[CIG-SHORT] PyLith-build test fails

Wed Mar 18 15:48:37 PDT 2015

Brad,

Thanks a lot for checking the mpich version compatibility with PyLith. I
started over from the scratch but in vain, with the same error. I have
PyLith binary (not built) in another partition of the hard drive which I
run for practising sample problems. Do you think that might have anything
to do with it?

Thanks again,
Mamun

On Wed, Mar 18, 2015 at 3:07 PM, Brad Aagaard <baagaard at usgs.gov> wrote:

> Mamun,
>
> I have verified that mpich-3.1.3 works with PETSc and PyLith. The PyLith
> installer will build this version of mpich for you, and you do not need
> admin privileges. See the INSTALL file with the pylith installer for
> instructions. If you rebuild mpich, you will want to delete all of the
> previously built PyLith and dependencies and start over to insure things
> are built consistently.
>
> Note: If you are building on a cluster, you may need to setup MPI to use
> the available hardware, such as Infiniband. This is why we recommend using
> MPI installed by a system administrator on clusters.
>
> Regards,
> Brad
>
>
>
> On 03/18/2015 01:58 PM, Mamun Miah wrote:
>
>> Thanks, Brad. I have built mpich-3.1.4 as the admin using the following
>> commands:
>>
>> ./configure --enable-shared CFLAGS=-fPIC CXXFLAGS=-fPIC
>> --prefix=/home/lawrence/mpich-install 2>&1 | tee c.txt
>> make 2>&1 | tee m.txt
>> make install 2>&1 | tee mi.txt
>> PATH=/home/lawrence/mpich-install/bin:$PATH ; export PATH
>>
>> Thanks again,
>> Mamun
>>
>> On Wed, Mar 18, 2015 at 12:24 PM, Brad Aagaard <baagaard at usgs.gov> wrote:
>>
>>  The test-suite.log file lists the following error:
>>>
>>> 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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>>
>>
>>
>>
>>
>>
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>>
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-- 
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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