On Thursday, January 29, 2015 04:11 AM, Lu Lu wrote:
Hi,
I have installed the fenics from the Ubuntu PPA. However, when I tried
to import dolfin in Python, I met the following error:
Python 2.7.6 (default, Mar 22 2014, 22:59:56)
[GCC 4.8.2] on linux2
>>> import dolfin
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python2.7/dist-packages/dolfin/__init__.py", line 16,
in <module>
from . import cpp
File "/usr/lib/python2.7/dist-packages/dolfin/cpp/__init__.py", line
42, in <module>
exec("from . import %s" % module_name)
File "<string>", line 1, in <module>
File "/usr/lib/python2.7/dist-packages/dolfin/cpp/common.py", line
32, in <module>
_common = swig_import_helper()
File "/usr/lib/python2.7/dist-packages/dolfin/cpp/common.py", line
28, in swig_import_helper
_mod = imp.load_module('_common', fp, pathname, description)
ImportError: /usr/lib/libmpi_f77.so.1: undefined symbol: opal_uses_threads
I found the same question here:
https://www.mail-archive.com/[email protected]/msg01011.html.
But I still don't know how to solve this problem.
The output of 'ldd /usr/lib/libmpi_f77.so.1' is:
linux-vdso.so.1 => (0x00007fff0d1fe000)
libmpi.so.1 => /usr/local/lib/libmpi.so.1 (0x00007f8ba71aa000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
(0x00007f8ba6f8c000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f8ba6bc5000)
libopen-rte.so.7 => /usr/local/lib/libopen-rte.so.7
(0x00007f8ba6949000)
libopen-pal.so.6 => /usr/local/lib/libopen-pal.so.6
(0x00007f8ba6663000)
/lib64/ld-linux-x86-64.so.2 (0x00007f8ba76e5000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f8ba645e000)
librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f8ba6256000)
libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007f8ba6053000)
The output of 'ldd ./x86_64-linux-gnu/libdolfin.so | grep -i mpi' is:
libmpi_cxx.so.1 => /usr/local/lib/libmpi_cxx.so.1 (0x00007f0f0b265000)
libmpi.so.1 => /usr/local/lib/libmpi.so.1 (0x00007f0f0af89000)
libscalapack-openmpi.so.1 => /usr/lib/libscalapack-openmpi.so.1
(0x00007f0f03f81000)
libfftw3_mpi.so.3 => /usr/lib/x86_64-linux-gnu/libfftw3_mpi.so.3
(0x00007f0f01610000)
libmpi_f90.so.1 => /usr/lib/libmpi_f90.so.1 (0x00007f0f0140b000)
libmpi_f77.so.1 => /usr/lib/libmpi_f77.so.1 (0x00007f0f011d6000)
libblacs-openmpi.so.1 => /usr/lib/libblacs-openmpi.so.1
(0x00007f0ef883e000)
libblacsCinit-openmpi.so.1 => /usr/lib/libblacsCinit-openmpi.so.1
(0x00007f0ef863c000)
I have confirmed that /usr/lib, /usr/local/lib, /lib/x86_64-linux-gnu,
/usr/lib/x86_64-linux-gnu, and /lib64 are in my LD_LIBRARY_PATH.
I don't know where is wrong? Thank you for your help.
Lu
Hi Lu,
It seems you have 2 copies of MPI installed, one under /usr and the
other under /usr/local -- the latter most probably by you. See if the
problem goes away if you remove it.
Regards,
ST
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