I am trying to build fenics on an Ubuntu 12.04 cluster (not as root).
Using fenics-install.sh it goes further than it did with Dolfin, but I
still had problems, which all seems python-related. I asusme they are
do to local variations in where python is installed.
They could be fixed by
mkdir
/pfs/nobackup/home/b/bbrydsoe/fenics_working_build/bld/python/vocgqpztn6ne/lib
ln -s /usr/lib/libpython2.7.so
/pfs/nobackup/home/b/bbrydsoe/fenics_working_build/bld/python/vocgqpztn6ne/lib/libpython2.7.so
and the first run-time error was due to our local numpy not being
in /usr/share/pyshared/numpy/
but installed as a loadable module in
/lap/python-numpy/1.8.0/gcc-lapack-openblas/lib/python2.7/site-packages/numpy/
I fixed that with a symlink.
So it built (but is there a way to get fenics to find the correct python
directories? I did set PYTHONPATH, but it did not seem to help).
I now tried to run a small test case, and I have no idea what the error
message means:
[t-cn1123.hpc2n.umu.se:23001] [[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_ess_base_std_prolog failed
--> Returned value Attempt to redefine an existing data type (-31)
instead of ORTE_SUCCESS
--------------------------------------------------------------------------
[t-cn1123.hpc2n.umu.se:23001] [[INVALID],INVALID] ORTE_ERROR_LOG: Attempt
to redefine an existing data type in file
../../../orte/runtime/orte_init.c at line 132
[t-cn1123:23001] *** Process received signal ***
[t-cn1123:23001] Signal: Segmentation fault (11)
[t-cn1123:23001] Signal code: Invalid permissions (2)
[t-cn1123:23001] Failing at address: 0x2add7336fce0
[t-cn1123:23001] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0)
[0x2add67f27cb0]
[t-cn1123:23001] [ 1]
/lap/openmpi/1.6.5/gcc-4.6/lib/libmpi.so.1(opal_show_help+0)
[0x2add7336fce0]
[t-cn1123:23001] *** End of error message ***
Any ideas?
--
Birgitte Maria E. Brydsö
HPC2N, MIT-Huset
Umeå University
SE-901 87 Umeå
Telephone: +46(0)90-786 64 55
Email: [email protected]
_______________________________________________
fenics-support mailing list
[email protected]
http://fenicsproject.org/mailman/listinfo/fenics-support
