[CIG-SHORT] Pylith 1.0.2 binary runtime error on Linux
Matthew Knepley
knepley at gmail.com
Fri Dec 21 05:50:27 PST 2007
The signature of this method changed in petsc-dev. It appears you are using
the release version 2.3.3. You will have to upgrade to the development version.
Thanks,
Matt
On Dec 21, 2007 12:28 AM, Ravi Kanda <rkanda at gps.caltech.edu> 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
>
> ----------------------------------------------------------------------
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>
--
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which
their experiments lead.
-- Norbert Wiener
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