[CIG-SHORT] PyLith-build test fails

[Brad Aagaard]

Mamun,

If did a "make" and "make install" in the PETSc directory after making 
the change to petscconf.h, then going into the build directory for 
PyLith and doing "make" should cause PyLith to rebuild because it will 
see that the PETSc header file petscconf.h changed.

Brad

On 03/19/2015 03:07 PM, Mamun Miah 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-
>
> 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.
>
> 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.
>>>>
>>>>
>>>>
>>>> _______________________________________________
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>>>> 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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>
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