[CIG-SHORT] Pylith 1.0.2 binary runtime error on Linux
Ravi Kanda
rkanda at gps.caltech.edu
Fri Dec 21 16:12:09 PST 2007
Brad and Matt,
Thank you for your prompt response. Brad, I ran the location checks below. My
problem seems to be that "topologymodule.so" points to the (older) petsc-dev
libraries I had installed in July. So, the simplest thing I could think of was
to create a script to clean up my paths of the petsc-dev libraries. Pylith now
runs without error and I can view the VTK files.
Looks like an alternative (and a more long-term solution) would be to update my
petsc-dev as Matt suggested, and then I should be able to run without having to
clean-up my paths.
Happy Holidays!
Ravi.
----------------------------------------------------------------------------------
Brad Aagaard wrote:
> 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
>>
>
>
--
---------------------------------------------------------------------
Ravi Kanda
Seismological Laboratory, MC 252-21
Division of Geological and Planetary Sciences
California Institute of Technology
1200 E. California Blvd., Pasadena, CA 91125
Phone: 626-395-6971, Fax: 626-564-0715
Web Page: http://www.gps.caltech.edu/~rkanda
----------------------------------------------------------------------
For a human being, the unexamined life is not worth living - SOCRATES
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