<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><br class=""></div><div class="">Hi Gabor-</div><div class=""><br class=""></div><div class="">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) </div><div class=""><br class=""></div><div class="">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.</div><div class=""><br class=""></div><div class="">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)</div><div class=""><br class=""></div><div class="">-Lance</div><div class=""><br class=""></div><br class=""><div><blockquote type="cite" class=""><div class="">On Aug 18, 2017, at 5:08 AM, Gabor Bunkoczi <<a href="mailto:gabor.bunkoczi@googlemail.com" class="">gabor.bunkoczi@googlemail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="">Hi Lance,</div><div class=""><br class=""></div><div class="">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 class=""><br class=""></div><div class="">BTW, I am unsure whether the entire cctbx is c++11 compliant.</div><div class=""><br class=""></div><div class="">BW, Gabor</div><div class=""><br class=""></div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Thu, Aug 17, 2017 at 10:03 PM, Lance Westerhoff <span dir="ltr" class=""><<a href="mailto:lance@quantumbioinc.com" target="_blank" class="">lance@quantumbioinc.com</a>></span> wrote:<br class=""><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;" class=""><div class="">Hi Billy-</div><div class=""><br class=""></div><div class="">That one worked - thanks!</div><div class=""><br class=""></div><div class="">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 class=""><br class=""></div><div class="">Thanks for your help!</div><span class=""><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)" class="">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)" class="">/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)" class=""><br class=""></div></span><div class=""><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)" class="">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)" class="">Using built-in specs.</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)" class="">COLLECT_GCC=gcc</div><span class=""><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)" class="">COLLECT_LTO_WRAPPER=/opt/gcc/<wbr class="">gcc-6.3.0-08092017/libexec/<wbr class="">gcc/x86_64-apple-darwin11.4.2/<wbr class="">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)" class="">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)" class="">Configured with: ../gcc-6.3.0/configure --prefix=/opt/gcc/gcc-6.3.0-<wbr class="">08092017 --enable-languages=c,c++,<wbr class="">fortran,objc --with-gmp=/opt/gcc/gcc-6.3.0-<wbr class="">08092017 --with-mpfr=/opt/gcc/gcc-6.3.<wbr class="">0-08092017 --with-mpc=/opt/gcc/gcc-6.3.0-<wbr class="">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)" class="">Thread model: posix</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)" class="">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)" class=""><br class=""></div><div class=""><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)" class="">mac-build64:build jenkins$ /opt/python/current/bin/python ../modules/cctbx_project/<wbr class="">libtbx/configure.py cctbx iotbx --compiler=gcc --enable-cxx11</div></div><div class=""><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)" class="">Python: 2.7.9 "/opt/python/current/bin/<wbr class="">python"</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)" class="">Compiler: gcc</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)" class="">Build mode: release</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)" class="">Warning level: 0</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)" class="">Precompiled Headers: False</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)" class="">Static libraries: False</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)" class="">Static exe: False</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)" class="">Scan Boost headers: False</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)" class="">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)" class="">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)" class="">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)" class="">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)" class="">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)" class="">Boost threads enabled: False</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)" class="">Enable CUDA: False</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)" class="">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)" class="">Use environment flags: False</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)" class="">Enable C++11: True</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)" class="">Force true division: True</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)" class="">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)" class="">.....</div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)" class=""><br class=""></div><div style="margin:0px;color:rgb(0,249,0);font-family:"Andale Mono";background-color:rgb(0,0,0)" class="">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)" class=""><span class=""><div style="margin:0px" class="">./bin/libtbx.scons -j "`./bin/libtbx.show_number_of_<wbr class="">processors`"</div><div style="margin:0px" class="">scons: Reading SConscript files ...</div></span><div style="margin:0px" class="">On MacOS, using gcc 6.3.0Xcode 4.6.3</div><div style="margin:0px" class="">Build version 4H1503</div><div style="margin:0px;min-height:14px" class=""><br class=""></div><div style="margin:0px" class="">libtbx.scons: OpenMP is disabled.</div><div style="margin:0px" class="">BOOST_VERSION: 105600</div><div class="">......</div><div class=""><br class=""></div><div class=""><div style="margin:0px" class=""><div style="margin:0px" class="">/private/var/lib/jenkins-<wbr class="">release/workspace/tmp/<wbr class="">newbuild-1131/modules/cctbx_<wbr class="">project/boost_adaptbx/graph/<wbr class="">graph_ext.cpp:337:5: required from here</div><div style="margin:0px" class="">/opt/gcc/gcc-6.3.0-08092017/<wbr class="">include/c++/6.3.0/bits/stl_<wbr class="">construct.h:75:7: error: use of deleted function ‘boost::detail::stored_edge_<wbr class="">property<long unsigned int, boost::property<boost::edge_<wbr class="">weight_t, boost::python::api::object> >::stored_edge_property(const boost::detail::stored_edge_<wbr class="">property<long unsigned int, boost::property<boost::edge_<wbr class="">weight_t, boost::python::api::object> >&)’</div><div style="margin:0px" class=""> { ::new(static_cast<void*>(__p)) _T1(std::forward<_Args>(__<wbr class="">args)...); }</div><div style="margin:0px" class=""> ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<wbr class="">~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<wbr class="">~~~~~~</div><div style="margin:0px" class="">In file included from /private/var/lib/jenkins-<wbr class="">release/workspace/tmp/<wbr class="">newbuild-1131/modules/boost/<wbr class="">boost/graph/adjacency_list.<wbr class="">hpp:246:0,</div><div style="margin:0px" class=""> from /private/var/lib/jenkins-<wbr class="">release/workspace/tmp/<wbr class="">newbuild-1131/modules/cctbx_<wbr class="">project/boost_adaptbx/graph/<wbr class="">graph_type.hpp:5,</div><div style="margin:0px" class=""> from /private/var/lib/jenkins-<wbr class="">release/workspace/tmp/<wbr class="">newbuild-1131/modules/cctbx_<wbr class="">project/boost_adaptbx/graph/<wbr class="">graph_ext.cpp:1:</div><div style="margin:0px" class="">/private/var/lib/jenkins-<wbr class="">release/workspace/tmp/<wbr class="">newbuild-1131/modules/boost/<wbr class="">boost/graph/detail/adjacency_<wbr class="">list.hpp:290:11: note: ‘boost::detail::stored_edge_<wbr class="">property<long unsigned int, boost::property<boost::edge_<wbr class="">weight_t, boost::python::api::object> >::stored_edge_property(const boost::detail::stored_edge_<wbr class="">property<long unsigned int, boost::property<boost::edge_<wbr class="">weight_t, boost::python::api::object> >&)’ is implicitly declared as deleted because ‘boost::detail::stored_edge_<wbr class="">property<long unsigned int, boost::property<boost::edge_<wbr class="">weight_t, boost::python::api::object> >’ declares a move constructor or move assignment operator</div><div style="margin:0px" class=""> class stored_edge_property : public stored_edge<Vertex> {</div><div style="margin:0px" class=""> ^~~~~~~~~~~~~~~~~~~~</div><div style="margin:0px" class="">g++ -o boost_adaptbx/graph/maximum_<wbr class="">clique_ext.o -c -DBOOST_ALL_NO_LIB -std=c++11 -DBOOST_PYTHON_MAX_BASES=2 -I/private/var/lib/jenkins-<wbr class="">release/workspace/tmp/<wbr class="">newbuild-1131/modules/boost -fPIC -fno-strict-aliasing -w -DNDEBUG -O3 -ffast-math -I/private/var/lib/jenkins-<wbr class="">release/workspace/tmp/<wbr class="">newbuild-1131/modules/cctbx_<wbr class="">project -I/private/var/lib/jenkins-<wbr class="">release/workspace/tmp/<wbr class="">newbuild-1131/build/include -I/private/var/lib/jenkins-<wbr class="">release/workspace/tmp/<wbr class="">newbuild-1131/build/include -I/opt/python/Python-2.7.9-<wbr class="">01292015/include/python2.7 /private/var/lib/jenkins-<wbr class="">release/workspace/tmp/<wbr class="">newbuild-1131/modules/cctbx_<wbr class="">project/boost_adaptbx/graph/<wbr class="">maximum_clique_ext.cpp</div><div style="margin:0px" class="">scons: *** [boost_adaptbx/graph/graph_<wbr class="">ext.o] Error 1</div><div style="margin:0px" class="">scons: building terminated because of errors.</div><div style="margin:0px" class="">usr+sys time: 4.25 seconds</div><div style="margin:0px" class="">wall clock time: 2 minutes 15.94 seconds (135.94 seconds total)</div><div style="margin:0px" class="">make: *** [default] Error 2</div></div></div></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div>-Lance<br class=""><div class=""><span class="">
____________________<br class="">Lance M. Westerhoff, Ph.D.<br class="">President and General Manager<br class="">QuantumBio Inc. <br class=""><br class="">WWW: <a href="http://www.quantumbioinc.com/" target="_blank" class="">http://www.quantumbioinc.com</a><br class="">Email: <a href="mailto:lance@quantumbioinc.com" target="_blank" class="">lance@quantumbioinc.com</a><br class=""><br class=""></span>Phone: <a href="tel:(814)%20235-6908" target="_blank" value="+18142356908" class="">814-235-6908</a><br class="">Fax: <a href="tel:(814)%20235-6909" target="_blank" value="+18142356909" class="">814-235-6909</a><br class=""><br class=""><br class="">This message and any attachments are solely for the intended recipient and<br class="">should be considered confidential. If you are not the intended recipient,<br class="">please immediately and permanently delete.
</div><div class=""><div class="h5">
<br class=""><div class=""><blockquote type="cite" class=""><div class="">On Aug 16, 2017, at 6:42 PM, Billy Poon <<a href="mailto:BKPoon@lbl.gov" target="_blank" class="">BKPoon@lbl.gov</a>> wrote:</div><br class="m_-138754997085060984Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi Lance,<div class=""><br class=""></div><div class="">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" class=""><div class=""><div class="m_-138754997085060984gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div class=""><div class="">--</div><div class=""><span style="font-size:12.8px" class="">Billy K. Poon</span><br class=""></div></div><div class="">Research Scientist, Molecular Biophysics and Integrated Bioimaging</div><div class="">Lawrence Berkeley National Laboratory</div><div class="">1 Cyclotron Road, M/S 33R0345</div><div class="">Berkeley, CA 94720</div><div class="">Tel: <a href="tel:(510)%20486-5709" target="_blank" value="+15104865709" class="">(510) 486-5709</a></div><div class="">Fax: <a href="tel:(510)%20486-5909" target="_blank" value="+15104865909" class="">(510) 486-5909</a></div><div class="">Web: <a href="https://phenix-online.org/" target="_blank" class="">https://phenix-online.org</a></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br class=""><div class="gmail_quote">On Wed, Aug 16, 2017 at 2:49 PM, Lance Westerhoff <span dir="ltr" class=""><<a href="mailto:lance@quantumbioinc.com" target="_blank" class="">lance@quantumbioinc.com</a>></span> wrote:<br class=""><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 class="">
Hello All-<br class="">
<br class="">
How does one introduce an alternate gcc compiler for CCTBX on Mac? I must be missing it in the documentation.<br class="">
<br class="">
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 $CC, etc) but to no avail. These environment variables seem to be disregarded. We do use this compiler for building CCTBX on linux without too much trouble, so I think the support should be there.<br class="">
<br class="">
Specifically:<br class="">
<br class="">
mac-build64:build jenkins$ env | grep CXX<br class="">
CXX=/opt/gcc/current/bin/g++<br class="">
<br class="">
mac-build64:build jenkins$ env | grep CC<br class="">
CC=/opt/gcc/current/bin/gcc<br class="">
<br class="">
mac-build64:build jenkins$ which gcc<br class="">
/opt/gcc/current/bin/gcc<br class="">
<br class="">
mac-build64:build jenkins$ g++ -v<br class="">
Using built-in specs.<br class="">
COLLECT_GCC=g++<br class="">
COLLECT_LTO_WRAPPER=/opt/gcc/g<wbr class="">cc-6.3.0-08092017/libexec/gcc/<wbr class="">x86_64-apple-darwin11.4.2/6.3.<wbr class="">0/lto-wrapper<br class="">
Target: x86_64-apple-darwin11.4.2<br class="">
Configured with: ../gcc-6.3.0/configure --prefix=/opt/gcc/gcc-6.3.0-08<wbr class="">092017 --enable-languages=c,c++,fortr<wbr class="">an,objc --with-gmp=/opt/gcc/gcc-6.3.0-<wbr class="">08092017 --with-mpfr=/opt/gcc/gcc-6.3.0<wbr class="">-08092017 --with-mpc=/opt/gcc/gcc-6.3.0-<wbr class="">08092017 --enable-libgomp --disable-multilib<br class="">
Thread model: posix<br class="">
gcc version 6.3.0 (GCC)<br class="">
<br class="">
mac-build64:build jenkins$ /opt/python/current/bin/python ../modules/cctbx_project/libtb<wbr class="">x/configure.py cctbx<br class="">
Python: 2.7.9 "/opt/python/current/bin/pytho<wbr class="">n"<br class="">
Compiler: default<br class="">
....<br class="">
This script is only applicable to Linux - exiting.<br class="">
Done.<br class="">
<br class="">
mac-build64:build jenkins$ make<br class="">
./bin/libtbx.scons -j "`./bin/libtbx.show_number_of_<wbr class="">processors`"<br class="">
scons: Reading SConscript files ...<br class="">
On MacOS, using clang 4.2.0<br class="">
Xcode 4.6.3<br class="">
Build version 4H1503<br class="">
...<br class="">
<br class="">
<br class="">
Thanks for your help!<br class="">
<br class="">
-Lance<br class="">
____________________<br class="">
Lance M. Westerhoff, Ph.D.<br class="">
President and General Manager<br class="">
QuantumBio Inc.<br class="">
<br class="">
WWW: <a href="http://www.quantumbioinc.com/" target="_blank" rel="noreferrer" class="">http://www.quantumbioinc.com</a><br class="">
Email: <a href="mailto:lance@quantumbioinc.com" target="_blank" class="">lance@quantumbioinc.com</a><br class="">
<br class="">
<br class="">
<br class="">
<br class="">
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