@Jan&Johannes. Thanks again. I tried on CentOS with GCC 4.8.2 and dolfin still fails to compile with the same error. What is the minimum GCC version required for dolfin?
On Mon, Dec 8, 2014 at 3:26 PM, Johannes Ring <[email protected]> wrote: > On Mon, Dec 8, 2014 at 8:20 PM, Lizao Li <[email protected]> wrote: > > > > > > On Mon, Dec 8, 2014 at 11:00 AM, Johannes Ring <[email protected]> > wrote: > >> > >> On Mon, Dec 8, 2014 at 5:05 PM, Lizao Li <[email protected]> wrote: > >> > @Johannes. It almost get through on the CentOS cluster now. Dolfin > fails > >> > to > >> > build at > >> >> > >> >> tail -f > >> >> > >> >> > /panfs/roc/groups/5/arnoldd/lil1/.hashdist/tmp/dolfin-hkxoe2xhroe3-1/build.log > >> >> 2014/12/08 09:30:21 - INFO: [package:run_job] > >> >> > >> >> > /panfs/roc/groups/5/arnoldd/lil1/.hashdist/tmp/dolfin-hkxoe2xhroe3-1/dolfin/parameter/Parameters.h:159: > >> >> note: void dolfin::Parameters::add(std::string, const > >> >> char*) > >> >> 2014/12/08 09:30:21 - INFO: [package:run_job] > >> >> > >> >> > /panfs/roc/groups/5/arnoldd/lil1/.hashdist/tmp/dolfin-hkxoe2xhroe3-1/dolfin/parameter/Parameters.h:162: > >> >> note: void dolfin::Parameters::add(std::string, > >> >> std::string, > >> >> std::set<std::basic_string<char, std::char_traits<char>, > >> >> std::allocator<char> >, std::less<std::basic_string<char, > >> >> std::char_traits<char>, std::allocator<char> > >, > >> >> std::allocator<std::basic_string<char, std::char_traits<char>, > >> >> std::allocator<char> > > >) > >> >> 2014/12/08 09:30:21 - INFO: [package:run_job] > >> >> > >> >> > /panfs/roc/groups/5/arnoldd/lil1/.hashdist/tmp/dolfin-hkxoe2xhroe3-1/dolfin/parameter/Parameters.h:165: > >> >> note: void dolfin::Parameters::add(std::string, const > >> >> char*, > >> >> std::set<std::basic_string<char, std::char_traits<char>, > >> >> std::allocator<char> >, std::less<std::basic_string<char, > >> >> std::char_traits<char>, std::allocator<char> > >, > >> >> std::allocator<std::basic_string<char, std::char_traits<char>, > >> >> std::allocator<char> > > >) > >> >> 2014/12/08 09:30:21 - INFO: [package:run_job] > >> >> > >> >> > /panfs/roc/groups/5/arnoldd/lil1/.hashdist/tmp/dolfin-hkxoe2xhroe3-1/dolfin/parameter/Parameters.h:168: > >> >> note: void dolfin::Parameters::add(std::string, bool) > >> >> 2014/12/08 09:30:21 - INFO: [package:run_job] > >> >> > >> >> > /panfs/roc/groups/5/arnoldd/lil1/.hashdist/tmp/dolfin-hkxoe2xhroe3-1/dolfin/parameter/Parameters.h:171: > >> >> note: void dolfin::Parameters::add(const > >> >> dolfin::Parameters&) > >> >> 2014/12/08 09:30:22 - INFO: [package:run_job] gmake[2]: *** > >> >> [dolfin/CMakeFiles/dolfin.dir/ale/HarmonicSmoothing.cpp.o] Error 1 > >> >> 2014/12/08 09:30:22 - INFO: [package:run_job] gmake[1]: *** > >> >> [dolfin/CMakeFiles/dolfin.dir/all] Error 2 > >> >> 2014/12/08 09:30:22 - INFO: [package:run_job] gmake: *** [all] Error > 2 > >> >> 2014/12/08 09:30:22 - ERROR: [package:run_job] Command > '[u'/bin/bash', > >> >> '_hashdist/build.sh']' returned non-zero exit status 2 > >> >> 2014/12/08 09:30:22 - ERROR: [package:run_job] command failed > (code=2); > >> >> raising > >> > >> I'm not sure if the actual error is shown here. Can you include more > >> of build.log? > > > > > > I digged further. I think the meaningful error message is somewhere in > the > > middle of build.log: > > 2014/12/08 11:30:25 - INFO: [package:run_job] > > > xxx/.hashdist/tmp/dolfin-4kidvbj2v52z/dolfin/parameter/GlobalParameters.h:84: > > error: no matching function for call to 'dolfin::Parameters::add(const > char > > [21], std::string&, <brace-enclosed initializer list>)' > > I also attached the full build.log at the end. Does Hashdist has its own > gcc > > or use the system gcc? > > It uses the system gcc by default, but you can build gcc with hashdist > and then use this gcc to build FEniCS. However, this will not be part > of the script, so you will have to download hashdist and hashstack and > setup a profile to build gcc. > > Note also that there are two examples in hashstack for building FEniCS > on clusters (Abel and SciNet) that uses the modules system, which > might be helpful > > > On CentOS, a somewhat old gcc is used > > gcc --version > > gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-4) > > Might this be the problem? > > > >> > >> > On Arch, it still fails at boost, where the wrong python include is > >> > used. I > >> > guess python paths are probably not set by the python package by > >> > default. > >> >> > >> >> tail -f /home/larry/.hashdist/tmp/boost-43vhthk4e2bi/build.log > >> >> [boost|ERROR] Command '[u'/bin/bash', '_hashdist/build.sh']' returned > >> >> non-zero exit status 1 > >> >> [boost|ERROR] command failed (code=1); raising > >> >> [larry@quetzalcoatlus temp]$ tail -f > >> >> /home/larry/.hashdist/tmp/boost-43vhthk4e2bi/build.log > >> >> 2014/12/08 09:44:04 - INFO: [package:run_job] > ^ > >> >> 2014/12/08 09:44:04 - INFO: [package:run_job] compilation terminated. > >> >> 2014/12/08 09:44:04 - INFO: [package:run_job] > >> >> 2014/12/08 09:44:04 - INFO: [package:run_job] "g++" > >> >> -ftemplate-depth-128 -O3 -finline-functions -Wno-inline -Wall > -pthread > >> >> -fPIC > >> >> -m64 -DBOOST_ALL_NO_LIB=1 -DBOOST_PYTHON_SOURCE -DNDEBUG -I"." > >> >> -I"/usr/include/python3.4" -c -o > >> >> > >> >> > "_build/boost/bin.v2/libs/python/build/gcc-4.9.2/release/address-model-64/threading-multi/numeric.o" > >> >> "libs/python/src/numeric.cpp" > >> >> 2014/12/08 09:44:04 - INFO: [package:run_job] > >> >> 2014/12/08 09:44:04 - INFO: [package:run_job] ...failed > gcc.compile.c++ > >> >> > >> >> > _build/boost/bin.v2/libs/python/build/gcc-4.9.2/release/address-model-64/threading-multi/numeric.o... > >> >> 2014/12/08 09:44:04 - INFO: [package:run_job] ...failed updating 1 > >> >> target... > >> >> 2014/12/08 09:44:04 - INFO: [package:run_job] ...updated 10689 > >> >> targets... > >> >> 2014/12/08 09:44:04 - ERROR: [package:run_job] Command > '[u'/bin/bash', > >> >> '_hashdist/build.sh']' returned non-zero exit status 1 > >> >> 2014/12/08 09:44:04 - ERROR: [package:run_job] command failed > (code=1); > >> >> raising > >> > >> I think I know what the problem is and I have made a fix. Please try > >> again with the latest script. > >> > > Thanks, that worked~ Boost is successfully compiled. But the installation > > failed at slepc: > > tail -f /home/larry/.hashdist/tmp/slepc-qzbng3rjmb5i/build.log > > 2014/12/08 12:30:28 - INFO: [package:run_job] u'PATCHELF_DIR': > > u'/home/larry/.hashdist/bld/patchelf/k3rloj265ogt', > > 2014/12/08 12:30:28 - INFO: [package:run_job] u'PATCHELF_ID': > > u'patchelf/k3rloj265ogtl4dmmmbmyt34dnffryka', > > 2014/12/08 12:30:28 - INFO: [package:run_job] 'PATH': > u'/usr/bin:/bin', > > 2014/12/08 12:30:28 - INFO: [package:run_job] u'PETSC_DIR': > > u'/home/larry/.hashdist/bld/petsc/zr5ml62hgwp6', > > 2014/12/08 12:30:28 - INFO: [package:run_job] u'PETSC_ID': > > u'petsc/zr5ml62hgwp6wgpoyob36cvcr5ugyzht', > > 2014/12/08 12:30:28 - INFO: [package:run_job] 'PWD': > > u'/home/larry/.hashdist/tmp/slepc-qzbng3rjmb5i'} > > 2014/12/08 12:30:28 - INFO: [package:run_job] Configure does not support > > Python 3 yet, please run as > > 2014/12/08 12:30:28 - INFO: [package:run_job] python2 './configure' > > '--prefix=/home/larry/.hashdist/bld/slepc/qzbng3rjmb5i' > > 2014/12/08 12:30:28 - ERROR: [package:run_job] Command '[u'/bin/bash', > > '_hashdist/build.sh']' returned non-zero exit status 1 > > 2014/12/08 12:30:28 - ERROR: [package:run_job] command failed (code=1); > > raising > > It seems slepc had its own PATH setting which did not use my local > python2 > > link. > > It looks like the slepc package in hashstack is missing a build > dependency on python. I will fix this tomorrow. > > Johannes > -- Lizao (Larry) Li Univeristy of Minnesota
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