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 _______________________________________________ fenics mailing list [email protected] http://fenicsproject.org/mailman/listinfo/fenics
