[CIG-SHORT] Pylith 1.0.2 binary runtime error on Linux
Ravi Kanda
rkanda at gps.caltech.edu
Thu Dec 20 22:28:54 PST 2007
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.
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LINUX VERSION:
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[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
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ENVIRONMENT VARIABLES:
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[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
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PYLITH ERROR:
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[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>
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Ravi Kanda
Seismological Laboratory, MC 252-21
Division of Geological and Planetary Sciences
California Institute of Technology
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For a human being, the unexamined life is not worth living - SOCRATES
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