importing petsc4py.PETSc results in segfault

Bug #232036 reported by Neilen Marais
12
This bug affects 1 person
Affects Status Importance Assigned to Milestone
petsc4py (Ubuntu)
Invalid
Undecided
Unassigned

Bug Description

Binary package hint: python-petsc4py

Runnin ubuntu hardy (8.04), AMD64 arch:

$ python
Python 2.5.2 (r252:60911, Apr 21 2008, 11:17:30)
[GCC 4.2.3 (Ubuntu 4.2.3-2ubuntu7)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import petsc4py.PETSc
Segmentation fault

Some pacake info:

$ wajig detail petsc-dev | grep Version
Version: 2.3.3-6ubuntu1

$ wajig detail python-petsc4py | grep Version
Version: 0.7.5-4
Python-Version: 2.4, 2.5

$ wajig detail python-numpy | grep Version
Version: 1:1.0.4-6ubuntu3
Python-Version: 2.4, 2.5

Not sure if it's ubuntu specific. I also get a segfault if I use numpy SVN and compile petsc4py 0.7.5 myself.

Revision history for this message
Gabriel de Perthuis (g2p) wrote :

The real cause is bug #260027 (though that's hard to guess, so I did not mark it as a duplicate).

Revision history for this message
Luis (luis94855510) wrote :

Binary package hint: python-petsc4py

Runnin ubuntu jaunty (9.04), i386 arch:

$ python
Python 2.6.2 (release26-maint, Apr 19 2009, 01:56:41)
[GCC 4.3.3] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import petsc4py.PETSc
python: symbol lookup error: /usr/lib/openmpi/lib/openmpi/mca_paffinity_linux.so: undefined symbol: mca_base_param_reg_int

Some pacake info:

$ wajig detail petsc-dev | grep Version
Version: 2.3.3-15ubuntu2

$ wajig detail python-petsc4py | grep Version
Version: 0.7.5-5build1
Python-Version: 2.5, 2.6

$ wajig detail python-numpy | grep Version
Version: 1:1.2.1-1ubuntu1
Python-Version: 2.5, 2.6

regards,
Luis.

Revision history for this message
Nizamov Shawkat (nizamov-shawkat) wrote :

This is a bug in OpenMPI and I also came across it. Workaround for python is quite simple :

from ctypes import *
mpi = CDLL('libmpi.so.0', RTLD_GLOBAL)

proposed in OpenMPI FAQ at http://www.open-mpi.org/faq/?category=running#loading-libmpi-dynamically

If I recoll correctly, I didn't observe this behaviour previously (in 8.10) with OpenMPI 1.2 series.

My guess is that this bug should be attached to libopenmpi

wbr
Shawkat

Revision history for this message
Nizamov Shawkat (nizamov-shawkat) wrote :

Also, as mentioned in
http://www.open-mpi.org/community/lists/users/2009/02/8135.php
bug may be resolved compiling OpenMPI 1.3 using --enable-shared --enable-static

Revision history for this message
Thomas Hotz (thotz-deactivatedaccount) wrote :

This package is not in our software archive any more, so I close this bug.

Changed in petsc4py (Ubuntu):
status: New → Invalid
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