Hi.
After several attempts, I have succeeded in installing fenics, but when I
try to run any of the tests, I get python problems:
[/pfs/nobackup/home/b/bbrydsoe/fenics_localpython_install/tmp/dolfin-w5erxesok5bt-1/test/unit/la/python]$
python LinearOperator.py
Traceback (most recent call last):
File "LinearOperator.py", line 22, in <module>
from dolfin import *
File
"/pfs/nobackup/home/b/bbrydsoe/fenics_localpython_install/bld/profile/thqp2gid4zyu/lib/python2.7/site-packages/dolfin/__init__.py",
line 4, in <module>
import dolfin.importhandler
File
"/pfs/nobackup/home/b/bbrydsoe/fenics_localpython_install/bld/profile/thqp2gid4zyu/lib/python2.7/site-packages/dolfin/importhandler/__init__.py",
line 13, in <module>
import numpy
File
"/pfs/nobackup/home/b/bbrydsoe/fenics_localpython_install/bld/profile/thqp2gid4zyu/lib/python2.7/site-packages/numpy/__init__.py",
line 137, in <module>
import add_newdocs
File
"/pfs/nobackup/home/b/bbrydsoe/fenics_localpython_install/bld/profile/thqp2gid4zyu/lib/python2.7/site-packages/numpy/add_newdocs.py",
line 9, in <module>
from numpy.lib import add_newdoc
File
"/pfs/nobackup/home/b/bbrydsoe/fenics_localpython_install/bld/profile/thqp2gid4zyu/lib/python2.7/site-packages/numpy/lib/__init__.py",
line 4, in <module>
from type_check import *
File
"/pfs/nobackup/home/b/bbrydsoe/fenics_localpython_install/bld/profile/thqp2gid4zyu/lib/python2.7/site-packages/numpy/lib/type_check.py",
line 8, in <module>
import numpy.core.numeric as _nx
File
"/pfs/nobackup/home/b/bbrydsoe/fenics_localpython_install/bld/profile/thqp2gid4zyu/lib/python2.7/site-packages/numpy/core/__init__.py",
line 5, in <module>
import multiarray
ImportError: No module named multiarray
I suspect that there is some sort of confusion with the system
installed python and what fenics builds. So I told fenics to use the
system python, but I still get the above error. This is my config
file:
=====================
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-c-opt
# HOST_SLEPC_DIR: /lap/slepc/3.4.3/gcc/ompi/opt
HOST_BLAS_DIR: /lap/openblas/0.2.9/lib/gcc
DOLFIN_ENABLE_TESTING: true
packages:
blas:
use: host-blas
# alternative to system blas:
# use: openblas
mpi:
# On debian: apt-get install mpich
use: host-mpi
# alternative to system mpi:
# use: openmpi
zlib:
nose:
launcher:
jinja2:
python:
link: shared
host: true
use_python_host_packages: true
numpy:
use: host-numpy
cmake:
use: host-cmake
petsc:
# use: host-petsc
# build with: |
# parmetis, openblas, scotch, suitesparse
# download: |
# hypre, mumps, scalapack, blacs
# coptflags: -=2
# link: shared
# debug: false
slepc:
# use: host-slepc
swig:
# build_with: |
# perl
use: host-swig
scotch:
boost:
toolset: gcc
address_model: 64
fiat:
sources:
- key: git:d88253e16bce0dc84d148be65a83538cc3a4844c
url: https://bitbucket.org/fenics-project/fiat.git
ufl:
sources:
- key: git:18f8afc58fe02588336fafc4c74bc4d4c9fdfe1a
url: https://bitbucket.org/fenics-project/ufl.git
ffc:
sources:
- key: git:86d4931c8d6062806b06305beb5adf9f4d1edc94
url: https://bitbucket.org/fenics-project/ffc.git
instant:
sources:
- key: git:df4ca503985853a7ed83ecffe2ac1a6168fa0752
url: https://bitbucket.org/fenics-project/instant.git
dolfin:
sources:
- key: git:04e0f27510d409e0e3d3ac6e9feef7ba50279529
url: https://bitbucket.org/fenics-project/dolfin.git
build_with: |
suitesparse, scotch, parmetis, petsc, slepc, zlib, hdf5
build_type: Developer
=================================
I tried setting pythonpath (also to include six, mpmath, and sympy which
I built locally), but it seems to make no difference:
export
PYTHONPATH="${PYTHONPATH}:/usr/lib/python2.7/:/usr/lib/:/usr/lib/pymodules/python2.7/:/home/b/bbrydsoe/pfs/fenics_test1123/python-six/lib/python2.7/site-packages/:/pfs/nobackup/home/b/bbrydsoe/fenics_test1123/python-mpmath/lib/python2.7/site-packages/:/pfs/nobackup/home/b/bbrydsoe/fenics_test1123/python-sympy/lib/python2.7/site-packages/:$PYTHONPATH"
Also, during build it breaks with an error twice, and I have to add this
to /bld/fiat/ulechmm57ewo/lib/python2.7/site-packages/FIAT/expansions.py
import sys
sys.path.append('/pfs/nobackup/home/b/bbrydsoe/fenics_test1123/python-sympy/lib/python2.7/site-packages')
and then do
mkdir
/pfs/nobackup/home/b/bbrydsoe/fenics_localpython_install/bld/python/vocgqpztn6ne/lib
t-cn1123 [/pfs/nobackup/home/b/bbrydsoe/fenics_localpython]$ ln -s
/usr/lib/libpython2.7.so
/pfs/nobackup/home/b/bbrydsoe/fenics_localpython_install/bld/python/vocgqpztn6ne/lib/libpython2.7.so
Clearly, something is wrong with the python-path, but I can't figure out
what to do.
--
Birgitte Maria E. Brydsö
HPC2N, MIT-Huset
Umeå University
SE-901 87 Umeå
Telephone: +46(0)90-786 64 55
Email: [email protected]
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