[CIG-SHORT] PyLith-build test fails

[Brad Aagaard]

On 03/18/2015 03:48 PM, Mamun Miah wrote:
> 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?

You should check PATH, PYTHONPATH, and LD_LIBRARY_PATH (assuming Linux) 
to make sure they see the correct PyLith directories.

If you plan to switch between the binary and a manual build, then you 
should setup your environment so that you can switch back and forth. 
Never put both sets of directories in your paths.

Is there a specific reason why you are building from source rather than 
using the binary?

Regards,
Brad


>
> 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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