[CIG-SHORT] PyLith-build test fails

Fri Mar 20 10:34:51 PDT 2015

Dear Matt,

I have run a sample problem from PyLith tutorial and got the following
PETSc errors:

[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 PetscSFReduceBegin() line 990 in
/home/lawrence/build/pylith/petsc-pylith/src/vec/is/sf/interface/sf.c
[0]PETSC ERROR: #6 DMLocalToGlobalBegin() line 1893 in
/home/lawrence/build/pylith/petsc-pylith/src/dm/interface/dm.c
[0]PETSC ERROR: #7 void pylith::topology::Field::complete()() line 710 in
../../../pylith-2.1.0/libsrc/pylith/topology/Field.cc
Fatal error. Calling MPI_Abort() to abort PyLith application.

Looks like the IBARRIER is still causing the problem.

On Thu, Mar 19, 2015 at 3:30 PM, Matthew Knepley <knepley at mcs.anl.gov>
wrote:

> 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
>>>>>
>>>>>
>>>> _______________________________________________
>>>> CIG-SHORT mailing list
>>>> CIG-SHORT at geodynamics.org
>>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>>
>>>
>>>
>>>
>>> --
>>> 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
>>
>> _______________________________________________
>> CIG-SHORT mailing list
>> CIG-SHORT at geodynamics.org
>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>>
>
>
>
> --
> 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.geodynamics.org/pipermail/cig-short/attachments/20150320/5c3d8005/attachment-0001.html>