[CIG-SHORT] PyLith install problem?

[Brad Aagaard]

Will,

There was a problem with trapping errors under Mac OS X in the PyLith 
1.9.0 release. Please try to use the v2.0.0 binary (we plan to send out 
the release announcement later today). The URL is

https://github.com/geodynamics/pylith/releases/download/v2.0.0rc2/pylith-2.0.0-darwin-10.6.8.tgz

At a minimum this should give you a better error message. If you still 
get an error, please send the entire output from running
"pylith axialdisp.cfg". You can do this by capturing it to a log:
pylith axialdisp.cfg >& log.

Regards,
Brad


On 06/05/2014 10:48 AM, William Brower Levandowski wrote:
> 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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