[CIG-SHORT] PyLith-build test fails

Thu Mar 19 15:30:57 PDT 2015

On Thu, Mar 19, 2015 at 4:07 PM, Mamun Miah <mmiah at go.olemiss.edu> wrote:

> Deat Matt,
>
> I have tried rebuilding PETSc after removing HAVE_MPI_IBARRIER from the
> petscconf.h file. It did not show any error. Then I went on building in the
> pylith directory. It shows the message as follows-
>

This is fine. PyLith does not need to be rebuilt for this change.

> lawrence at petaluma:~/build/pylith$ make
> Making all in bin
> make[1]: Entering directory `/home/lawrence/build/pylith/bin'
> make[1]: Nothing to be done for `all'.
> make[1]: Leaving directory `/home/lawrence/build/pylith/bin'
> make[1]: Entering directory `/home/lawrence/build/pylith'
> make[1]: Nothing to be done for `all-am'.
> make[1]: Leaving directory `/home/lawrence/build/pylith'
> lawrence at petaluma:~/build/pylith$
>
> Also, rebuilding PETSc after removing IBARRIER does not seem to have any
> effect on the $PETSC_DIR/config.log file.
>

Also fine, you did not reconfigure.

Please run your example again and see if it works.

  Thanks,

    Matt

> Thanks,
> Mamun
>
> 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
>>
>> _______________________________________________
>> CIG-SHORT mailing list
>> CIG-SHORT at geodynamics.org
>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>
>
>
>
> --
> 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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>

-- 
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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