[CIG-SHORT] PyLith-build test fails

Thu Mar 19 07:02:48 PDT 2015

On Wed, Mar 18, 2015 at 4:40 PM, Mamun Miah <mmiah at go.olemiss.edu> wrote:

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

So this machine is plainly reporting that Ibarrier is there, and the link
works for PyLith, so
the check worked. It appears that MPI is broken here. Can you follow the
directions in
the last email to rebuild PETSc and try your run again?

  Thanks,

    Matt

> 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.
>>>>
>>>>
>>>>
>>>> _______________________________________________
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>>>> CIG-SHORT at geodynamics.org
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>>>>
>>>>
>>> _______________________________________________
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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
>>
>> _______________________________________________
>> CIG-SHORT mailing list
>> CIG-SHORT at geodynamics.org
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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
>
> _______________________________________________
> CIG-SHORT mailing list
> 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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