[CIG-SHORT] PyLith-build test fails

Wed Mar 18 15:40:23 PDT 2015

Thanks, Matt. Please see the attached $PETSC_DIR/configure.log

Regards,
Mamun Miah

On Wed, Mar 18, 2015 at 1:57 PM, Matthew Knepley <knepley at mcs.anl.gov>
wrote:

> On Wed, Mar 18, 2015 at 1:24 PM, Brad Aagaard <baagaard at usgs.gov> wrote:
>
>> The test-suite.log file lists the following error:
>>
>
> Yes, it is possible that we are finding the MPI_Ibarrier() function in our
> test, but the implementation
> actually just crashes. We have seen this before with incomplete MPI
> implementations. You can
> remove
>
>   HAVE_MPI_IBARRIER
>
> from
>
>   $PETSC_DIR/$PETSC_ARCH/include/petscconf.h
>
> and rebuild PETSc using
>
>   cd $PETSC_DIR
>   make
>
> Please send
>
>   $PETSC_DIR/configure.log
>
> so I can look at the test for that function.
>
>   Thanks,
>
>      Matt
>
>
>> test_writeData (TestOutputSolnPoints.TestOutputSolnPoints) ... [0]PETSC
>> ERROR: #1 PetscCommBuildTwoSided_Ibarrier() line 122 in
>> /home/lawrence/build/pylith/petsc-pylith/src/sys/utils/mpits.c
>> [0]PETSC ERROR: #2 PetscCommBuildTwoSided() line 231 in
>> /home/lawrence/build/pylith/petsc-pylith/src/sys/utils/mpits.c
>> [0]PETSC ERROR: #3 PetscSFSetUp_Basic() line 552 in
>> /home/lawrence/build/pylith/petsc-pylith/src/vec/is/sf/
>> impls/basic/sfbasic.c
>> [0]PETSC ERROR: #4 PetscSFSetUp() line 192 in /home/lawrence/build/pylith/
>> petsc-pylith/src/vec/is/sf/interface/sf.c
>> [0]PETSC ERROR: #5 PetscSFBcastBegin() line 923 in
>> /home/lawrence/build/pylith/petsc-pylith/src/vec/is/sf/interface/sf.c
>> [0]PETSC ERROR: #6 DMGlobalToLocalBegin() line 1692 in
>> /home/lawrence/build/pylith/petsc-pylith/src/dm/interface/dm.c
>> [0]PETSC ERROR: #7 void pylith::topology::Field::scatterGlobalToLocal(PetscVec,
>> const char*) const() line 1168 in ../../../pylith-2.1.0/libsrc/
>> pylith/topology/Field.cc
>> ERROR
>>
>> ======================================================================
>> ERROR: test_writeData (TestOutputSolnPoints.TestOutputSolnPoints)
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>   File "/home/lawrence/build/pylith/pylith-2.1.0/unittests/
>> pytests/meshio/TestOutputSolnPoints.py", line 194, in test_writeData
>>     output.writeData(2.0, self.fields)
>>   File "/home/lawrence/pylith/lib/python2.7/site-packages/
>> pylith/meshio/OutputManager.py", line 252, in writeData
>>     self._appendVertexField(t, field, mesh)
>>   File "/home/lawrence/pylith/lib/python2.7/site-packages/
>> pylith/meshio/OutputManager.py", line 439, in _appendVertexField
>>     ModuleOutputManager.appendVertexField(self, t, field, mesh)
>>   File "/home/lawrence/pylith/lib/python2.7/site-packages/pylith/meshio/meshio.py",
>> line 300, in appendVertexField
>>     def appendVertexField(self, *args): return _meshio.OutputManager_appendVertexField(self,
>> *args)
>> RuntimeError: Error detected while in PETSc function.
>>
>> This looks like it may be an MPI issue. I don't get this error on any of
>> the machines I have tested using OpenMPI and MPICH. What version of MPI are
>> you using? How was MPI installed (installer, sys admin, you, someone else)?
>>
>> Regards,
>> Brad
>>
>>
>>
>> On 03/18/2015 11:52 AM, Mamun Miah wrote:
>>
>>> Dear developers,
>>>
>>> I have been trying to build PyLith from the source code but apparently
>>> reached an impasse. I am getting the following test failure.
>>>
>>> FAIL: testmeshio.py
>>>
>>> ============================================================
>>> ================
>>> Testsuite summary for PyLith 2.1.0
>>> ============================================================
>>> ================
>>> # TOTAL: 3
>>> # PASS:  2
>>> # SKIP:  0
>>> # XFAIL: 0
>>> # FAIL:  1
>>> # XPASS: 0
>>> # ERROR: 0
>>> ============================================================
>>> ================
>>> See unittests/pytests/meshio/test-suite.log
>>> Please report to cig-short at geodynamics.org
>>> ============================================================
>>> ================
>>> make[8]: *** [test-suite.log] Error 1
>>> make[8]: Leaving directory
>>> `/home/lawrence/build/pylith/pylith-build/unittests/pytests/meshio'
>>> make[7]: *** [check-TESTS] Error 2
>>> make[7]: Leaving directory
>>> `/home/lawrence/build/pylith/pylith-build/unittests/pytests/meshio'
>>> make[6]: *** [check-am] Error 2
>>> make[6]: Leaving directory
>>> `/home/lawrence/build/pylith/pylith-build/unittests/pytests/meshio'
>>> make[5]: *** [check-recursive] Error 1
>>> make[5]: Leaving directory
>>> `/home/lawrence/build/pylith/pylith-build/unittests/pytests/meshio'
>>> make[4]: *** [check-recursive] Error 1
>>> make[4]: Leaving directory
>>> `/home/lawrence/build/pylith/pylith-build/unittests/pytests'
>>> make[3]: *** [check-recursive] Error 1
>>> make[3]: Leaving directory
>>> `/home/lawrence/build/pylith/pylith-build/unittests'
>>> make[2]: *** [check-recursive] Error 1
>>> make[2]: Leaving directory `/home/lawrence/build/pylith/pylith-build'
>>> make[1]: *** [pylith] Error 2
>>> make[1]: Leaving directory `/home/lawrence/build/pylith'
>>> make: *** [installed_pylith] Error 2
>>>
>>> I have found this CIG-SHORT post here:
>>> http://lists.geodynamics.org/pipermail/cig-short/2014-August/001833.html
>>> But it did not help. Attached are the test*.log files along with the
>>> testsuite.log file
>>>
>>> I would appreciate any help in regards to fixing this problem.
>>>
>>>
>>>
>>> _______________________________________________
>>> CIG-SHORT mailing list
>>> CIG-SHORT at geodynamics.org
>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>>
>>>
>> _______________________________________________
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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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-- 
Thanks & Best Regards,

Mamun Miah
Graduate Research Assistant
Department of Civil Engineering
The University of Mississippi
Oxford, MS 38655
Phone: (662)-801-1904
Website: http://www.linkedin.com/pub/mamun-miah-eit/21/53/339
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