho<wbr>n"<br>
Compiler: default<br>
....<br>
This script is only applicable to Linux - exiting.<br>
Done.<br>
<br>
mac-build64:build jenkins$ make<br>
./bin/libtbx.scons -j "`./bin/libtbx.show_number_of_<wbr>processors`"<br>
scons: Reading SConscript files ...<br>
On MacOS, using clang 4.2.0<br>
Xcode 4.6.3<br>
Build version 4H1503<br>
...<br>
<br>
<br>
Thanks for your help!<br>
<br>
-Lance<br>
____________________<br>
Lance M. Westerhoff, Ph.D.<br>
President and General Manager<br>
QuantumBio Inc.<br>
<br>
WWW: <a href="http://www.quantumbioinc.com/" target="_blank" rel="noreferrer">http://www.quantumbioinc.com</a><br>
Email: <a href="mailto:lance@quantumbioinc.com" target="_blank">lance@quantumbioinc.com</a><br>
<br>
<br>
<br>
<br>
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</blockquote></div><br></div>
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