[CIG-SHORT] PyLith-build test fails

Fri Mar 20 11:09:55 PDT 2015

On Fri, Mar 20, 2015 at 11:34 AM, Mamun Miah <mmiah at go.olemiss.edu> wrote:

> 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.
>

This makes it clear that you did not rebuild PETSc. Here is the source:

https://bitbucket.org/petsc/petsc/src/6d5951fb15cef55c0a1c902bab2c56b27935b002/src/sys/utils/mpits.c?at=master#cl-86

The function listed will not even be compiled if you rebuilt with that
#ifdef removed. Please
remove that statement from petscconf.h, rebuild PETSc, which will recreate
the shared library.

  Thanks,

     Matt

> 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
>
> _______________________________________________
> 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
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