/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.
Yes. It's a module.
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?
No, that was an error.
After adding the module to prologue, using openblas, and indenting the
PATH, I got a bit longer. Fenics builds, I can import dolfin into python,
and I no longer get the ORTE error. It is using the correct MPI version,
so that is great, thanks!
I now have a problem with incompatible versions of SWIG. The one installed
on the system is 2.0.4, and fenics seems to have built 2.0.11. For some
reason it then tries to use the system version during running, I think?
This is the error message I get when trying to run a short test program
bvp_01.py:
Incompatible swig versions detected. UFC swig version is not the same as
extension module swig version: '2.0.11' != '2.0.4'
Traceback (most recent call last):
File "./bvp_01.py", line 119, in <module>
bvp_01 ( 8 )
File "./bvp_01.py", line 47, in bvp_01
V = FunctionSpace ( mesh, "Lagrange", 1 )
File
"/pfs/nobackup/home/b/bbrydsoe/fenics_MPIMODULE_build/bld/profile/hztejro3ksqb/lib/python2.7/site-packages/dolfin/functions/functionspace.py",
line 456, in __init__
FunctionSpaceBase.__init__(self, mesh, element, constrained_domain)
File
"/pfs/nobackup/home/b/bbrydsoe/fenics_MPIMODULE_build/bld/profile/hztejro3ksqb/lib/python2.7/site-packages/dolfin/functions/functionspace.py",
line 147, in __init__
ufc_element, ufc_dofmap = jit(self._ufl_element)
File
"/pfs/nobackup/home/b/bbrydsoe/fenics_MPIMODULE_build/bld/profile/hztejro3ksqb/lib/python2.7/site-packages/dolfin/compilemodules/jit.py",
line 66, in mpi_jit
output = local_jit(*args, **kwargs)
File
"/pfs/nobackup/home/b/bbrydsoe/fenics_MPIMODULE_build/bld/profile/hztejro3ksqb/lib/python2.7/site-packages/dolfin/compilemodules/jit.py",
line 126, in jit
return jit_compile(form, parameters=p)
File
"/pfs/nobackup/home/b/bbrydsoe/fenics_MPIMODULE_build/bld/profile/hztejro3ksqb/lib/python2.7/site-packages/ffc/jitcompiler.py",
line 75, in jit
return jit_element(ufl_object, parameters)
File
"/pfs/nobackup/home/b/bbrydsoe/fenics_MPIMODULE_build/bld/profile/hztejro3ksqb/lib/python2.7/site-packages/ffc/jitcompiler.py",
line 186, in jit_element
compiled_form, module, form_data, prefix = jit_form(form, parameters)
File
"/pfs/nobackup/home/b/bbrydsoe/fenics_MPIMODULE_build/bld/profile/hztejro3ksqb/lib/python2.7/site-packages/ffc/jitcompiler.py",
line 164, in jit_form
check_swig_version(module)
File
"/pfs/nobackup/home/b/bbrydsoe/fenics_MPIMODULE_build/bld/profile/hztejro3ksqb/lib/python2.7/site-packages/ffc/jitcompiler.py",
line 86, in check_swig_version
(ufc.__swigversion__, compiled_module.swigversion))
File "<string>", line 1, in <lambda>
File
"/pfs/nobackup/home/b/bbrydsoe/fenics_MPIMODULE_build/bld/profile/hztejro3ksqb/lib/python2.7/site-packages/ufl/log.py",
line 151, in error
raise self._exception_type(self._format_raw(*message))
Exception: Incompatible swig versions detected. UFC swig version is not
the same as extension module swig version: '2.0.11' != '2.0.4'
Also attaching the new version of my yaml file.
Is there something I need to set differently in order for fenics to run
with the swig it has built?
Thanks, Birgitte
--
Birgitte Maria E. Brydsö
HPC2N, MIT-Huset
Umeå University
SE-901 87 Umeå
Telephone: +46(0)90-786 64 55
Email: [email protected]
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: |
source /lap/modules/init/bash; module load openmpi/gcc/1.6.5; module load
cmake; export CC=gcc; export CXX=g++; export FC=gfortran; export F77=gfortran;
export F90=gfortran; export CPP=cpp; CCP=/lap/openmpi/1.6.5/gcc-4.6/bin/mpicc;
mpicc=/lap/openmpi/1.6.5/gcc-4.6/bin/mpicc;
PATH:
/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:/lap/openmpi/1.6.5/gcc-4.6/bin/mpicc:/usr/bin:/bin
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
# use: openmpi
blas:
# use: host-blas
use: openblas
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
use: openblas
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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