[CIG-SHORT] PyLith-build test fails

[Brad Aagaard]

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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