[CIG-SHORT] Running on cluster

[Matthew Knepley]

On Mon, Jul 28, 2014 at 4:44 PM, Ma, Xiao <xiaoma5 at illinois.edu> wrote:

>  Hi,
> I am running pylith on a cluster.
> Here is the input part :
> ***************************************
>  [pylithapp]
> scheduler = pbs
> [pylithapp.pbs]
> shell = /bin/bash
> # Export all environment variables to the batch job
> # Send email to johndoe at mydomain.org when the job begins, ends, or aborts
> qsub-options = -V -m bea -M xiaoma5 at illinois.edu
> [pylithapp.launcher]
> command = mpirun -np ${nodes} -machinefile ${PBS_NODEFILE}
>
>  *********************************************
> Error message
> **********************************************
>  Traceback (most recent call last):
>   File "<string>", line 1, in <module>
>   File
> "/home/xiaoma5/project-cse/pylith-1.9.0-linux-x86_64/lib/python2.7/site-packages/pythia-0.8.1.15-py2.7.egg/pyre/schedulers/__init__.py",
> line 53, in jobstart
>     kwds = kwds)
>   File
> "/home/xiaoma5/project-cse/pylith-1.9.0-linux-x86_64/lib/python2.7/site-packages/pythia-0.8.1.15-py2.7.egg/pyre/applications/__init__.py",
> line 41, in start
>     shell.run(**kwds)
>   File
> "/home/xiaoma5/project-cse/pylith-1.9.0-linux-x86_64/lib/python2.7/site-packages/pythia-0.8.1.15-py2.7.egg/pyre/applications/Shell.py",
> line 143, in run
>     method(*args, **kwds)
>   File
> "/home/xiaoma5/project-cse/pylith-1.9.0-linux-x86_64/lib/python2.7/site-packages/pythia-0.8.1.15-py2.7.egg/pyre/applications/SuperScript.py",
> line 47, in execute
>     self.subscript = self.createSubscript(subscriptName)
>   File
> "/home/xiaoma5/project-cse/pylith-1.9.0-linux-x86_64/lib/python2.7/site-packages/pythia-0.8.1.15-py2.7.egg/pyre/applications/AppRunner.py",
> line 25, in createSubscript
>     cls = loadObject(name)
>   File
> "/home/xiaoma5/project-cse/pylith-1.9.0-linux-x86_64/lib/python2.7/site-packages/pythia-0.8.1.15-py2.7.egg/pyre/util/__init__.py",
> line 54, in loadObject
>     obj = __import__(module, globals(), globals(), ['__name__'])
>   File
> "/home/xiaoma5/project-cse/pylith-1.9.0-linux-x86_64/lib/python2.7/site-packages/pylith/apps/PyLithApp.py",
> line 23, in <module>
>     from PetscApplication import PetscApplication
>   File
> "/home/xiaoma5/project-cse/pylith-1.9.0-linux-x86_64/lib/python2.7/site-packages/pylith/apps/PetscApplication.py",
> line 27, in <module>
>     class PetscApplication(Application):
>   File
> "/home/xiaoma5/project-cse/pylith-1.9.0-linux-x86_64/lib/python2.7/site-packages/pylith/apps/PetscApplication.py",
> line 41, in PetscApplication
>     from pylith.utils.PetscManager import PetscManager
>   File
> "/home/xiaoma5/project-cse/pylith-1.9.0-linux-x86_64/lib/python2.7/site-packages/pylith/utils/PetscManager.py",
> line 29, in <module>
>     import pylith.utils.petsc as petsc
>   File
> "/home/xiaoma5/project-cse/pylith-1.9.0-linux-x86_64/lib/python2.7/site-packages/pylith/utils/petsc.py",
> line 25, in <module>
>     _petsc = swig_import_helper()
>   File
> "/home/xiaoma5/project-cse/pylith-1.9.0-linux-x86_64/lib/python2.7/site-packages/pylith/utils/petsc.py",
> line 21, in swig_import_helper
>     _mod = imp.load_module('_petsc', fp, pathname, description)
> ImportError: /usr/lib64/libgfortran.so.3: version `GFORTRAN_1.4' not found
> (required by
> /home/xiaoma5/project-cse/pylith-1.9.0-linux-x86_64/lib/libpetsc.so)
>

The problem here is that the environment where you built PyLith,
specifically the gfortran compiler, is different
from the nodes on which you are trying to run. Possible solutions:

  1) Build on the cluster itself

  2) Build PETSc without Fortran using --with-fc=0 in configure

   Thanks,

     Matt


> ----------------------------------------
>
> *****************************************************************************
> The program is running when I am not using the cluster, so there must be
> something not right in this cluster command lines.
>
> *****************************************************************************
> %%Command Lines:
>
>  pylith test1.cfg --job.queue=test \
> --job.name=test1 --job.stdout=example1.log --job.stderr=example1.err \
> --job.walltime=5*minute \
> --nodes=4
>
>  I will really appriciate your help
> Best,
> Xiao
>
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> CIG-SHORT at geodynamics.org
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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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