On Mon, Mar 9, 2015 at 11:42 AM, Birgitte Maria Elisabeth Brydso <[email protected]> wrote: >> I rebuilt letting fenics build petsc instead of using the system petsc, >> and the above error is gone. Fenics compiles, and I can load dolfin in >> python. However, if I try to run a test-case, any test-case, I get this >> error: >> >> [t-cn0109.hpc2n.umu.se:31129] [[INVALID],INVALID] ORTE_ERROR_LOG: Attempt >> to redefine an existing data type in file >> ../../../orte/runtime/orte_globals.c at line 189 >> [t-cn0109.hpc2n.umu.se:31130] [[INVALID],INVALID] ORTE_ERROR_LOG: Attempt >> to redefine an existing data type in file >> ../../../orte/runtime/orte_globals.c at line 189 >> [t-cn0109.hpc2n.umu.se:31131] [[INVALID],INVALID] ORTE_ERROR_LOG: Attempt >> to redefine an existing data type in file >> ../../../orte/runtime/orte_globals.c at line 189 >> [t-cn0109.hpc2n.umu.se:31132] [[INVALID],INVALID] ORTE_ERROR_LOG: Attempt >> to redefine an existing data type in file >> ../../../orte/runtime/orte_globals.c at line 189 >> -------------------------------------------------------------------------- >> It looks like orte_init failed for some reason; your parallel process is >> likely to abort. There are many reasons that a parallel process can >> fail during orte_init; some of which are due to configuration or >> environment problems. This failure appears to be an internal failure; >> here's some additional information (which may only be relevant to an >> Open MPI developer): >> >> orte_dt_init failed >> --> Returned value Attempt to redefine an existing data type (-31) >> instead of ORTE_SUCCESS >> -------------------------------------------------------------------------- >> -------------------------------------------------------------------------- >> It looks like orte_init failed for some reason; your parallel process is >> likely to abort. There are many reasons that a parallel process can >> fail during orte_init; some of which are due to configuration or >> environment problems. This failure appears to be an internal failure; >> here's some additional information (which may only be relevant to an >> Open MPI developer): >> >> orte_dt_init failed >> --> Returned value Attempt to redefine an existing data type (-31) >> instead of ORTE_SUCCESS >> >> >> ... (repeated) >> >> >> If my version of MPI a problem? The compilers, perhaps? I have compiled >> with GCC 4.6.3 and OpenMPI 1.6.5. >> >> Attaching my yaml file. >> > > > I took a look at the libraries linked to dolfin, and it looks as if there is > indeed a MPI problem - it links in not just the MPI version I want it to use > (OpenMPI 1.6.5 which is installed as a module), but also the one installed > with the OS. This causes some sort of conflict I am guessing, but I have > absolutely no idea how to stop this from happening. > > This is the output from ldd libdolfin.so > > linux-vdso.so.1 => (0x00007fff691d0000) > libxml2.so.2 => > /pfs/nobackup/home/b/bbrydsoe/fenics_5_build/bld/libxml2/ohwsguokc2rl/lib/libxml2.so.2 > (0x00002b7d50c58000) > libboost_filesystem.so.1.55.0 => > /pfs/nobackup/home/b/bbrydsoe/fenics_5_build/bld/boost/pgpg4cjabhlf/lib/libboost_filesystem.so.1.55.0 > (0x00002b7d50fc0000) > libboost_program_options.so.1.55.0 => > /pfs/nobackup/home/b/bbrydsoe/fenics_5_build/bld/boost/pgpg4cjabhlf/lib/libboost_program_options.so.1.55.0 > (0x00002b7d511d8000) > libboost_system.so.1.55.0 => > /pfs/nobackup/home/b/bbrydsoe/fenics_5_build/bld/boost/pgpg4cjabhlf/lib/libboost_system.so.1.55.0 > (0x00002b7d51450000) > libboost_thread.so.1.55.0 => > /pfs/nobackup/home/b/bbrydsoe/fenics_5_build/bld/boost/pgpg4cjabhlf/lib/libboost_thread.so.1.55.0 > (0x00002b7d51658000) > libboost_iostreams.so.1.55.0 => > /pfs/nobackup/home/b/bbrydsoe/fenics_5_build/bld/boost/pgpg4cjabhlf/lib/libboost_iostreams.so.1.55.0 > (0x00002b7d51870000) > libhdf5.so.8 => > /pfs/nobackup/home/b/bbrydsoe/fenics_5_build/bld/hdf5/5wwfxxazmvaz/lib/libhdf5.so.8 > (0x00002b7d51a88000) > libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 > (0x00002b7d51f78000) > libz.so.1 => > /pfs/nobackup/home/b/bbrydsoe/fenics_5_build/bld/zlib/ybkphsca7v4h/lib/libz.so.1 > (0x00002b7d52198000) > libml.so.11 => > /pfs/nobackup/home/b/bbrydsoe/fenics_5_build/bld/trilinos/qcaqlx2soyjs/lib/libml.so.11 > (0x00002b7d523b0000) > libzoltan.so.11 => > /pfs/nobackup/home/b/bbrydsoe/fenics_5_build/bld/trilinos/qcaqlx2soyjs/lib/libzoltan.so.11 > (0x00002b7d528c0000) > libifpack.so.11 => > /pfs/nobackup/home/b/bbrydsoe/fenics_5_build/bld/trilinos/qcaqlx2soyjs/lib/libifpack.so.11 > (0x00002b7d52bb8000) > libamesos.so.11 => > /pfs/nobackup/home/b/bbrydsoe/fenics_5_build/bld/trilinos/qcaqlx2soyjs/lib/libamesos.so.11 > (0x00002b7d52f98000) > libepetraext.so.11 => > /pfs/nobackup/home/b/bbrydsoe/fenics_5_build/bld/trilinos/qcaqlx2soyjs/lib/libepetraext.so.11 > (0x00002b7d53270000) > libbelosepetra.so.11 => > /pfs/nobackup/home/b/bbrydsoe/fenics_5_build/bld/trilinos/qcaqlx2soyjs/lib/libbelosepetra.so.11 > (0x00002b7d53580000) > libbelos.so.11 => > /pfs/nobackup/home/b/bbrydsoe/fenics_5_build/bld/trilinos/qcaqlx2soyjs/lib/libbelos.so.11 > (0x00002b7d538c0000) > libepetra.so.11 => > /pfs/nobackup/home/b/bbrydsoe/fenics_5_build/bld/trilinos/qcaqlx2soyjs/lib/libepetra.so.11 > (0x00002b7d53ac8000) > libkokkosdisttsqr.so.11 => > /pfs/nobackup/home/b/bbrydsoe/fenics_5_build/bld/trilinos/qcaqlx2soyjs/lib/libkokkosdisttsqr.so.11 > (0x00002b7d53e30000) > libkokkosnodetsqr.so.11 => > /pfs/nobackup/home/b/bbrydsoe/fenics_5_build/bld/trilinos/qcaqlx2soyjs/lib/libkokkosnodetsqr.so.11 > (0x00002b7d54048000) > libteuchosnumerics.so.11 => > /pfs/nobackup/home/b/bbrydsoe/fenics_5_build/bld/trilinos/qcaqlx2soyjs/lib/libteuchosnumerics.so.11 > (0x00002b7d542c0000) > libteuchoscomm.so.11 => > /pfs/nobackup/home/b/bbrydsoe/fenics_5_build/bld/trilinos/qcaqlx2soyjs/lib/libteuchoscomm.so.11 > (0x00002b7d544e8000) > libteuchosparameterlist.so.11 => > /pfs/nobackup/home/b/bbrydsoe/fenics_5_build/bld/trilinos/qcaqlx2soyjs/lib/libteuchosparameterlist.so.11 > (0x00002b7d547c8000) > libteuchoscore.so.11 => > /pfs/nobackup/home/b/bbrydsoe/fenics_5_build/bld/trilinos/qcaqlx2soyjs/lib/libteuchoscore.so.11 > (0x00002b7d54d20000) > libopenblas.so.0 => > /pfs/nobackup/home/b/bbrydsoe/fenics_5_build/bld/openblas/4lzg23k34ugh/lib/libopenblas.so.0 > (0x00002b7d54f88000) > libparmetis.so => > /pfs/nobackup/home/b/bbrydsoe/fenics_5_build/bld/parmetis/geuhf7fxgppt/lib/libparmetis.so > (0x00002b7d55f70000) > libmpi_cxx.so.0 => /usr/lib/libmpi_cxx.so.0 (0x00002b7d561f0000) > libmpi.so.0 => /usr/lib/libmpi.so.0 (0x00002b7d56410000) > libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00002b7d566c8000) > libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 > (0x00002b7d569c8000) > libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1 > (0x00002b7d56cc8000) > libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 > (0x00002b7d56ed8000) > libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00002b7d570f0000) > libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00002b7d574b0000) > liblzma.so.5 => /usr/lib/x86_64-linux-gnu/liblzma.so.5 > (0x00002b7d576b8000) > librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00002b7d578e0000) > libbz2.so.1.0 => > /pfs/nobackup/home/b/bbrydsoe/fenics_5_build/bld/bzip2/36p53sj2wv7t/lib/libbz2.so.1.0 > (0x00002b7d57af0000) > libmpi.so.1 => /lap/openmpi/1.8.1/gcc-4.6/lib/libmpi.so.1 > (0x00002b7d57d00000) > /lib64/ld-linux-x86-64.so.2 (0x00002b7d50008000) > libgaleri.so.11 => > /pfs/nobackup/home/b/bbrydsoe/fenics_5_build/bld/trilinos/qcaqlx2soyjs/lib/libgaleri.so.11 > (0x00002b7d57fd8000) > libaztecoo.so.11 => > /pfs/nobackup/home/b/bbrydsoe/fenics_5_build/bld/trilinos/qcaqlx2soyjs/lib/libaztecoo.so.11 > (0x00002b7d58220000) > libmpi_cxx.so.1 => /lap/openmpi/1.8.1/gcc-4.6/lib/libmpi_cxx.so.1 > (0x00002b7d584b8000) > libteuchosremainder.so.11 => > /pfs/nobackup/home/b/bbrydsoe/fenics_5_build/bld/trilinos/qcaqlx2soyjs/lib/libteuchosremainder.so.11 > (0x00002b7d586d8000) > libtriutils.so.11 => > /pfs/nobackup/home/b/bbrydsoe/fenics_5_build/bld/trilinos/qcaqlx2soyjs/lib/libtriutils.so.11 > (0x00002b7d588f8000) > libgfortran.so.3 => /usr/lib/x86_64-linux-gnu/libgfortran.so.3 > (0x00002b7d58b58000) > libopen-rte.so.0 => /usr/lib/libopen-rte.so.0 (0x00002b7d58e70000) > libopen-rte.so.7 => /lap/openmpi/1.8.1/gcc-4.6/lib/libopen-rte.so.7 > (0x00002b7d590c0000) > libopen-pal.so.6 => /lap/openmpi/1.8.1/gcc-4.6/lib/libopen-pal.so.6 > (0x00002b7d59340000) > libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 > (0x00002b7d59618000) > libopen-pal.so.0 => /usr/lib/libopen-pal.so.0 (0x00002b7d59850000) > libnuma.so.1 => /usr/lib/libnuma.so.1 (0x00002b7d59aa8000) > libpciaccess.so.0 => /usr/lib/x86_64-linux-gnu/libpciaccess.so.0 > (0x00002b7d59cb8000) > libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 > (0x00002b7d59ec8000) > > > > How do I set it in the yaml file so that fenics only grabs the MPI in > > /lap/openmpi/1.8.1/gcc-4.6/
Is this a module? In that case you should add "module load <modulename>" to PROLOGUE. See for instance some of the examples in hashstack. Some comments about your profile: - You should use openblas for blas and lapack since you build petsc and dolfin with openblas. - It looks like the PATH is not indented correctly. Is that on purpose? Johannes _______________________________________________ fenics-support mailing list [email protected] http://fenicsproject.org/mailman/listinfo/fenics-support
