[CIG-SHORT] PyLith-build test fails

[Matthew Knepley]

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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