[CIG-SHORT] PyLith install problem?

William Brower Levandowski Will.Levandowski at Colorado.EDU
Thu Jun 5 10:48:19 PDT 2014


Hello--
I am working through setting up and testing PyLith for the first time on
OSX 10.8.
In attempting to verify proper installation, I tried the tutorial
axialdisp. (i.e., *pylith axialdisp.cfg* in directory
~/src/pylith/pylith-1.9.0/examples/twocells/twotri3)
The initialization and mesh building seem fine, but then the following
abnormal ending message occurs:

*Fatal error. Calling MPI_Abort() to abort PyLith application.*
*Traceback (most recent call last):*
*  File
"/Users/wlevandowski/pylith/lib/python2.7/site-packages/pylith/apps/PetscApplication.py",
line 65, in onComputeNodes*
*    self.main(*args, **kwds)*
*  File
"/Users/wlevandowski/pylith/lib/python2.7/site-packages/pylith/apps/PyLithApp.py",
line 111, in main*
*    self.problem.preinitialize(mesh)*
*  File
"/Users/wlevandowski/pylith/lib/python2.7/site-packages/pylith/problems/TimeDependent.py",
line 95, in preinitialize*
*    self.formulation.preinitialize(mesh, self.materials, self.bc,
self.interfaces, self.gravityField)*
*  File
"/Users/wlevandowski/pylith/lib/python2.7/site-packages/pylith/problems/Formulation.py",
line 183, in preinitialize*
*    self._setupMaterials(materials)*
*  File
"/Users/wlevandowski/pylith/lib/python2.7/site-packages/pylith/problems/Formulation.py",
line 398, in _setupMaterials*
*    integrator.preinitialize(self.mesh(), material)*
*  File
"/Users/wlevandowski/pylith/lib/python2.7/site-packages/pylith/feassemble/IntegratorElasticity.py",
line 63, in preinitialize*
*    material.preinitialize(mesh)*
*  File
"/Users/wlevandowski/pylith/lib/python2.7/site-packages/pylith/materials/Material.py",
line 128, in preinitialize*
*    self.ncells = MeshOps_numMaterialCells(mesh, self.id
<http://self.id>())*
*SystemError: error return without exception set*
*--------------------------------------------------------------------------*
*MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD *
*with errorcode -1.*

*NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.*
*You may or may not see output from other processes, depending on*
*exactly when Open MPI kills them.*
*--------------------------------------------------------------------------*
*--------------------------------------------------------------------------*
*mpirun has exited due to process rank 0 with PID 89491 on*
*node engr2-2-94-241-dhcp.int.colorado.edu
<http://engr2-2-94-241-dhcp.int.colorado.edu> exiting without calling
"finalize". This may*
*have caused other processes in the application to be*
*terminated by signals sent by mpirun (as reported here).*
*--------------------------------------------------------------------------*
*/Users/wlevandowski/pylith/bin/nemesis: mpirun: exit 255*
*/Users/wlevandowski/pylith/bin/pylith:
/Users/wlevandowski/pylith/bin/nemesis: exit 1*


No vtk files are produced.

Does anyone see an obvious goof on my part, or did I mess something up in
the install? (I notice that the directory structure is slightly different
from that described in the tutorial. I configured using the desktop-darwin
instructions and already had Python 3.4 installed, if that matters.)
If the latter, removing and reinstalling PyLith should be straightforward.

Thanks so much for your help,
Will
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