[CIG-SHORT] Pylith 1.0.2 binary runtime error on Linux
Brad Aagaard
baagaard at usgs.gov
Fri Dec 21 08:38:35 PST 2007
Ravi-
On linux systems the relevant environment variables are PATH,
PYTHONPATH, and LD_LIBRARY_PATH. If these are not all consistent, then
odd things will happen. I would follow the following steps to make sure
you are getting a consistent set of files:
1. Verify location of nemesis binary.
which nemesis
2. Verify location of pylith script.
which pylith
3. Check location of libraries linked with nemesis
ldd `which nemesis`
4. Check location of pylith Python files
python
import pylith
pylith.__file__
5. Check libaries linked to pylith Python modules
cd PREFIX/lib/python2.5/site-packages
ldd topologymodule.so
When testing the linux binaries, I clear out my PATH, PYTHONPATH, and
LD_LIBRARY_PATH variables so that they only see the system directories
and none of the PyLith, etc development files.
Brad
Ravi Kanda wrote:
> Hi,
>
> I am trying to run the TWOTRI example with Pylith 1.0.2 (from binary
> tarball).
>
> However, I get an error during the mesh-reading process:
> ".....site-packages/pylith/topology/topologymodule.so: undefined symbol:
> _Z12MatSetOptionP6_p_Mat9MatOption10PetscTruth" (full traceback copied
> below).
>
> I am trying to figure out if this is because pylith is trying to access
> the Pythia (0.8.1.4) files in my PYTHON_LIBDIR site-packages
> (/export/scratch1/rkanda/sw/lib/python2.5/site-packages/), instead of
> those within the PYTHON BINARY TREE
> (/home/subdyna3/rkanda/geoframe/Pylith/pylith-1.0.2-linux-i686/lib/python2.5/site-packages).
> If so, I don't understand why pylith is seeking PYTHON_LIBDIR even
> though the PYLITH ROOT DIRECTORY equivalents appear first in PATH,
> LD_LIBRARY_PATH, & PYTHONPATH. Each time I have run this, I used a
> fresh terminal to make sure I start with the correct paths - so I don't
> understand why PYTHON_LIBDIR is getting precedence.
>
> I looked under the CIG-SHORT archives to see if other people encountered
> this problem. I could not find anything other than suggestions for
> setting the appropriate paths in the startup script pointing to the
> PYLITH BINARY TREE. But I had already added the necessary paths to my
> environment variables (see below) before running pylith. I also tried
> running outside the PYLITH BINARY TREE (by copying the TWOTRI3 folder to
> another location), but get the same error message.
>
> I will really appreciate any suggestions.
>
> Thanks,
> Ravi.
>
> -------------------------------------------------------------------------------------------------------------------------------------------------
>
> LINUX VERSION:
> -------------------------------------------------------------------------------------------------------------------------------------------------
>
> [subdyna:~]rkanda> uname -a
> Linux subdyna 2.6.12-1.1381_FC3smp #1 SMP Fri Oct 21 04:03:26 EDT 2005
> i686 i686 i386 GNU/Linux
>
> -------------------------------------------------------------------------------------------------------------------------------------------------
>
> ENVIRONMENT VARIABLES:
> -------------------------------------------------------------------------------------------------------------------------------------------------
>
> [subdyna:twotri3]rkanda> echo $PATH
> /home/subdyna3/rkanda/geoframe/Pylith/pylith-1.0.2-linux-i686/bin:/export/scratch1/rkanda/sw/Adobe/Reader8/bin:/home/subdyna3/rkanda/geoframe/petsc/petsc-dev/externalpackages/mpich2-1.0.5p4/bin:/export/scratch1/rkanda/sw/bin:/usr/X11R6/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/intel/cc/10.0/bin:/opt/intel/fc/10.0/bin:/opt/intel/idb/10.0/bin:/opt/pgi/linux86/7.0/bin:/opt/util/bin:/opt/util/autorun/files:.:/home/subdyna3/rkanda/geoframe/export/pythia-0.8:/export/scratch1/rkanda/dv/products/bin:/home/subdyna3/rkanda/geoframe/config/make:/home/subdyna3/rkanda/geoframe/Cubit_10.2
>
>
> [subdyna:twotri3]rkanda> echo $LD_LIBRARY_PATH
> /home/subdyna3/rkanda/geoframe/Pylith/pylith-1.0.2-linux-i686/lib:/export/scratch1/rkanda/sw/lib/atlas:/opt/intel/lib:/opt/intel/mkl/lib/32:/opt/GMT/lib:/usr/local/lib:/usr/X11R6/lib:/usr/lib:/lib:/export/scratch1/rkanda/sw/lib:/export/scratch1/rkanda/sw/lib/vtk-5.0:/home/subdyna3/rkanda/geoframe/export/pythia-0.8:/export/scratch1/rkanda/dv/products/lib:/home/subdyna3/rkanda/geoframe/petsc/petsc-dev/linux-mpich2sock-opt/lib:/home/subdyna3/rkanda/geoframe/petsc/petsc-dev/externalpackages/mpich2-1.0.5p4/lib
>
>
> [subdyna:twotri3]rkanda> echo $PYTHONPATH
> /home/subdyna3/rkanda/geoframe/Pylith/pylith-1.0.2-linux-i686/lib/python2.5/site-packages:/export/scratch1/rkanda/dv/products/modules:/home/rkanda/Python/Python-2.5/Modules:/export/scratch1/rkanda/sw/lib/python2.5/site-packages:/home/rkanda/Python/VTK/VTK-build/Wrapping/Python:/export/scratch1/rkanda/sw/lib/vtk-5.0
>
>
> -------------------------------------------------------------------------------------------------------------------------------------------------
>
> PYLITH ERROR:
> -------------------------------------------------------------------------------------------------------------------------------------------------
>
> [subdyna:twotri3]rkanda> pylith dislocation.cfg
> >>
> /home/buildbot/install/x86_linux_single_nosched_binbot/lib/python2.5/site-packages/pylith/utils/PetscManager.py:47:initialize
>
> -- petsc(info)
> -- Initializing PETSc.
> >>
> /home/buildbot/install/x86_linux_single_nosched_binbot/lib/python2.5/site-packages/pylith/meshio/MeshIO.py:45:read
>
> -- meshioascii(info)
> -- Reading finite-element mesh
> Traceback (most recent call last):
> File "<string>", line 1, in <module>
> File
> "/export/scratch1/rkanda/sw/lib/python2.5/site-packages/pythia-0.8.1.4-py2.5.egg/mpi/__init__.py",
> line 42, in mpistart
> kwds = kwds)
> File
> "/export/scratch1/rkanda/sw/lib/python2.5/site-packages/pythia-0.8.1.4-py2.5.egg/pyre/applications/__init__.py",
> line 41, in start
> shell.run(**kwds)
> File
> "/export/scratch1/rkanda/sw/lib/python2.5/site-packages/pythia-0.8.1.4-py2.5.egg/pyre/applications/Shell.py",
> line 139, in run
> method(*args, **kwds)
> File
> "/export/scratch1/rkanda/sw/lib/python2.5/site-packages/pythia-0.8.1.4-py2.5.egg/pyre/applications/SuperScript.py",
> line 49, in execute
> self.main(*args, **kwds)
> File
> "/export/scratch1/rkanda/sw/lib/python2.5/site-packages/pythia-0.8.1.4-py2.5.egg/pyre/applications/SuperScript.py",
> line 58, in main
> self.runSubscript(*args, **kwds)
> File
> "/export/scratch1/rkanda/sw/lib/python2.5/site-packages/pythia-0.8.1.4-py2.5.egg/pyre/applications/SuperScript.py",
> line 62, in runSubscript
> self.subscript.run(*args, **kwds)
> File
> "/export/scratch1/rkanda/sw/lib/python2.5/site-packages/pythia-0.8.1.4-py2.5.egg/pyre/applications/Application.py",
> line 42, in run
> shell.run(*args, **kwds)
> File
> "/export/scratch1/rkanda/sw/lib/python2.5/site-packages/pythia-0.8.1.4-py2.5.egg/pyre/applications/Shell.py",
> line 139, in run
> method(*args, **kwds)
> File
> "/export/scratch1/rkanda/sw/lib/python2.5/site-packages/pythia-0.8.1.4-py2.5.egg/mpi/Application.py",
> line 118, in _onComputeNodes
> self.onComputeNodes(*args, **kwds)
> File
> "/export/scratch1/rkanda/sw/lib/python2.5/site-packages/pythia-0.8.1.4-py2.5.egg/mpi/Application.py",
> line 124, in onComputeNodes
> self.main(*args, **kwds)
> File
> "/home/buildbot/install/x86_linux_single_nosched_binbot/lib/python2.5/site-packages/pylith/PyLithApp.py",
> line 90, in main
> File
> "/home/buildbot/install/x86_linux_single_nosched_binbot/lib/python2.5/site-packages/pylith/topology/MeshImporter.py",
> line 79, in create
> File
> "/home/buildbot/install/x86_linux_single_nosched_binbot/lib/python2.5/site-packages/pylith/meshio/MeshIO.py",
> line 59, in read
> File
> "/home/buildbot/install/x86_linux_single_nosched_binbot/lib/python2.5/site-packages/pylith/topology/Mesh.py",
> line 44, in initialize
> File
> "/home/buildbot/install/x86_linux_single_nosched_binbot/lib/python2.5/site-packages/pylith/topology/Mesh.py",
> line 136, in _createCppHandle
> ImportError:
> /home/subdyna3/rkanda/geoframe/Pylith/pylith-1.0.2-linux-i686/lib/python2.5/site-packages/pylith/topology/topologymodule.so:
> undefined symbol: _Z12MatSetOptionP6_p_Mat9MatOption10PetscTruth
> --pyre-start: mpiexec: exit 1
> /home/subdyna3/rkanda/geoframe/Pylith/pylith-1.0.2-linux-i686/bin/pylith:
> /home/subdyna3/rkanda/geoframe/Pylith/pylith-1.0.2-linux-i686/bin/nemesis:
> exit 1
> [subdyna:twotri3]rkanda>
> -------------------------------------------------------------------------------------------------------------------------------------------------
>
>
>
>
>
> ---------------------------------------------------------------------
> Ravi Kanda
> Seismological Laboratory, MC 252-21
> Division of Geological and Planetary Sciences
> California Institute of Technology
> ----------------------------------------------------------------------
>
> For a human being, the unexamined life is not worth living - SOCRATES
>
> ----------------------------------------------------------------------
> _______________________________________________
> CIG-SHORT mailing list
> CIG-SHORT at geodynamics.org
> http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>
More information about the CIG-SHORT
mailing list