On Mon, 2 Mar 2015, Birgitte Maria Elisabeth Brydso wrote:
I haven't been able to find out what the problem is still. Fenics builds, but
I cannot run anything.
If I try loading dolfin in python, I get:
Python 2.7.3 (default, Dec 18 2014, 19:10:20)
[GCC 4.6.3] on linux2
Type "help", "copyright", "credits" or "license" for more information.
import dolfin
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File
"/pfs/nobackup/home/b/bbrydsoe/fenics_4_build/bld/profile/r63cg2noaejh/lib/python2.7/site-packages/dolfin/__init__.py",
line 16, in <module>
import cpp
File
"/pfs/nobackup/home/b/bbrydsoe/fenics_4_build/bld/profile/r63cg2noaejh/lib/python2.7/site-packages/dolfin/cpp/__init__.py",
line 42, in <module>
exec("import %s" % module_name)
File "<string>", line 1, in <module>
File
"/pfs/nobackup/home/b/bbrydsoe/fenics_4_build/bld/profile/r63cg2noaejh/lib/python2.7/site-packages/dolfin/cpp/common.py",
line 30, in <module>
_common = swig_import_helper()
File
"/pfs/nobackup/home/b/bbrydsoe/fenics_4_build/bld/profile/r63cg2noaejh/lib/python2.7/site-packages/dolfin/cpp/common.py",
line 26, in swig_import_helper
_mod = imp.load_module('_common', fp, pathname, description)
ImportError:
/pfs/nobackup/home/b/bbrydsoe/fenics_4_build/bld/trilinos/lpxvrylngji5/lib/libepetra.so.11:
undefined symbol: sgecon_
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.
-Birgitte
extends:
- name: hashstack
urls: ['https://github.com/hashdist/hashstack.git']
key: 'git:1a97d560b12d86d8c36f8e574a1ebb3ea00067b7'
file: debian.yaml
parameters:
HOST_MPICC: /lap/openmpi/1.6.5/gcc-4.6/bin/mpicc
HOST_MPICXX: /lap/openmpi/1.6.5/gcc-4.6/bin/mpic++
HOST_MPIF77: /lap/openmpi/1.6.5/gcc-4.6/bin/mpif77
HOST_MPIF90: /lap/openmpi/1.6.5/gcc-4.6/bin/mpif90
HOST_MPIEXEC: /lap/openmpi/1.6.5/gcc-4.6/bin/mpiexec
HOST_CMAKE: /lap/cmake/2.8.12.1/bin/cmake
HOST_PYTHON: /usr/bin/python
# HOST_SWIG_EXECUTABLE: /usr/bin/swig
# HOST_PETSC_DIR: /lap/petsc/3.4.3/gcc/ompi/opt
HOST_PETSC_ARCH: linux-gnu-cxx-opt
# HOST_SLEPC_DIR: /lap/slepc/3.4.3/gcc/ompi/opt
# HOST_BLAS_DIR: /lap/openblas/0.2.9/lib/gcc
# HOST_LAPACK: /lap/acml/5.3.1/gfortran64_fma4/lib
python_host_packages:
/lap/python-numpy/1.8.0/gcc-lapack-openblas/lib/python2.7/site-packages/numpy
DOLFIN_ENABLE_TESTING: true
PROLOGUE: |
export CC=gcc; export CXX=g++; export FC=gfortran; export F77=gfortran;
export F90=gfortran; export CPP=cpp;
PATH:
/usr/bin:/bin:/lap/python-numpy/1.8.0/gcc-lapack-openblas/lib/python2.7/site-packages/numpy:/usr/lib/python2.7/:/usr/lib/pymodules/python2.7/:/home/b/bbrydsoe/pfs/fenics_test1123/python-six/lib/python2.7/site-packages/:/pfs/nobackup/home/b/bbrydsoe/fenics_test1123/python-mpmath/lib/python2.7/site-packages/:/pfs/nobackup/home/b/bbrydsoe/fenics_test1123/python-sympy/lib/python2.7/site-packages/::/lap/acml/5.3.1/gfortran64_fma4/lib
packages:
launcher:
cmake:
use: host-cmake
python:
host: true
# build_with: |
# openssl, bzip2, sqlite
link: shared
use_python_host_packages: true
mpi:
use: host-mpi
blas:
use: host-blas
hdf5:
petsc:
build_with: |
parmetis, openblas, scotch, suitesparse
download: |
superlu, superlu_dist, hypre, scalapack, blacs, mumps
coptflags: -02
link: shared
debug: false
boost:
toolset: gcc
address_model: 64
swig:
pkg-config:
ipython:
zlib:
nose:
jinja2:
lapack:
use: host-lapack
numpy:
trilinos:
parmetis:
slepc:
scotch:
matplotlib:
fiat:
ufl:
ffc:
instant:
dolfin:
build_with: |
openblas, suitesparse, scotch, parmetis, petsc, petsc4py, slepc, zlib,
hdf5, bzip2, trilinos
build_type: Developer
mpi4py:
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