On Mon, 23 Feb 2015, Birgitte Maria Elisabeth Brydso wrote:
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.
List of problems snipped.
I gave up on that track, and are trying to compile with different
settings. It compiles and I now get different runtime errors, which are
related to trilinos:
Traceback (most recent call last):
File "circle.py", line 18, in <module>
from dolfin import *
File
"/pfs/nobackup/home/b/bbrydsoe/fenics_4_build/bld/profile/v2hvayjs3g2y/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/v2hvayjs3g2y/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/v2hvayjs3g2y/lib/python2.7/site-packages/dolfin/cpp/common.py",
line 32, in <module>
_common = swig_import_helper()
File
"/pfs/nobackup/home/b/bbrydsoe/fenics_4_build/bld/profile/v2hvayjs3g2y/lib/python2.7/site-packages/dolfin/cpp/common.py",
line 28, in swig_import_helper
_mod = imp.load_module('_common', fp, pathname, description)
ImportError:
/pfs/nobackup/home/b/bbrydsoe/fenics_4_build/bld/trilinos/tk5bfy4ns5ff/lib/libepetra.so.11:
undefined symbol: sgecon_
Looking into libepetra.so.11:
ldd
/pfs/nobackup/home/b/bbrydsoe/fenics_4_build/bld/trilinos/tk5bfy4ns5ff/lib/libepetra.so.11
linux-vdso.so.1 => (0x00007fffac1f8000)
libopenblas.so.0 =>
/pfs/nobackup/home/b/bbrydsoe/fenics_4_build/bld/openblas/g5qqrconxz6t/lib/libopenblas.so.0
(0x00002b4879540000)
libmpi_cxx.so.0 => /usr/lib/libmpi_cxx.so.0 (0x00002b487a540000)
libmpi.so.0 => /usr/lib/libmpi.so.0 (0x00002b487a760000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00002b487aa18000)
libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
(0x00002b487ad18000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1
(0x00002b487b018000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
(0x00002b487b230000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00002b487b450000)
libgfortran.so.3 => /usr/lib/x86_64-linux-gnu/libgfortran.so.3
(0x00002b487b810000)
libopen-rte.so.0 => /usr/lib/libopen-rte.so.0 (0x00002b487bb28000)
/lib64/ld-linux-x86-64.so.2 (0x00002b4878fb0000)
libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0
(0x00002b487bd78000)
libopen-pal.so.0 => /usr/lib/libopen-pal.so.0 (0x00002b487bfb0000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2
(0x00002b487c208000)
libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1
(0x00002b487c410000)
I don't see any errors. Has anyone experienced this/have any suggestions?
Attaching my local.yaml file
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-c-opt
HOST_SLEPC_DIR: /lap/slepc/3.4.3/gcc/ompi/opt
HOST_BLAS_DIR: /lap/openblas/0.2.9/lib/gcc
python_host_packages:
/lap/python-numpy/1.8.0/gcc-lapack-openblas/lib/python2.7/site-packages/numpy
DOLFIN_ENABLE_TESTING: true
PATH:
/usr/lib:/usr/local/bin:/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/scotch/6.0.0/:/lap/parmetis/4.0.2/
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
lapack:
use: openblas
# hypre:
# with_openblas: true
numpy:
use: host-numpy
cmake:
use: host-cmake
trilinos:
parmetis:
petsc:
use: host-petsc
# build with: |
# parmetis, openblas, scotch, suitesparse, superlu_dist, hypre
# download: |
# hypre, mumps, scalapack, blacs, ml
# coptflags: -=2
# link: shared
# debug: false
slepc:
# use: host-slepc
swig:
# build_with: |
# perl
# use: host-swig
scotch:
boost:
toolset: gcc
address_model: 64
build_with: python
ipython:
matplotlib:
fiat:
ufl:
ffc:
instant:
dolfin:
build_with: |
openblas, hdf5, parmetis, petsc, suitesparse, scotch, slepc, zlib,
trilinos
build_type: Developer
mpi4py:
_______________________________________________
fenics-support mailing list
[email protected]
http://fenicsproject.org/mailman/listinfo/fenics-support
