On Wed, Jul 23, 2014 at 3:07 PM, Jan Blechta <[email protected]> wrote: > Have you tried running in debugger, interrupting in a deadlocked state > and printing backtrace?
Thanks for the tip. I started the test with "mpirun -np 2 python test_hdf5.py" and then did "gdb -pid <pid>" to attach the debugger. The output is attached. Does it make sense to anyone? Johannes
johannr@gpc-f104n084:~$ gdb -pid 1260 GNU gdb (GDB) 7.3.1 Copyright (C) 2011 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html> This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Type "show copying" and "show warranty" for details. This GDB was configured as "x86_64-unknown-linux-gnu". For bug reporting instructions, please see: <http://www.gnu.org/software/gdb/bugs/>. Attaching to process 1260 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/bin/python2.7...done. Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libpython2.7.so.1.0...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libpython2.7.so.1.0 Reading symbols from /lib64/libdl.so.2...(no debugging symbols found)...done. Loaded symbols for /lib64/libdl.so.2 Reading symbols from /lib64/libm.so.6...(no debugging symbols found)...done. Loaded symbols for /lib64/libm.so.6 Reading symbols from /scinet/gpc/mpi/openmpi/1.4.4-gcc-v4.6.1/lib/libmpi.so.0...done. Loaded symbols for /scinet/gpc/mpi/openmpi/1.4.4-gcc-v4.6.1/lib/libmpi.so.0 Reading symbols from /scinet/gpc/mpi/openmpi/1.4.4-gcc-v4.6.1/lib/libopen-rte.so.0...(no debugging symbols found)...done. Loaded symbols for /scinet/gpc/mpi/openmpi/1.4.4-gcc-v4.6.1/lib/libopen-rte.so.0 Reading symbols from /scinet/gpc/mpi/openmpi/1.4.4-gcc-v4.6.1/lib/libopen-pal.so.0...(no debugging symbols found)...done. Loaded symbols for /scinet/gpc/mpi/openmpi/1.4.4-gcc-v4.6.1/lib/libopen-pal.so.0 Reading symbols from /usr/lib64/librdmacm.so.1...(no debugging symbols found)...done. Loaded symbols for /usr/lib64/librdmacm.so.1 Reading symbols from /usr/lib64/libibverbs.so.1...(no debugging symbols found)...done. Loaded symbols for /usr/lib64/libibverbs.so.1 Reading symbols from /opt/torque/lib/libtorque.so.2...done. Loaded symbols for /opt/torque/lib/libtorque.so.2 Reading symbols from /lib64/libnsl.so.1...(no debugging symbols found)...done. Loaded symbols for /lib64/libnsl.so.1 Reading symbols from /lib64/libutil.so.1...(no debugging symbols found)...done. Loaded symbols for /lib64/libutil.so.1 Reading symbols from /lib64/libpthread.so.0...(no debugging symbols found)...done. [Thread debugging using libthread_db enabled] Loaded symbols for /lib64/libpthread.so.0 Reading symbols from /lib64/libc.so.6...(no debugging symbols found)...done. Loaded symbols for /lib64/libc.so.6 Reading symbols from /lib64/ld-linux-x86-64.so.2...(no debugging symbols found)...done. Loaded symbols for /lib64/ld-linux-x86-64.so.2 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/site-packages/numpy/core/multiarray.so...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/site-packages/numpy/core/multiarray.so Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/site-packages/numpy/core/umath.so...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/site-packages/numpy/core/umath.so Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/site-packages/numpy/core/_sort.so...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/site-packages/numpy/core/_sort.so Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/cPickle.so...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/cPickle.so Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/cStringIO.so...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/cStringIO.so Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/site-packages/numpy/core/scalarmath.so...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/site-packages/numpy/core/scalarmath.so Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/_collections.so...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/_collections.so Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/operator.so...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/operator.so Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/itertools.so...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/itertools.so Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/_bisect.so...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/_bisect.so Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/_heapq.so...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/_heapq.so Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/_functools.so...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/_functools.so Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/time.so...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/time.so Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/math.so...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/math.so Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/site-packages/numpy/lib/_compiled_base.so...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/site-packages/numpy/lib/_compiled_base.so Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so Reading symbols from /scinet/gpc/compilers/gcc-4.6.1/lib64/libgfortran.so.3...done. Loaded symbols for /scinet/gpc/compilers/gcc-4.6.1/lib64/libgfortran.so.3 Reading symbols from /scinet/gpc/compilers/gcc-4.6.1/lib64/libgcc_s.so.1...done. Loaded symbols for /scinet/gpc/compilers/gcc-4.6.1/lib64/libgcc_s.so.1 Reading symbols from /scinet/gpc/compilers/gcc-4.6.1/lib64/libquadmath.so.0...done. Loaded symbols for /scinet/gpc/compilers/gcc-4.6.1/lib64/libquadmath.so.0 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/grp.so...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/grp.so Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/site-packages/numpy/fft/fftpack_lite.so...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/site-packages/numpy/fft/fftpack_lite.so Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/strop.so...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/strop.so Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/site-packages/numpy/random/mtrand.so...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/site-packages/numpy/random/mtrand.so Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/_ctypes.so...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/_ctypes.so Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/_struct.so...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/_struct.so Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/_io.so...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/_io.so Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/select.so...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/select.so Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/fcntl.so...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/fcntl.so Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/binascii.so...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/binascii.so Reading symbols from /lib64/libz.so.1...(no debugging symbols found)...done. Loaded symbols for /lib64/libz.so.1 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/_hashlib.so...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/_hashlib.so Reading symbols from /usr/lib64/libssl.so.10...(no debugging symbols found)...done. Loaded symbols for /usr/lib64/libssl.so.10 Reading symbols from /usr/lib64/libcrypto.so.10...(no debugging symbols found)...done. Loaded symbols for /usr/lib64/libcrypto.so.10 Reading symbols from /lib64/libgssapi_krb5.so.2...(no debugging symbols found)...done. Loaded symbols for /lib64/libgssapi_krb5.so.2 Reading symbols from /lib64/libkrb5.so.3...(no debugging symbols found)...done. Loaded symbols for /lib64/libkrb5.so.3 Reading symbols from /lib64/libcom_err.so.2...(no debugging symbols found)...done. Loaded symbols for /lib64/libcom_err.so.2 Reading symbols from /lib64/libk5crypto.so.3...(no debugging symbols found)...done. Loaded symbols for /lib64/libk5crypto.so.3 Reading symbols from /lib64/libkrb5support.so.0...(no debugging symbols found)...done. Loaded symbols for /lib64/libkrb5support.so.0 Reading symbols from /lib64/libkeyutils.so.1...(no debugging symbols found)...done. Loaded symbols for /lib64/libkeyutils.so.1 Reading symbols from /lib64/libresolv.so.2...(no debugging symbols found)...done. Loaded symbols for /lib64/libresolv.so.2 Reading symbols from /lib64/libselinux.so.1...(no debugging symbols found)...done. Loaded symbols for /lib64/libselinux.so.1 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/site-packages/Scientific/linux2/Scientific_numerics_package_id.so...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/site-packages/Scientific/linux2/Scientific_numerics_package_id.so Reading symbols from /home/s/steinman/johannr/fenics/fenics-1.4.0/lib/python2.7/site-packages/ffc/time_elements_ext.so...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-1.4.0/lib/python2.7/site-packages/ffc/time_elements_ext.so Reading symbols from /scinet/gpc/mpi/openmpi/1.4.4-gcc-v4.6.1/lib/libmpi_cxx.so.0...(no debugging symbols found)...done. Loaded symbols for /scinet/gpc/mpi/openmpi/1.4.4-gcc-v4.6.1/lib/libmpi_cxx.so.0 Reading symbols from /scinet/gpc/compilers/gcc-4.6.1/lib64/libstdc++.so.6...done. Loaded symbols for /scinet/gpc/compilers/gcc-4.6.1/lib64/libstdc++.so.6 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/_random.so...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/python2.7/lib-dynload/_random.so Reading symbols from /home/s/steinman/johannr/fenics/fenics-1.4.0/lib/python2.7/site-packages/ufc/_ufc.so...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-1.4.0/lib/python2.7/site-packages/ufc/_ufc.so Reading symbols from /home/s/steinman/johannr/fenics/fenics-1.4.0/lib/python2.7/site-packages/dolfin/cpp/_common.so...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-1.4.0/lib/python2.7/site-packages/dolfin/cpp/_common.so Reading symbols from /home/s/steinman/johannr/fenics/fenics-1.4.0/lib/libdolfin.so.1.4...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-1.4.0/lib/libdolfin.so.1.4 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libxml2.so.2...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libxml2.so.2 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libboost_filesystem.so.1.51.0...(no debugging symbols found)...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libboost_filesystem.so.1.51.0 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libboost_program_options.so.1.51.0...(no debugging symbols found)...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libboost_program_options.so.1.51.0 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libboost_system.so.1.51.0...(no debugging symbols found)...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libboost_system.so.1.51.0 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libboost_thread.so.1.51.0...(no debugging symbols found)...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libboost_thread.so.1.51.0 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libboost_iostreams.so.1.51.0...(no debugging symbols found)...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libboost_iostreams.so.1.51.0 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libhdf5.so.7...(no debugging symbols found)...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libhdf5.so.7 Reading symbols from /lib64/librt.so.1...(no debugging symbols found)...done. Loaded symbols for /lib64/librt.so.1 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libml.so.11...(no debugging symbols found)...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libml.so.11 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libgaleri-xpetra.so.11...(no debugging symbols found)...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libgaleri-xpetra.so.11 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libgaleri.so.11...(no debugging symbols found)...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libgaleri.so.11 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libisorropia.so.11...(no debugging symbols found)...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libisorropia.so.11 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libxpetra-sup.so.11...(no debugging symbols found)...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libxpetra-sup.so.11 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libxpetra-ext.so.11...(no debugging symbols found)...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libxpetra-ext.so.11 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libxpetra.so.11...(no debugging symbols found)...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libxpetra.so.11 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libzoltan.so.11...(no debugging symbols found)...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libzoltan.so.11 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libifpack.so.11...(no debugging symbols found)...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libifpack.so.11 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libaztecoo.so.11...(no debugging symbols found)...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libaztecoo.so.11 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libamesos.so.11...(no debugging symbols found)...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libamesos.so.11 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libepetraext.so.11...(no debugging symbols found)...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libepetraext.so.11 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libtriutils.so.11...(no debugging symbols found)...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libtriutils.so.11 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libbelostpetra.so.11...(no debugging symbols found)...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libbelostpetra.so.11 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libbelosepetra.so.11...(no debugging symbols found)...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libbelosepetra.so.11 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libbelos.so.11...(no debugging symbols found)...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libbelos.so.11 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libtpetraext.so.11...(no debugging symbols found)...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libtpetraext.so.11 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libtpetrainout.so.11...(no debugging symbols found)...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libtpetrainout.so.11 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libtpetra.so.11...(no debugging symbols found)...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libtpetra.so.11 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libepetra.so.11...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libepetra.so.11 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libkokkosdisttsqr.so.11...(no debugging symbols found)...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libkokkosdisttsqr.so.11 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libkokkosnodetsqr.so.11...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libkokkosnodetsqr.so.11 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libkokkoslinalg.so.11...(no debugging symbols found)...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libkokkoslinalg.so.11 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libkokkosnodeapi.so.11...(no debugging symbols found)...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libkokkosnodeapi.so.11 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libkokkos.so.11...(no debugging symbols found)...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libkokkos.so.11 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libtpi.so.11...(no debugging symbols found)...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libtpi.so.11 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libteuchosremainder.so.11...(no debugging symbols found)...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libteuchosremainder.so.11 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libteuchosnumerics.so.11...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libteuchosnumerics.so.11 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libteuchoscomm.so.11...(no debugging symbols found)...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libteuchoscomm.so.11 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libteuchosparameterlist.so.11...(no debugging symbols found)...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libteuchosparameterlist.so.11 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libteuchoscore.so.11...(no debugging symbols found)...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libteuchoscore.so.11 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libpetsc.so...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libpetsc.so Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libparmetis.so...(no debugging symbols found)...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libparmetis.so Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libmetis.so...(no debugging symbols found)...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libmetis.so Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libCGAL.so.10...(no debugging symbols found)...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libCGAL.so.10 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libgmp.so.10...(no debugging symbols found)...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libgmp.so.10 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libmpfr.so.4...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libmpfr.so.4 Reading symbols from /scinet/gpc/compilers/gcc-4.6.1/lib64/libgomp.so.1...done. Loaded symbols for /scinet/gpc/compilers/gcc-4.6.1/lib64/libgomp.so.1 Reading symbols from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libboost_chrono.so.1.51.0...(no debugging symbols found)...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libboost_chrono.so.1.51.0 Reading symbols from /lib64/libbz2.so.1...(no debugging symbols found)...done. Loaded symbols for /lib64/libbz2.so.1 Reading symbols from /scinet/gpc/mpi/openmpi/1.4.4-gcc-v4.6.1/lib/libmpi_f90.so.0...(no debugging symbols found)...done. Loaded symbols for /scinet/gpc/mpi/openmpi/1.4.4-gcc-v4.6.1/lib/libmpi_f90.so.0 Reading symbols from /scinet/gpc/mpi/openmpi/1.4.4-gcc-v4.6.1/lib/libmpi_f77.so.0...(no debugging symbols found)...done. Loaded symbols for /scinet/gpc/mpi/openmpi/1.4.4-gcc-v4.6.1/lib/libmpi_f77.so.0 Reading symbols from /scinet/gpc/lib64_6.4/libX11.so.6...(no debugging symbols found)...done. Loaded symbols for /scinet/gpc/lib64_6.4/libX11.so.6 Reading symbols from /scinet/gpc/lib64_6.4/libxcb.so.1...(no debugging symbols found)...done. Loaded symbols for /scinet/gpc/lib64_6.4/libxcb.so.1 Reading symbols from /scinet/gpc/lib64_6.4/libXau.so.6...(no debugging symbols found)...done. Loaded symbols for /scinet/gpc/lib64_6.4/libXau.so.6 Reading symbols from /home/s/steinman/johannr/fenics/fenics-1.4.0/lib/python2.7/site-packages/dolfin/cpp/_la.so...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-1.4.0/lib/python2.7/site-packages/dolfin/cpp/_la.so Reading symbols from /home/s/steinman/johannr/fenics/fenics-1.4.0/lib/python2.7/site-packages/dolfin/cpp/_function.so...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-1.4.0/lib/python2.7/site-packages/dolfin/cpp/_function.so Reading symbols from /home/s/steinman/johannr/fenics/fenics-1.4.0/lib/python2.7/site-packages/dolfin/cpp/_mesh.so...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-1.4.0/lib/python2.7/site-packages/dolfin/cpp/_mesh.so Reading symbols from /home/s/steinman/johannr/fenics/fenics-1.4.0/lib/python2.7/site-packages/dolfin/cpp/_fem.so...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-1.4.0/lib/python2.7/site-packages/dolfin/cpp/_fem.so Reading symbols from /home/s/steinman/johannr/fenics/fenics-1.4.0/lib/python2.7/site-packages/dolfin/cpp/_io.so...done. Loaded symbols for /home/s/steinman/johannr/fenics/fenics-1.4.0/lib/python2.7/site-packages/dolfin/cpp/_io.so Reading symbols from /lib64/libnss_files.so.2...(no debugging symbols found)...done. Loaded symbols for /lib64/libnss_files.so.2 Reading symbols from /lib64/libnss_sss.so.2...(no debugging symbols found)...done. Loaded symbols for /lib64/libnss_sss.so.2 0x00007fe44eef7054 in __lll_lock_wait () from /lib64/libpthread.so.0 (gdb) backtrace #0 0x00007fe44eef7054 in __lll_lock_wait () from /lib64/libpthread.so.0 #1 0x00007fe44eef2388 in _L_lock_854 () from /lib64/libpthread.so.0 #2 0x00007fe44eef2257 in pthread_mutex_lock () from /lib64/libpthread.so.0 #3 0x00007fe4502074a4 in progress () from /scinet/gpc/mpi/openmpi/1.4.4-gcc-v4.6.1/lib/libmpi.so.0 #4 0x00007fe4502050ca in mca_io_base_component_run_progress () from /scinet/gpc/mpi/openmpi/1.4.4-gcc-v4.6.1/lib/libmpi.so.0 #5 0x00007fe44fc4acdb in opal_progress () from /scinet/gpc/mpi/openmpi/1.4.4-gcc-v4.6.1/lib/libopen-pal.so.0 #6 0x00007fe45016e80d in ompi_request_default_wait_all () from /scinet/gpc/mpi/openmpi/1.4.4-gcc-v4.6.1/lib/libmpi.so.0 #7 0x00007fe4501e30a6 in ompi_coll_tuned_sendrecv_actual () from /scinet/gpc/mpi/openmpi/1.4.4-gcc-v4.6.1/lib/libmpi.so.0 #8 0x00007fe4501eb2cf in ompi_coll_tuned_barrier_intra_two_procs () from /scinet/gpc/mpi/openmpi/1.4.4-gcc-v4.6.1/lib/libmpi.so.0 #9 0x00007fe450184c5e in PMPI_Barrier () from /scinet/gpc/mpi/openmpi/1.4.4-gcc-v4.6.1/lib/libmpi.so.0 #10 0x00007fe4502269cf in mca_io_romio_dist_MPI_File_set_view () from /scinet/gpc/mpi/openmpi/1.4.4-gcc-v4.6.1/lib/libmpi.so.0 #11 0x00007fe450207c22 in mca_io_romio_file_set_view () from /scinet/gpc/mpi/openmpi/1.4.4-gcc-v4.6.1/lib/libmpi.so.0 #12 0x00007fe4501a9cef in PMPI_File_set_view () from /scinet/gpc/mpi/openmpi/1.4.4-gcc-v4.6.1/lib/libmpi.so.0 #13 0x00007fe445468dfe in H5FD_mpio_write () from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libhdf5.so.7 #14 0x00007fe445465f3a in H5FD_write () from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libhdf5.so.7 #15 0x00007fe445455659 in H5F_accum_write () from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libhdf5.so.7 #16 0x00007fe445457f46 in H5F_block_write () from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libhdf5.so.7 #17 0x00007fe44543b5d9 in H5D__mpio_select_write () from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libhdf5.so.7 #18 0x00007fe4454398a6 in H5D__final_collective_io () from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libhdf5.so.7 #19 0x00007fe4454399ed in H5D__inter_collective_io () from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libhdf5.so.7 #20 0x00007fe44543d2db in H5D__contig_collective_write () from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libhdf5.so.7 #21 0x00007fe445437ec2 in H5D__write () from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libhdf5.so.7 #22 0x00007fe445438757 in H5Dwrite () from /home/s/steinman/johannr/fenics/fenics-deps-gnu-2014-01-28/lib/libhdf5.so.7 #23 0x00007fe4471d9384 in dolfin::HDF5Interface::write_dataset<double> (file_handle=16777216, dataset_name=Cannot access memory at address 0x7fff04000002 ) at /home/s/steinman/johannr/fenics/fenics-1.4.0/src/dolfin-1.4.0/dolfin/io/HDF5Interface.h:301 #24 0x00007fe4471d9656 in dolfin::HDF5File::write_data<double> (this=0x17c3d40, dataset_name="/my_mesh/coordinates", data=std::vector of length 26, capacity 30 = {...}, global_size=<optimized out>, use_mpi_io=true) at /home/s/steinman/johannr/fenics/fenics-1.4.0/src/dolfin-1.4.0/dolfin/io/HDF5File.h:225 #25 0x00007fe4472085e4 in dolfin::HDF5File::write (this=0x17c3d40, mesh=..., cell_dim=2, name="/my_mesh") at /home/s/steinman/johannr/fenics/fenics-1.4.0/src/dolfin-1.4.0/dolfin/io/HDF5File.cpp:274 #26 0x00007fe44720985c in dolfin::HDF5File::write (this=0x17c3d40, mesh=..., name=<optimized out>) at /home/s/steinman/johannr/fenics/fenics-1.4.0/src/dolfin-1.4.0/dolfin/io/HDF5File.cpp:248 #27 0x00007fe43bbccd4e in _wrap_HDF5File_write__SWIG_3 (nobjs=<optimized out>, swig_obj=<optimized out>) at /home/s/steinman/johannr/fenics/fenics-1.4.0/src/dolfin-1.4.0/dorsal_build_dir/dolfin/swig/modules/io/modulePYTHON_wrap.cxx:23661 #28 0x00007fe43bbcd91b in _wrap_HDF5File_write (self=<optimized out>, args=<optimized out>) at /home/s/steinman/johannr/fenics/fenics-1.4.0/src/dolfin-1.4.0/dorsal_build_dir/dolfin/swig/modules/io/modulePYTHON_wrap.cxx:24917 #29 0x00007fe450acfabb in do_call (nk=<optimized out>, na=<optimized out>, pp_stack=0x7fff09b179c0, func=0x7fe43c18ab48) at Python/ceval.c:4228 ---Type <return> to continue, or q <return> to quit--- #30 call_function (oparg=<optimized out>, pp_stack=0x7fff09b179c0) at Python/ceval.c:4036 #31 PyEval_EvalFrameEx (f=<optimized out>, throwflag=<optimized out>) at Python/ceval.c:2666 #32 0x00007fe450ad1175 in PyEval_EvalCodeEx (co=<optimized out>, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:3253 #33 0x00007fe450ad12b2 in PyEval_EvalCode (co=<optimized out>, globals=<optimized out>, locals=<optimized out>) at Python/ceval.c:667 #34 0x00007fe450af3770 in run_mod (arena=0xf909a0, flags=0x7fff09b17cd0, locals=0xf08440, globals=0xf08440, filename=<optimized out>, mod=0xfa0b28) at Python/pythonrun.c:1346 #35 PyRun_FileExFlags (fp=0xf90760, filename=<optimized out>, start=<optimized out>, globals=0xf08440, locals=0xf08440, closeit=1, flags=0x7fff09b17cd0) at Python/pythonrun.c:1332 #36 0x00007fe450af420f in PyRun_SimpleFileExFlags (fp=0xf90760, filename=0x7fff09b18778 "test_hdf5.py", closeit=1, flags=0x7fff09b17cd0) at Python/pythonrun.c:936 #37 0x00007fe450b06f7b in Py_Main (argc=<optimized out>, argv=<optimized out>) at Modules/main.c:599 #38 0x00007fe44eb74cdd in __libc_start_main () from /lib64/libc.so.6 #39 0x0000000000400699 in _start () (gdb)
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