@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 > 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 looked further into Hashdist. Is my understanding correct that this approach is basically a more sophisticaed implementation of dorsal writing in python 2? On Sun, Dec 7, 2014 at 7:20 AM, Johannes Ring <[email protected]> wrote: > On Sat, Dec 6, 2014 at 10:55 PM, Lizao Li <[email protected]> wrote: > > > > On Sat, Dec 6, 2014 at 2:50 PM, Johannes Ring <[email protected]> wrote: > >> > >> On Sat, Dec 6, 2014 at 9:29 PM, Lizao Li <[email protected]> wrote: > >> > @Johannes. Indeed, on Arch `python` is linked to py3 and `python2` is > >> > linked > >> > to py2. Is there a way to make it work by changing the default python > >> > binary > >> > path? > >> > >> You can make a symbolic link to python2 in some directory > >> > >> ln -s /usr/bin/python2 python > >> > >> and then add this directory first in PATH. > >> > > > > Thanks. The first hurdle is passed. After > >> > >> ln -s /usr/bin/python2 python > >> export PATH=$PWD:$PATH > >> wget -O - http://fenicsproject.org/fenics-install.sh | bash > > > > the installation failed at "boost": > > Output of `tail -f > /home/larry/.hashdist/tmp/boost-tyvhwearpzdg/build.log` > >> > >> 2014/12/06 15:18:08 - INFO: [package:run_job] > >> 2014/12/06 15:18:08 - INFO: [package:run_job] compilation terminated. > >> 2014/12/06 15:18:08 - INFO: [package:run_job] > >> 2014/12/06 15:18:08 - 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" > >> 2014/12/06 15:18:08 - INFO: [package:run_job] > >> 2014/12/06 15:18:08 - 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... > >> 2014/12/06 15:18:08 - INFO: [package:run_job] ...failed updating 1 > >> target... > >> 2014/12/06 15:18:08 - INFO: [package:run_job] ...updated 10689 > targets... > >> 2014/12/06 15:18:08 - ERROR: [package:run_job] Command '[u'/bin/bash', > >> '_hashdist/build.sh']' returned non-zero exit status 1 > >> 2014/12/06 15:18:08 - ERROR: [package:run_job] command failed (code=1); > >> raising > > > > It seems the python path is still wrong. Is there a way to set the > > python_lib and pythong_include path? > > I have updated the script now to build its own python. That should > hopefully fix this problem. > > > > >> > >> Johannes > >> > >> > I also tried it on a production cluster with CentOS 6.5. It failed at > >> > package "eigen" > >> >> > >> >> [eigen] Building eigen/hfjxjswpo5ct, follow log with: > >> >> [eigen] tail -f > >> >> > >> >> > /panfs/roc/groups/5/arnoldd/lil1/.hashdist/tmp/eigen-hfjxjswpo5ct/build.log > >> > >> Take a look at this file. > > > > > > Thanks for pointing that out. I thought when it said "[eigen] tail -f > ...." > > it meant "what follows is the output from tail -f ..." already. > Apparently > > it is not. The full log revealed that cmake is missing. Is there an easy > to > > add that? (I do not have sudo on that cluster)) > > Yes, this is easy and it is fixed now in the latest version of the script. > > Johannes > -- Lizao (Larry) Li Univeristy of Minnesota
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