On Mon, 8 Dec 2014 13:20:20 -0600 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? 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? Yes, exactly this has been already observed http://fenicsproject.org/pipermail/fenics/2014-November/002038.html Jan > > > > > > > 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. > > > > > > I looked further into Hashdist. Is my understanding correct that > > > this approach is basically a more sophisticaed implementation of > > > dorsal > > writing > > > in python 2? > > > > Well, I guess you can say that. > > > > > > Johannes > > > > > _______________________________________________ fenics mailing list [email protected] http://fenicsproject.org/mailman/listinfo/fenics
