dolfin builds but doesn't work

On 3/9/10 2:18 AM, <email address hidden> wrote:
> New question #103680 on Dorsal:
> https://answers.launchpad.net/dorsal/+question/103680
>
> Using dorsal-0.6.0 I built FEniCS. It seems to build without problems (under Fedora 11). However, it doesn't
> work. I source the file dolfin.conf, but python fails already at "from dolfin import *":
>
>>>> from dolfin import *
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> File "/home/faculty/arnold/workshop/FEniCS-0.6.0/build/lib/python2.6/site-packages/dolfin/__init__.py", line 13, in <module>
> import dolfin.cpp as cpp
> File "/home/faculty/arnold/workshop/FEniCS-0.6.0/build/lib/python2.6/site-packages/dolfin/cpp.py", line 28, in <module>
> _cpp = swig_import_helper()
> File "/home/faculty/arnold/workshop/FEniCS-0.6.0/build/lib/python2.6/site-packages/dolfin/cpp.py", line 24, in swig_import_helper
> _mod = imp.load_module('_cpp', fp, pathname, description)
> ImportError: /home/faculty/arnold/workshop/FEniCS-0.6.0/build/lib/python2.6/site-packages/dolfin/_cpp.so: undefined symbol: _ZNK6dolfin20IntersectionOperator24all_intersected_entitiesERKNS_4MeshERSt3setIjSt4lessIjESaIjEE
>
> Any ideas?

I think this might have something to do with CGAL. I will investigate.

Harish

Any more thoughts on this. I am stuck (without dolfin)!

Did you try to build DOLFIN without CGAL?

On Tuesday 9. March 2010 02.18.43 <email address hidden> wrote:
> New question #103680 on Dorsal:
> https://answers.launchpad.net/dorsal/+question/103680
>
> Using dorsal-0.6.0 I built FEniCS. It seems to build without problems
> (under Fedora 11). However, it doesn't
>
> work. I source the file dolfin.conf, but python fails already at "from dolfin
import *":
> >>> from dolfin import *
>
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> File
> "/home/faculty/arnold/workshop/FEniCS-0.6.0/build/lib/python2.6/site-packa
> ges/dolfin/__init__.py", line 13, in <module> import dolfin.cpp as cpp
> File
> "/home/faculty/arnold/workshop/FEniCS-0.6.0/build/lib/python2.6/site-packa
> ges/dolfin/cpp.py", line 28, in <module> _cpp = swig_import_helper()
> File
> "/home/faculty/arnold/workshop/FEniCS-0.6.0/build/lib/python2.6/site-packa
> ges/dolfin/cpp.py", line 24, in swig_import_helper _mod =
> imp.load_module('_cpp', fp, pathname, description)
> ImportError:
> /home/faculty/arnold/workshop/FEniCS-0.6.0/build/lib/python2.6/site-packag
> es/dolfin/_cpp.so: undefined symbol:
> _ZNK6dolfin20IntersectionOperator24all_intersected_entitiesERKNS_4MeshERSt
> 3setIjSt4lessIjESaIjEE
>
> Any ideas?

The only idea I came up is that you maybe have somewhere an old libdolfin.so
lying around which does not contain those symbols which has to be resolved in
_cpp.so. Could you do an (should be one line)

ldd /home/faculty/arnold/workshop/FEniCS-0.6.0/build/lib/python2.6/site-
packages/dolfin/_cpp.so

to check which libs _cpp.so are actually linked to it. The entry for
libdolfin.so.0 is important, make sure that this one is really pointing to your
recently installed libdolfin.so.

Thank you Andre! The ldd command returned

 libCGAL.so.4 => /home/faculty/arnold/workshop/FEniCS-0.6.0/build/lib/libCGAL.so.4 (0x00bf7000)
 libCGAL_Core.so.4 => /home/faculty/arnold/workshop/FEniCS-0.6.0/build/lib/libCGAL_Core.so.4 (0x00110000)
 libslepc.so => /home/faculty/arnold/workshop/FEniCS-0.5.0/build/lib/libslepc.so (0x00722000)
 libpetscts.so => /home/faculty/arnold/workshop/FEniCS-0.5.0/build/lib/libpetscts.so (0x00a24000)

with some libraries pointing to FEniCS-0.6.0 (the version compiled with dorsal 0.6.0) and some my older version
FEniCS-0.5.0. I don't know why this is, because I had sourced dolfin.conf from 0.6.0 and my LD_LIBRARY_PATH
was set to /home/faculty/arnold/workshop/FEniCS-0.6.0/build/lib:

In any case, when I renamed the directory /home/faculty/arnold/workshop/FEniCS-0.5.0 ldd showed that
everything resolved to the new libraries, and my problem was solved.