[CIG-SHORT] PyLith-build test fails
Mamun Miah
mmiah at go.olemiss.edu
Wed Mar 18 16:26:22 PDT 2015
Thanks. Actually, I contacted you earlier telling you about my PhD research
which is to simulate induced seismicity from fluid injection. We (with
people from LBNL) are developing a coupled hydro-geomechanical code by
linking TOUGH2 and PyLith to implement pore pressure and calculate
effective stress field. We have already linked and run our coupled
simulator by passing parameters back and forth between the two codes but we
might need to modify PyLith to reflect the changes in constitutive
relations due to fluid pressure. So, that is the motivation behind building
PyLith from the source.
Best Regards,
Mamun Miah
On Wed, Mar 18, 2015 at 3:54 PM, Brad Aagaard <baagaard at usgs.gov> wrote:
> 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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>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
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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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