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_
My best guess is that it is related to problems with SWIG? I have tried
building with the already installed SWIG, and lettng Fenics build, but no
changes. Nothing works.
Any ideas?
-Birgitte
On Thu, 26 Feb 2015, Birgitte Maria Elisabeth Brydso wrote:
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]
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