@Johannes, the SLEPc patched worked. Thanks~ On Archlinux, these two lines builds FEniCS successfully:
TMP=/tmp/test; mkdir $TMP; cd $TMP; ln -s `which python2` python wget -O - http://fenicsproject.org/fenics-install.sh | bash Since python is included in the package, it is probably a good idea to include ipython as well. The default repl is a pain to use. @Jan, I tried GCC4.8.2 on the same CentOS and it still fails with the same error. Upon digging further into the build log, it seems dolfin did something funny: 2014/12/09 14:50:53 - INFO: [package:run_job] -- The C compiler identification is GNU 4.4.7 2014/12/09 14:50:53 - INFO: [package:run_job] -- The CXX compiler identification is GNU 4.4.7 2014/12/09 14:50:53 - INFO: [package:run_job] -- Check for working C compiler: */usr/bin/cc* 2014/12/09 14:50:54 - INFO: [package:run_job] -- Check for working C compiler: */usr/bin/cc* -- works 2014/12/09 14:50:54 - INFO: [package:run_job] -- Detecting C compiler ABI info 2014/12/09 14:50:54 - INFO: [package:run_job] -- Detecting C compiler ABI info - done 2014/12/09 14:50:54 - INFO: [package:run_job] -- Check for working CXX compiler: /usr/bin/c++ 2014/12/09 14:50:54 - INFO: [package:run_job] -- Check for working CXX compiler: /usr/bin/c++ -- works Note that in the above cc and c++ (wrong version), not gcc and g++ (correct version), were used. I think symlink gcc probably won't work here because libc and includes are also going to be wrong, unlike the python case where the symlinked python is only used to run the hashdist script. Shouldn't dolfin cmake choose the compiler following some priority like mpic++>g++>c++ ? On Tue, Dec 9, 2014 at 11:16 AM, Jan Blechta <[email protected]> wrote: > Building mpi4py fails on Ubuntu 12.04 because of some problem with > system Cython (see below for full log) > > ImportError: /usr/lib/pymodules/python2.7/Cython/Compiler/Code.so: > undefined symbol: PyUnicodeUCS4_DecodeUTF8 > > Shouldn't be Cython built also? > > Jan > > > 2014/12/09 18:02:56 - INFO: [package:run_job] running install > 2014/12/09 18:02:56 - INFO: [package:run_job] running build > 2014/12/09 18:02:56 - INFO: [package:run_job] running build_src > 2014/12/09 18:02:56 - INFO: [package:run_job] cythonizing > 'mpi4py.MPI.pyx' -> 'mpi4py.MPI.c' 2014/12/09 18:02:56 - INFO: > [package:run_job] Traceback (most recent call last): 2014/12/09 > 18:02:56 - INFO: [package:run_job] File "setup.py", line 624, in > <module> 2014/12/09 18:02:56 - INFO: [package:run_job] main() > 2014/12/09 18:02:56 - INFO: [package:run_job] File "setup.py", line > 621, in main 2014/12/09 18:02:56 - INFO: [package:run_job] > run_setup() 2014/12/09 18:02:56 - INFO: [package:run_job] File > "setup.py", line 493, in run_setup 2014/12/09 18:02:56 - INFO: > [package:run_job] **metadata) 2014/12/09 18:02:56 - INFO: > [package:run_job] File > > "/srv/groot/blechta/.hashdist/tmp/mpi4py-dps5vsljzl7g-1/conf/mpidistutils.py", > line 441, in setup 2014/12/09 18:02:56 - INFO: [package:run_job] > return fcn_setup(**attrs) 2014/12/09 18:02:56 - INFO: > [package:run_job] File > > "/srv/groot/blechta/.hashdist/bld/python/ctzx2dm36c6d/lib/python2.7/distutils/core.py", > line 151, in setup 2014/12/09 18:02:56 - INFO: [package:run_job] > dist.run_commands() 2014/12/09 18:02:56 - INFO: [package:run_job] > File > > "/srv/groot/blechta/.hashdist/bld/python/ctzx2dm36c6d/lib/python2.7/distutils/dist.py", > line 953, in run_commands 2014/12/09 18:02:56 - INFO: > [package:run_job] self.run_command(cmd) 2014/12/09 18:02:56 - INFO: > [package:run_job] File > > "/srv/groot/blechta/.hashdist/bld/python/ctzx2dm36c6d/lib/python2.7/distutils/dist.py", > line 972, in run_command 2014/12/09 18:02:56 - INFO: > [package:run_job] cmd_obj.run() 2014/12/09 18:02:56 - INFO: > [package:run_job] File > > "/srv/groot/blechta/.hashdist/bld/python/ctzx2dm36c6d/lib/python2.7/distutils/command/install.py", > line 563, in run 2014/12/09 18:02:56 - INFO: [package:run_job] > self.run_command('build') 2014/12/09 18:02:56 - INFO: > [package:run_job] File > > "/srv/groot/blechta/.hashdist/bld/python/ctzx2dm36c6d/lib/python2.7/distutils/cmd.py", > line 326, in run_command 2014/12/09 18:02:56 - INFO: > [package:run_job] self.distribution.run_command(command) 2014/12/09 > 18:02:56 - INFO: [package:run_job] File > > "/srv/groot/blechta/.hashdist/bld/python/ctzx2dm36c6d/lib/python2.7/distutils/dist.py", > line 972, in run_command 2014/12/09 18:02:56 - INFO: > [package:run_job] cmd_obj.run() 2014/12/09 18:02:56 - INFO: > [package:run_job] File > > "/srv/groot/blechta/.hashdist/bld/python/ctzx2dm36c6d/lib/python2.7/distutils/command/build.py", > line 127, in run 2014/12/09 18:02:56 - INFO: [package:run_job] > self.run_command(cmd_name) 2014/12/09 18:02:56 - INFO: > [package:run_job] File > > "/srv/groot/blechta/.hashdist/bld/python/ctzx2dm36c6d/lib/python2.7/distutils/cmd.py", > line 326, in run_command 2014/12/09 18:02:56 - INFO: > [package:run_job] self.distribution.run_command(command) 2014/12/09 > 18:02:56 - INFO: [package:run_job] File > > "/srv/groot/blechta/.hashdist/bld/python/ctzx2dm36c6d/lib/python2.7/distutils/dist.py", > line 972, in run_command 2014/12/09 18:02:56 - INFO: > [package:run_job] cmd_obj.run() 2014/12/09 18:02:56 - INFO: > [package:run_job] File "setup.py", line 594, in build_sources > 2014/12/09 18:02:56 - INFO: [package:run_job] wdir='src', > force=cmd.force, VERSION=CYTHON) 2014/12/09 18:02:56 - INFO: > [package:run_job] File "setup.py", line 573, in run_cython 2014/12/09 > 18:02:56 - INFO: [package:run_job] wdir=wdir) 2014/12/09 18:02:56 - > INFO: [package:run_job] File > "/srv/groot/blechta/.hashdist/tmp/mpi4py-dps5vsljzl7g-1/conf/cythonize.py", > line 9, in cythonize 2014/12/09 18:02:56 - INFO: [package:run_job] > from Cython.Compiler.Main import \ 2014/12/09 18:02:56 - INFO: > [package:run_job] File > "/usr/lib/pymodules/python2.7/Cython/Compiler/Main.py", line 18, in > <module> 2014/12/09 18:02:56 - INFO: [package:run_job] import Code > 2014/12/09 18:02:56 - INFO: [package:run_job] > ImportError: /usr/lib/pymodules/python2.7/Cython/Compiler/Code.so: > undefined symbol: PyUnicodeUCS4_DecodeUTF8 2014/12/09 18:02:56 - ERROR: > [package:run_job] Command '[u'/bin/bash', '_hashdist/build.sh']' > returned non-zero exit status 1 2014/12/09 18:02:56 - ERROR: > [package:run_job] command failed (code=1); raising > _______________________________________________ > fenics mailing list > [email protected] > http://fenicsproject.org/mailman/listinfo/fenics > -- Lizao (Larry) Li Univeristy of Minnesota
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