[CIG-SHORT] fault opening with nonzero traction
Yasemin Korkusuz
yaseminkrksz at gmail.com
Mon Dec 11 06:16:43 PST 2017
Dear Aagaard,
Thank you very much for your support. I installed the latest version of
PyLith (2.2.1). Next, adding only large "zero_tolerance" and
"zero_tolerance_normal" values (on the order of 5) to pylithapp.cfg file
solved the rupture propagation problem for my smoothed 2 segments fault
model. I will work on it for further improvements.
Best Regards
Yasemin
2017-12-06 20:04 GMT+03:00 Brad Aagaard <baagaard at usgs.gov>:
> Here is the important part of the error message:
> > RuntimeError: WARNING! Fault opening with nonzero traction., v_fault:
> > 13506, opening: 1.01291e-10, normal traction: -0.00340407
>
> See this post from Nov 28 on the cig-short email list (note the discussion
> of the zero_tolerance and zero_tolerance_normal parameters):
> http://lists.geodynamics.org/pipermail/cig-short/2017-November/003068.html
>
> The PETSC_ERROR stuff is the other processes calling abort as a result of
> one process aborting and notifying the others. The number in square
> brackets before PETSC_ERROR is the process number.
>
> Regards,
> Brad
>
>
> On 12/06/2017 06:02 AM, Yasemin Korkusuz wrote:
>
>> Dear Aagaard,
>>
>> First, I am sorry for my late reply due to some problems. Thanks for your
>> quick response.
>>
>> I generally run my cases for 200m and 300m resolutions because I could
>> not get results for 100m grid size. Also, I did not get error messages for
>> the stability conditions, as they are satisfied.
>> I have copied an error message below this email. This is for a simple
>> around 120km long 2 segments fault. Both segments are vertical and the
>> angle between the segments is 10 degree. I attached a figure to represent
>> the geometry.
>>
>> Does it related to the MPI or what are your suggestions?
>>
>> Thanks a lot
>> Yasemin
>>
>>
>> ----------------------------------------------------------------------
>> ...
>> -- Advancing solution from t=4.74*s to t=4.75*s.
>> >> /home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pylith/problems/TimeDependent.py:208:run
>> -- timedependent(info)
>> -- Finishing advancing solution from t=4.74*s to t=4.75*s.
>> >> /home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pylith/feassemble/IntegratorEl
>> asticity.py:125:writeData
>> -- elasticityexplicittet4(info)
>> -- Writing material data.
>> >> /home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pylith/faults/Fault.py:191:writeData
>> -- faultcohesivedyn(info)
>> -- Writing fault data.
>> >> /home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pylith/problems/TimeDependent.py:184:run
>> -- timedependent(info)
>> -- Main time loop, current time is t=4.75*s
>> >> /home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pylith/problems/TimeDependent.py:195:run
>> -- timedependent(info)
>> -- Preparing to advance solution from time t=4.75*s to t=4.76*s.
>> >> /home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pylith/problems/TimeDependent.py:201:run
>> -- timedependent(info)
>> -- Advancing solution from t=4.75*s to t=4.76*s.
>> Fatal error. Calling MPI_Abort() to abort PyLith application.
>> Traceback (most recent call last):
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pylith/apps/PetscApplication.py", line 74,
>> in onComputeNodes
>> self.main(*args, **kwds)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pylith/apps/PyLithApp.py", line 135, in main
>> self.problem.run(self)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pylith/problems/TimeDependent.py", line 203,
>> in run
>> self.formulation.step(t, dt)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pylith/problems/Explicit.py", line 215, in
>> step
>> self._reformResidual(t, dt)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pylith/problems/Formulation.py", line 598,
>> in _reformResidual
>> self.reformResidual()
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pylith/problems/problems.py", line 88, in
>> reformResidual
>> def reformResidual(self, tmpResidualVec=None, tmpSolveSolnVec=None):
>> return _problems.Formulation_reformResidual(self, tmpResidualVec,
>> tmpSolveSolnVec)
>> RuntimeError: WARNING! Fault opening with nonzero traction., v_fault:
>> 13506, opening: 1.01291e-10, normal traction: -0.00340407
>>
>> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 17
>> Traceback (most recent call last):
>> File "<string>", line 1, in <module>
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pythia-0.8.1.17-py2.7.egg/mpi/__init__.py",
>> line 42, in mpistart
>> kwds = kwds)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pythia-0.8.1.17-py2.7.egg/
>> pyre/applications/__init__.py", line 41, in start
>> shell.run(**kwds)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pythia-0.8.1.17-py2.7.egg/pyre/applications/Shell.py",
>> line 143, in run
>> method(*args, **kwds)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pythia-0.8.1.17-py2.7.egg/
>> pyre/applications/SuperScript.py", line 49, in execute
>> self.main(*args, **kwds)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pythia-0.8.1.17-py2.7.egg/
>> pyre/applications/SuperScript.py", line 58, in main
>> self.runSubscriTraceback (most recent call last):
>> File "<string>", line 1, in <module>
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pythia-0.8.1.17-py2.7.egg/mpi/__init__.py",
>> line 42, in mpistart
>> kwds = kwds)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pythia-0.8.1.17-py2.7.egg/
>> pyre/applications/__init__.py", line 41, in start
>> shell.run(**kwds)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pythia-0.8.1.17-py2.7.egg/pyre/applications/Shell.py",
>> line 143, in run
>> method(*args, **kwds)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pythia-0.8.1.17-py2.7.egg/
>> pyre/applications/SuperScript.py", line 49, in execute
>> self.main(*args, **kwds)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pythia-0.8.1.17-py2.7.egg/
>> pyre/applications/SuperScript.py", line 58, in main
>> self.runSubscriTraceback (most recent call last):
>> File "<string>", line 1, in <module>
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pythia-0.8.1.17-py2.7.egg/mpi/__init__.py",
>> line 42, in mpistart
>> kwds = kwds)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pythia-0.8.1.17-py2.7.egg/
>> pyre/applications/__init__.py", line 41, in start
>> shell.run(**kwds)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pythia-0.8.1.17-py2.7.egg/pyre/applications/Shell.py",
>> line 143, in run
>> method(*args, **kwds)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pythia-0.8.1.17-py2.7.egg/
>> pyre/applications/SuperScript.py", line 49, in execute
>> self.main(*args, **kwds)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pythia-0.8.1.17-py2.7.egg/
>> pyre/applications/SuperScript.py", line 58, in main
>> self.runSubscri[3]PETSC ERROR: ------------------------------
>> ------------------------------------------
>> [3]PETSC ERROR: Caught signal number 3 Quit: Some other process (or the
>> batch system) has told this process to end
>> [3]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>> [3]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/d
>> ocumentation/faq.html#valgrind
>> [3]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS
>> X to find memory corruption errors
>> [3]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
>> and run
>> [3]PETSC ERROR: to get more information on the crash.
>> [3]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> [3]PETSC ERROR: Signal received
>> [3]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
>> for trouble shooting.
>> [3]PETSC ERROR: Petsc Development GIT revision: v3.7.2-876-g7e45237 GIT
>> Date: 2016-06-16 04:41:50 -0500
>> [3]PETSC ERROR: /home/yasemin/softwares/pylith
>> /pylith-2.1.4-linux-x86_64/[4]PETSC ERROR: ------------------------------
>> ------------------------------------------
>> [4]PETSC ERROR: Caught signal number 3 Quit: Some other process (or the
>> batch system) has told this process to end
>> [4]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>> [4]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/d
>> ocumentation/faq.html#valgrind
>> [4]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS
>> X to find memory corruption errors
>> [4]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
>> and run
>> [4]PETSC ERROR: to get more information on the crash.
>> [4]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> [4]PETSC ERROR: Signal received
>> [4]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
>> for trouble shooting.
>> [4]PETSC ERROR: Petsc Development GIT revision: v3.7.2-876-g7e45237 GIT
>> Date: 2016-06-16 04:41:50 -0500
>> [4]PETSC ERROR: /home/yasemin/softwares/pylith
>> /pylith-2.1.4-linux-x86_64/[5]PETSC ERROR: ------------------------------
>> ------------------------------------------
>> [5]PETSC ERROR: Caught signal number 3 Quit: Some other process (or the
>> batch system) has told this process to end
>> [5]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>> [5]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/d
>> ocumentation/faq.html#valgrind
>> [5]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS
>> X to find memory corruption errors
>> [5]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
>> and run
>> [5]PETSC ERROR: to get more information on the crash.
>> [5]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> [5]PETSC ERROR: Signal received
>> [5]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
>> for trouble shooting.
>> [5]PETSC ERROR: Petsc Development GIT revision: v3.7.2-876-g7e45237 GIT
>> Date: 2016-06-16 04:41:50 -0500
>> [5]PETSC ERROR: /home/yasemin/softwares/pylith
>> /pylith-2.1.4-linux-x86_64/[6]PETSC ERROR: ------------------------------
>> ------------------------------------------
>> [6]PETSC ERROR: Caught signal number 3 Quit: Some other process (or the
>> batch system) has told this process to end
>> [6]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>> [6]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/d
>> ocumentation/faq.html#valgrind
>> [6]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS
>> X to find memory corruption errors
>> [6]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
>> and run
>> [6]PETSC ERROR: to get more information on the crash.
>> [6]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> [6]PETSC ERROR: Signal received
>> [6]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
>> for trouble shooting.
>> [6]PETSC ERROR: Petsc Development GIT revision: v3.7.2-876-g7e45237 GIT
>> Date: 2016-06-16 04:41:50 -0500
>> [6]PETSC ERROR: /home/yasemin/softwares/pylith
>> /pylith-2.1.4-linux-x86_64/[7]PETSC ERROR: ------------------------------
>> ------------------------------------------
>> [7]PETSC ERROR: Caught signal number 3 Quit: Some other process (or the
>> batch system) has told this process to end
>> [7]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>> [7]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/d
>> ocumentation/faq.html#valgrind
>> [7]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS
>> X to find memory corruption errors
>> [7]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
>> and run
>> [7]PETSC ERROR: to get more information on the crash.
>> [7]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> [7]PETSC ERROR: Signal received
>> [7]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
>> for trouble shooting.
>> [7]PETSC ERROR: Petsc Development GIT revision: v3.7.2-876-g7e45237 GIT
>> Date: 2016-06-16 04:41:50 -0500
>> [7]PETSC ERROR: /home/yasemin/softwares/pylith
>> /pylith-2.1.4-linux-x86_64/[8]PETSC ERROR: ------------------------------
>> ------------------------------------------
>> [8]PETSC ERROR: Caught signal number 3 Quit: Some other process (or the
>> batch system) has told this process to end
>> [8]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>> [8]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/d
>> ocumentation/faq.html#valgrind
>> [8]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS
>> X to find memory corruption errors
>> [8]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
>> and run
>> [8]PETSC ERROR: to get more information on the crash.
>> [8]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> [8]PETSC ERROR: Signal received
>> [8]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
>> for trouble shooting.
>> [8]PETSC ERROR: Petsc Development GIT revision: v3.7.2-876-g7e45237 GIT
>> Date: 2016-06-16 04:41:50 -0500
>> [8]PETSC ERROR: /home/yasemin/softwares/pylith
>> /pylith-2.1.4-linux-x86_64/[9]PETSC ERROR: ------------------------------
>> ------------------------------------------
>> [9]PETSC ERROR: Caught signal number 3 Quit: Some other process (or the
>> batch system) has told this process to end
>> [9]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>> [9]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/d
>> ocumentation/faq.html#valgrind
>> [9]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS
>> X to find memory corruption errors
>> [9]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
>> and run
>> [9]PETSC ERROR: to get more information on the crash.
>> [9]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> [9]PETSC ERROR: Signal received
>> [9]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
>> for trouble shooting.
>> [9]PETSC ERROR: Petsc Development GIT revision: v3.7.2-876-g7e45237 GIT
>> Date: 2016-06-16 04:41:50 -0500
>> [9]PETSC ERROR: /home/yasemin/softwares/pylith
>> /pylith-2.1.4-linux-x86_64/[10]PETSC ERROR:
>> ------------------------------------------------------------------------
>> [10]PETSC ERROR: Caught signal number 3 Quit: Some other process (or the
>> batch system) has told this process to end
>> [10]PETSC ERROR: Try option -start_in_debugger or
>> -on_error_attach_debugger
>> [10]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/d
>> ocumentation/faq.html#valgrind
>> [10]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac
>> OS X to find memory corruption errors
>> [10]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
>> and run
>> [10]PETSC ERROR: to get more information on the crash.
>> [10]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> [10]PETSC ERROR: Signal received
>> [10]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
>> for trouble shooting.
>> [10]PETSC ERROR: Petsc Development GIT revision: v3.7.2-876-g7e45237 GIT
>> Date: 2016-06-16 04:41:50 -0500
>> [10]PETSC ERROR: /home/yasemin/softwares/pylith/pylith-2.1.4-l[11]PETSC
>> ERROR: ------------------------------------------------------------
>> ------------
>> [11]PETSC ERROR: Caught signal number 3 Quit: Some other process (or the
>> batch system) has told this process to end
>> [11]PETSC ERROR: Try option -start_in_debugger or
>> -on_error_attach_debugger
>> [11]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/d
>> ocumentation/faq.html#valgrind
>> [11]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac
>> OS X to find memory corruption errors
>> [11]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
>> and run
>> [11]PETSC ERROR: to get more information on the crash.
>> [11]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> [11]PETSC ERROR: Signal received
>> [11]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
>> for trouble shooting.
>> [11]PETSC ERROR: Petsc Development GIT revision: v3.7.2-876-g7e45237 GIT
>> Date: 2016-06-16 04:41:50 -0500
>> [11]PETSC ERROR: /home/yasemin/softwares/pylith/pylith-2.1.4-l[12]PETSC
>> ERROR: ------------------------------------------------------------
>> ------------
>> [12]PETSC ERROR: Caught signal number 3 Quit: Some other process (or the
>> batch system) has told this process to end
>> [12]PETSC ERROR: Try option -start_in_debugger or
>> -on_error_attach_debugger
>> [12]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/d
>> ocumentation/faq.html#valgrind
>> [12]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac
>> OS X to find memory corruption errors
>> [12]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
>> and run
>> [12]PETSC ERROR: to get more information on the crash.
>> [12]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> [12]PETSC ERROR: Signal received
>> [12]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
>> for trouble shooting.
>> [12]PETSC ERROR: Petsc Development GIT revision: v3.7.2-876-g7e45237 GIT
>> Date: 2016-06-16 04:41:50 -0500
>> [12]PETSC ERROR: /home/yasemin/softwares/pylith/pylith-2.1.4-l[13]PETSC
>> ERROR: ------------------------------------------------------------
>> ------------
>> [13]PETSC ERROR: Caught signal number 3 Quit: Some other process (or the
>> batch system) has told this process to end
>> [13]PETSC ERROR: Try option -start_in_debugger or
>> -on_error_attach_debugger
>> [13]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/d
>> ocumentation/faq.html#valgrind
>> [13]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac
>> OS X to find memory corruption errors
>> [13]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
>> and run
>> [13]PETSC ERROR: to get more information on the crash.
>> [13]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> [13]PETSC ERROR: Signal received
>> [13]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
>> for trouble shooting.
>> [13]PETSC ERROR: Petsc Development GIT revision: v3.7.2-876-g7e45237 GIT
>> Date: 2016-06-16 04:41:50 -0500
>> [13]PETSC ERROR: /home/yasemin/softwares/pylith/pylith-2.1.4-l[14]PETSC
>> ERROR: ------------------------------------------------------------
>> ------------
>> [14]PETSC ERROR: Caught signal number 3 Quit: Some other process (or the
>> batch system) has told this process to end
>> [14]PETSC ERROR: Try option -start_in_debugger or
>> -on_error_attach_debugger
>> [14]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/d
>> ocumentation/faq.html#valgrind
>> [14]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac
>> OS X to find memory corruption errors
>> [14]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
>> and run
>> [14]PETSC ERROR: to get more information on the crash.
>> [14]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> [14]PETSC ERROR: Signal received
>> [14]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
>> for trouble shooting.
>> [14]PETSC ERROR: Petsc Development GIT revision: v3.7.2-876-g7e45237 GIT
>> Date: 2016-06-16 04:41:50 -0500
>> [14]PETSC ERROR: /home/yasemin/softwares/pylith/pylith-2.1.4-l[15]PETSC
>> ERROR: ------------------------------------------------------------
>> ------------
>> [15]PETSC ERROR: Caught signal number 3 Quit: Some other process (or the
>> batch system) has told this process to end
>> [15]PETSC ERROR: Try option -start_in_debugger or
>> -on_error_attach_debugger
>> [15]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/d
>> ocumentation/faq.html#valgrind
>> [15]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac
>> OS X to find memory corruption errors
>> [15]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
>> and run
>> [15]PETSC ERROR: to get more information on the crash.
>> [15]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> [15]PETSC ERROR: Signal received
>> [15]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
>> for trouble shooting.
>> [15]PETSC ERROR: Petsc Development GIT revision: v3.7.2-876-g7e45237 GIT
>> Date: 2016-06-16 04:41:50 -0500
>> [15]PETSC ERROR: /home/yasemin/softwares/pylith/pylith-2.1.4-l[16]PETSC
>> ERROR: ------------------------------------------------------------
>> ------------
>> [16]PETSC ERROR: Caught signal number 3 Quit: Some other process (or the
>> batch system) has told this process to end
>> [16]PETSC ERROR: Try option -start_in_debugger or
>> -on_error_attach_debugger
>> [16]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/d
>> ocumentation/faq.html#valgrind
>> [16]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac
>> OS X to find memory corruption errors
>> [16]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
>> and run
>> [16]PETSC ERROR: to get more information on the crash.
>> [16]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> [16]PETSC ERROR: Signal received
>> [16]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
>> for trouble shooting.
>> [16]PETSC ERROR: Petsc Development GIT revision: v3.7.2-876-g7e45237 GIT
>> Date: 2016-06-16 04:41:50 -0500
>> [16]PETSC ERROR: /home/yasemin/softwares/pylith/pylith-2.1.4-lpt(*args,
>> **kwds)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pythia-0.8.1.17-py2.7.egg/
>> pyre/applications/SuperScript.py", line 62, in runSubscript
>> self.subscript.run(*args, **kwds)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pythia-0.8.1.17-py2.7.egg/
>> pyre/applications/Application.py", line 42, in run
>> shell.run(*args, **kwds)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pythia-0.8.1.17-py2.7.egg/pyre/applications/Shell.py",
>> line 143, in run
>> method(*args, **kwds)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pythia-0.8.1.17-py2.7.egg/mpi/Application.py",
>> line 118, in _onComputeNodes
>> self.onComputeNodes(*args, **kwds)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pylith/apps/PetscApplication.py", line 74,
>> in onComputeNodes
>> self.main(*args, **kwds)
>> File "pt(*args, **kwds)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pythia-0.8.1.17-py2.7.egg/
>> pyre/applications/SuperScript.py", line 62, in runSubscript
>> self.subscript.run(*args, **kwds)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pythia-0.8.1.17-py2.7.egg/
>> pyre/applications/Application.py", line 42, in run
>> shell.run(*args, **kwds)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pythia-0.8.1.17-py2.7.egg/pyre/applications/Shell.py",
>> line 143, in run
>> method(*args, **kwds)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pythia-0.8.1.17-py2.7.egg/mpi/Application.py",
>> line 118, in _onComputeNodes
>> self.onComputeNodes(*args, **kwds)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pylith/apps/PetscApplication.py", line 74,
>> in onComputeNodes
>> self.main(*args, **kwds)
>> File "pt(*args, **kwds)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pythia-0.8.1.17-py2.7.egg/
>> pyre/applications/SuperScript.py", line 62, in runSubscript
>> self.subscript.run(*args, **kwds)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pythia-0.8.1.17-py2.7.egg/
>> pyre/applications/Application.py", line 42, in run
>> shell.run(*args, **kwds)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pythia-0.8.1.17-py2.7.egg/pyre/applications/Shell.py",
>> line 143, in run
>> method(*args, **kwds)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pythia-0.8.1.17-py2.7.egg/mpi/Application.py",
>> line 118, in _onComputeNodes
>> self.onComputeNodes(*args, **kwds)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pylith/apps/PetscApplication.py", line 74,
>> in onComputeNodes
>> self.main(*args, **kwds)
>> File "bin/mpinemesis on a arch-pylith named agri by yasemin Wed Dec 6
>> 16:34:15 2017
>> [3]PETSC ERROR: Configure options --prefix=/home/brad/pylith-binary/dist
>> --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1
>> --with-debugging=0 --with-shared-libraries=1 --with-64-bit-points=1
>> --with-large-file-io=1 --download-chaco=1 --download-ml=1
>> --download-f2cblaslapack=1 --with-hwloc=0 --with-ssl=0 --with-x=0
>> --with-c2html=0 --with-lgrind=0 --with-hdf5=1 --with-hdf5-dir=/home/brad/pylith-binary/dist
>> --LIBS=-lz --with-fc=0 CPPFLAGS="-I/home/brad/pylith-binary/dist/include
>> " LDFLAGS="-L/home/brad/pylith-binary/dist/lib " CFLAGS="-g -O2"
>> CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS=
>> PETSC_DIR=/home/brad/pylith-binary/build/petsc-pylith
>> PETSC_ARCH=arch-pylith
>> [3]PETSC ERROR: #1 User provided function() line 0 in unknown file
>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 3
>> bin/mpinemesis on a arch-pylith named agri by yasemin Wed Dec 6 16:34:15
>> 2017
>> [4]PETSC ERROR: Configure options --prefix=/home/brad/pylith-binary/dist
>> --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1
>> --with-debugging=0 --with-shared-libraries=1 --with-64-bit-points=1
>> --with-large-file-io=1 --download-chaco=1 --download-ml=1
>> --download-f2cblaslapack=1 --with-hwloc=0 --with-ssl=0 --with-x=0
>> --with-c2html=0 --with-lgrind=0 --with-hdf5=1 --with-hdf5-dir=/home/brad/pylith-binary/dist
>> --LIBS=-lz --with-fc=0 CPPFLAGS="-I/home/brad/pylith-binary/dist/include
>> " LDFLAGS="-L/home/brad/pylith-binary/dist/lib " CFLAGS="-g -O2"
>> CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS=
>> PETSC_DIR=/home/brad/pylith-binary/build/petsc-pylith
>> PETSC_ARCH=arch-pylith
>> [4]PETSC ERROR: #1 User provided function() line 0 in unknown file
>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 4
>> bin/mpinemesis on a arch-pylith named agri by yasemin Wed Dec 6 16:34:15
>> 2017
>> [5]PETSC ERROR: Configure options --prefix=/home/brad/pylith-binary/dist
>> --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1
>> --with-debugging=0 --with-shared-libraries=1 --with-64-bit-points=1
>> --with-large-file-io=1 --download-chaco=1 --download-ml=1
>> --download-f2cblaslapack=1 --with-hwloc=0 --with-ssl=0 --with-x=0
>> --with-c2html=0 --with-lgrind=0 --with-hdf5=1 --with-hdf5-dir=/home/brad/pylith-binary/dist
>> --LIBS=-lz --with-fc=0 CPPFLAGS="-I/home/brad/pylith-binary/dist/include
>> " LDFLAGS="-L/home/brad/pylith-binary/dist/lib " CFLAGS="-g -O2"
>> CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS=
>> PETSC_DIR=/home/brad/pylith-binary/build/petsc-pylith
>> PETSC_ARCH=arch-pylith
>> [5]PETSC ERROR: #1 User provided function() line 0 in unknown file
>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 5
>> bin/mpinemesis on a arch-pylith named agri by yasemin Wed Dec 6 16:34:15
>> 2017
>> [6]PETSC ERROR: Configure options --prefix=/home/brad/pylith-binary/dist
>> --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1
>> --with-debugging=0 --with-shared-libraries=1 --with-64-bit-points=1
>> --with-large-file-io=1 --download-chaco=1 --download-ml=1
>> --download-f2cblaslapack=1 --with-hwloc=0 --with-ssl=0 --with-x=0
>> --with-c2html=0 --with-lgrind=0 --with-hdf5=1 --with-hdf5-dir=/home/brad/pylith-binary/dist
>> --LIBS=-lz --with-fc=0 CPPFLAGS="-I/home/brad/pylith-binary/dist/include
>> " LDFLAGS="-L/home/brad/pylith-binary/dist/lib " CFLAGS="-g -O2"
>> CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS=
>> PETSC_DIR=/home/brad/pylith-binary/build/petsc-pylith
>> PETSC_ARCH=arch-pylith
>> [6]PETSC ERROR: #1 User provided function() line 0 in unknown file
>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 6
>> bin/mpinemesis on a arch-pylith named agri by yasemin Wed Dec 6 16:34:15
>> 2017
>> [7]PETSC ERROR: Configure options --prefix=/home/brad/pylith-binary/dist
>> --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1
>> --with-debugging=0 --with-shared-libraries=1 --with-64-bit-points=1
>> --with-large-file-io=1 --download-chaco=1 --download-ml=1
>> --download-f2cblaslapack=1 --with-hwloc=0 --with-ssl=0 --with-x=0
>> --with-c2html=0 --with-lgrind=0 --with-hdf5=1 --with-hdf5-dir=/home/brad/pylith-binary/dist
>> --LIBS=-lz --with-fc=0 CPPFLAGS="-I/home/brad/pylith-binary/dist/include
>> " LDFLAGS="-L/home/brad/pylith-binary/dist/lib " CFLAGS="-g -O2"
>> CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS=
>> PETSC_DIR=/home/brad/pylith-binary/build/petsc-pylith
>> PETSC_ARCH=arch-pylith
>> [7]PETSC ERROR: #1 User provided function() line 0 in unknown file
>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 7
>> bin/mpinemesis on a arch-pylith named agri by yasemin Wed Dec 6 16:34:15
>> 2017
>> [8]PETSC ERROR: Configure options --prefix=/home/brad/pylith-binary/dist
>> --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1
>> --with-debugging=0 --with-shared-libraries=1 --with-64-bit-points=1
>> --with-large-file-io=1 --download-chaco=1 --download-ml=1
>> --download-f2cblaslapack=1 --with-hwloc=0 --with-ssl=0 --with-x=0
>> --with-c2html=0 --with-lgrind=0 --with-hdf5=1 --with-hdf5-dir=/home/brad/pylith-binary/dist
>> --LIBS=-lz --with-fc=0 CPPFLAGS="-I/home/brad/pylith-binary/dist/include
>> " LDFLAGS="-L/home/brad/pylith-binary/dist/lib " CFLAGS="-g -O2"
>> CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS=
>> PETSC_DIR=/home/brad/pylith-binary/build/petsc-pylith
>> PETSC_ARCH=arch-pylith
>> [8]PETSC ERROR: #1 User provided function() line 0 in unknown file
>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 8
>> bin/mpinemesis on a arch-pylith named agri by yasemin Wed Dec 6 16:34:15
>> 2017
>> [9]PETSC ERROR: Configure options --prefix=/home/brad/pylith-binary/dist
>> --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1
>> --with-debugging=0 --with-shared-libraries=1 --with-64-bit-points=1
>> --with-large-file-io=1 --download-chaco=1 --download-ml=1
>> --download-f2cblaslapack=1 --with-hwloc=0 --with-ssl=0 --with-x=0
>> --with-c2html=0 --with-lgrind=0 --with-hdf5=1 --with-hdf5-dir=/home/brad/pylith-binary/dist
>> --LIBS=-lz --with-fc=0 CPPFLAGS="-I/home/brad/pylith-binary/dist/include
>> " LDFLAGS="-L/home/brad/pylith-binary/dist/lib " CFLAGS="-g -O2"
>> CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS=
>> PETSC_DIR=/home/brad/pylith-binary/build/petsc-pylith
>> PETSC_ARCH=arch-pylith
>> [9]PETSC ERROR: #1 User provided function() line 0 in unknown file
>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 9
>> inux-x86_64/bin/mpinemesis on a arch-pylith named agri by yasemin Wed
>> Dec 6 16:34:15 2017
>> [10]PETSC ERROR: Configure options --prefix=/home/brad/pylith-binary/dist
>> --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1
>> --with-debugging=0 --with-shared-libraries=1 --with-64-bit-points=1
>> --with-large-file-io=1 --download-chaco=1 --download-ml=1
>> --download-f2cblaslapack=1 --with-hwloc=0 --with-ssl=0 --with-x=0
>> --with-c2html=0 --with-lgrind=0 --with-hdf5=1 --with-hdf5-dir=/home/brad/pylith-binary/dist
>> --LIBS=-lz --with-fc=0 CPPFLAGS="-I/home/brad/pylith-binary/dist/include
>> " LDFLAGS="-L/home/brad/pylith-binary/dist/lib " CFLAGS="-g -O2"
>> CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS=
>> PETSC_DIR=/home/brad/pylith-binary/build/petsc-pylith
>> PETSC_ARCH=arch-pylith
>> [10]PETSC ERROR: #1 User provided function() line 0 in unknown file
>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 10
>> inux-x86_64/bin/mpinemesis on a arch-pylith named agri by yasemin Wed
>> Dec 6 16:34:15 2017
>> [11]PETSC ERROR: Configure options --prefix=/home/brad/pylith-binary/dist
>> --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1
>> --with-debugging=0 --with-shared-libraries=1 --with-64-bit-points=1
>> --with-large-file-io=1 --download-chaco=1 --download-ml=1
>> --download-f2cblaslapack=1 --with-hwloc=0 --with-ssl=0 --with-x=0
>> --with-c2html=0 --with-lgrind=0 --with-hdf5=1 --with-hdf5-dir=/home/brad/pylith-binary/dist
>> --LIBS=-lz --with-fc=0 CPPFLAGS="-I/home/brad/pylith-binary/dist/include
>> " LDFLAGS="-L/home/brad/pylith-binary/dist/lib " CFLAGS="-g -O2"
>> CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS=
>> PETSC_DIR=/home/brad/pylith-binary/build/petsc-pylith
>> PETSC_ARCH=arch-pylith
>> [11]PETSC ERROR: #1 User provided function() line 0 in unknown file
>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 11
>> inux-x86_64/bin/mpinemesis on a arch-pylith named agri by yasemin Wed
>> Dec 6 16:34:15 2017
>> [12]PETSC ERROR: Configure options --prefix=/home/brad/pylith-binary/dist
>> --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1
>> --with-debugging=0 --with-shared-libraries=1 --with-64-bit-points=1
>> --with-large-file-io=1 --download-chaco=1 --download-ml=1
>> --download-f2cblaslapack=1 --with-hwloc=0 --with-ssl=0 --with-x=0
>> --with-c2html=0 --with-lgrind=0 --with-hdf5=1 --with-hdf5-dir=/home/brad/pylith-binary/dist
>> --LIBS=-lz --with-fc=0 CPPFLAGS="-I/home/brad/pylith-binary/dist/include
>> " LDFLAGS="-L/home/brad/pylith-binary/dist/lib " CFLAGS="-g -O2"
>> CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS=
>> PETSC_DIR=/home/brad/pylith-binary/build/petsc-pylith
>> PETSC_ARCH=arch-pylith
>> [12]PETSC ERROR: #1 User provided function() line 0 in unknown file
>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 12
>> inux-x86_64/bin/mpinemesis on a arch-pylith named agri by yasemin Wed
>> Dec 6 16:34:15 2017
>> [13]PETSC ERROR: Configure options --prefix=/home/brad/pylith-binary/dist
>> --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1
>> --with-debugging=0 --with-shared-libraries=1 --with-64-bit-points=1
>> --with-large-file-io=1 --download-chaco=1 --download-ml=1
>> --download-f2cblaslapack=1 --with-hwloc=0 --with-ssl=0 --with-x=0
>> --with-c2html=0 --with-lgrind=0 --with-hdf5=1 --with-hdf5-dir=/home/brad/pylith-binary/dist
>> --LIBS=-lz --with-fc=0 CPPFLAGS="-I/home/brad/pylith-binary/dist/include
>> " LDFLAGS="-L/home/brad/pylith-binary/dist/lib " CFLAGS="-g -O2"
>> CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS=
>> PETSC_DIR=/home/brad/pylith-binary/build/petsc-pylith
>> PETSC_ARCH=arch-pylith
>> [13]PETSC ERROR: #1 User provided function() line 0 in unknown file
>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 13
>> inux-x86_64/bin/mpinemesis on a arch-pylith named agri by yasemin Wed
>> Dec 6 16:34:15 2017
>> [14]PETSC ERROR: Configure options --prefix=/home/brad/pylith-binary/dist
>> --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1
>> --with-debugging=0 --with-shared-libraries=1 --with-64-bit-points=1
>> --with-large-file-io=1 --download-chaco=1 --download-ml=1
>> --download-f2cblaslapack=1 --with-hwloc=0 --with-ssl=0 --with-x=0
>> --with-c2html=0 --with-lgrind=0 --with-hdf5=1 --with-hdf5-dir=/home/brad/pylith-binary/dist
>> --LIBS=-lz --with-fc=0 CPPFLAGS="-I/home/brad/pylith-binary/dist/include
>> " LDFLAGS="-L/home/brad/pylith-binary/dist/lib " CFLAGS="-g -O2"
>> CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS=
>> PETSC_DIR=/home/brad/pylith-binary/build/petsc-pylith
>> PETSC_ARCH=arch-pylith
>> [14]PETSC ERROR: #1 User provided function() line 0 in unknown file
>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 14
>> inux-x86_64/bin/mpinemesis on a arch-pylith named agri by yasemin Wed
>> Dec 6 16:34:15 2017
>> [15]PETSC ERROR: Configure options --prefix=/home/brad/pylith-binary/dist
>> --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1
>> --with-debugging=0 --with-shared-libraries=1 --with-64-bit-points=1
>> --with-large-file-io=1 --download-chaco=1 --download-ml=1
>> --download-f2cblaslapack=1 --with-hwloc=0 --with-ssl=0 --with-x=0
>> --with-c2html=0 --with-lgrind=0 --with-hdf5=1 --with-hdf5-dir=/home/brad/pylith-binary/dist
>> --LIBS=-lz --with-fc=0 CPPFLAGS="-I/home/brad/pylith-binary/dist/include
>> " LDFLAGS="-L/home/brad/pylith-binary/dist/lib " CFLAGS="-g -O2"
>> CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS=
>> PETSC_DIR=/home/brad/pylith-binary/build/petsc-pylith
>> PETSC_ARCH=arch-pylith
>> [15]PETSC ERROR: #1 User provided function() line 0 in unknown file
>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 15
>> inux-x86_64/bin/mpinemesis on a arch-pylith named agri by yasemin Wed
>> Dec 6 16:34:15 2017
>> [16]PETSC ERROR: Configure options --prefix=/home/brad/pylith-binary/dist
>> --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1
>> --with-debugging=0 --with-shared-libraries=1 --with-64-bit-points=1
>> --with-large-file-io=1 --download-chaco=1 --download-ml=1
>> --download-f2cblaslapack=1 --with-hwloc=0 --with-ssl=0 --with-x=0
>> --with-c2html=0 --with-lgrind=0 --with-hdf5=1 --with-hdf5-dir=/home/brad/pylith-binary/dist
>> --LIBS=-lz --with-fc=0 CPPFLAGS="-I/home/brad/pylith-binary/dist/include
>> " LDFLAGS="-L/home/brad/pylith-binary/dist/lib " CFLAGS="-g -O2"
>> CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS=
>> PETSC_DIR=/home/brad/pylith-binary/build/petsc-pylith
>> PETSC_ARCH=arch-pylith
>> [16]PETSC ERROR: #1 User provided function() line 0 in unknown file
>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 16
>> /home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pylith/apps/PyLithApp.py", line 135, in main
>> self.problem.run(self)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pylith/problems/TimeDependent.py", line 203,
>> in run
>> self.formulation.step(t, dt)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pylith/problems/Explicit.py", line 215, in
>> step
>> self._reformResidual(t, dt)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pylith/problems/Formulation.py", line 598,
>> in _reformResidual
>> self.reformResidual()
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pylith/problems/problems.py", line 88, in
>> reformResidual
>> def reformResidual(self, tmpResidualVec=None, tmpSolveSolnVec=None):
>> return _problems.Formulation_reformResidual(self, tmpResidualVec,
>> tmpSolveSolnVec)
>> KeyboardInterrupt
>> [0]PETSC ER/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pylith/apps/PyLithApp.py", line 135, in main
>> self.problem.run(self)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pylith/problems/TimeDependent.py", line 203,
>> in run
>> self.formulation.step(t, dt)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pylith/problems/Explicit.py", line 215, in
>> step
>> self._reformResidual(t, dt)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pylith/problems/Formulation.py", line 598,
>> in _reformResidual
>> self.reformResidual()
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pylith/problems/problems.py", line 88, in
>> reformResidual
>> def reformResidual(self, tmpResidualVec=None, tmpSolveSolnVec=None):
>> return _problems.Formulation_reformResidual(self, tmpResidualVec,
>> tmpSolveSolnVec)
>> KeyboardInterrupt
>> [1]PETSC ER/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pylith/apps/PyLithApp.py", line 135, in main
>> self.problem.run(self)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pylith/problems/TimeDependent.py", line 203,
>> in run
>> self.formulation.step(t, dt)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pylith/problems/Explicit.py", line 215, in
>> step
>> self._reformResidual(t, dt)
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pylith/problems/Formulation.py", line 598,
>> in _reformResidual
>> self.reformResidual()
>> File "/home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/
>> lib/python2.7/site-packages/pylith/problems/problems.py", line 88, in
>> reformResidual
>> def reformResidual(self, tmpResidualVec=None, tmpSolveSolnVec=None):
>> return _problems.Formulation_reformResidual(self, tmpResidualVec,
>> tmpSolveSolnVec)
>> KeyboardInterrupt
>> [2]PETSC ERROR: ------------------------------
>> ------------------------------------------
>> [0]PETSC ERROR: Caught signal number 3 Quit: Some other process (or the
>> batch system) has told this process to end
>> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>> [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/d
>> ocumentation/faq.html#valgrind
>> [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS
>> X to find memory corruption errors
>> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
>> and run
>> [0]PETSC ERROR: to get more information on the crash.
>> [0]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> [0]PETSC ERROR: Signal received
>> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
>> for trouble shooting.
>> [0]PETSC ERROR: Petsc Development GIT revision: v3.7.2-876-g7e45237 GIT
>> Date: 2016-06-16 04:41:50 -0500
>> [0]PETSC ERROR: /home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/bin/mpinemeROR:
>> ------------------------------------------------------------------------
>> [1]PETSC ERROR: Caught signal number 3 Quit: Some other process (or the
>> batch system) has told this process to end
>> [1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>> [1]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/d
>> ocumentation/faq.html#valgrind
>> [1]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS
>> X to find memory corruption errors
>> [1]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
>> and run
>> [1]PETSC ERROR: to get more information on the crash.
>> [1]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> [1]PETSC ERROR: Signal received
>> [1]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
>> for trouble shooting.
>> [1]PETSC ERROR: Petsc Development GIT revision: v3.7.2-876-g7e45237 GIT
>> Date: 2016-06-16 04:41:50 -0500
>> [1]PETSC ERROR: /home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/bin/mpinemeROR:
>> ------------------------------------------------------------------------
>> [2]PETSC ERROR: Caught signal number 3 Quit: Some other process (or the
>> batch system) has told this process to end
>> [2]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>> [2]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/d
>> ocumentation/faq.html#valgrind
>> [2]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS
>> X to find memory corruption errors
>> [2]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
>> and run
>> [2]PETSC ERROR: to get more information on the crash.
>> [2]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> [2]PETSC ERROR: Signal received
>> [2]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
>> for trouble shooting.
>> [2]PETSC ERROR: Petsc Development GIT revision: v3.7.2-876-g7e45237 GIT
>> Date: 2016-06-16 04:41:50 -0500
>> [2]PETSC ERROR: /home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/bin/mpinemesis
>> on a arch-pylith named agri by yasemin Wed Dec 6 16:34:15 2017
>> [0]PETSC ERROR: Configure options --prefix=/home/brad/pylith-binary/dist
>> --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1
>> --with-debugging=0 --with-shared-libraries=1 --with-64-bit-points=1
>> --with-large-file-io=1 --download-chaco=1 --download-ml=1
>> --download-f2cblaslapack=1 --with-hwloc=0 --with-ssl=0 --with-x=0
>> --with-c2html=0 --with-lgrind=0 --with-hdf5=1 --with-hdf5-dir=/home/brad/pylith-binary/dist
>> --LIBS=-lz --with-fc=0 CPPFLAGS="-I/home/brad/pylith-binary/dist/include
>> " LDFLAGS="-L/home/brad/pylith-binary/dist/lib " CFLAGS="-g -O2"
>> CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS=
>> PETSC_DIR=/home/brad/pylith-binary/build/petsc-pylith
>> PETSC_ARCH=arch-pylith
>> [0]PETSC ERROR: #1 User provided function() line 0 in unknown file
>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
>> sis on a arch-pylith named agri by yasemin Wed Dec 6 16:34:15 2017
>> [1]PETSC ERROR: Configure options --prefix=/home/brad/pylith-binary/dist
>> --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1
>> --with-debugging=0 --with-shared-libraries=1 --with-64-bit-points=1
>> --with-large-file-io=1 --download-chaco=1 --download-ml=1
>> --download-f2cblaslapack=1 --with-hwloc=0 --with-ssl=0 --with-x=0
>> --with-c2html=0 --with-lgrind=0 --with-hdf5=1 --with-hdf5-dir=/home/brad/pylith-binary/dist
>> --LIBS=-lz --with-fc=0 CPPFLAGS="-I/home/brad/pylith-binary/dist/include
>> " LDFLAGS="-L/home/brad/pylith-binary/dist/lib " CFLAGS="-g -O2"
>> CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS=
>> PETSC_DIR=/home/brad/pylith-binary/build/petsc-pylith
>> PETSC_ARCH=arch-pylith
>> [1]PETSC ERROR: #1 User provided function() line 0 in unknown file
>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 1
>> sis on a arch-pylith named agri by yasemin Wed Dec 6 16:34:15 2017
>> [2]PETSC ERROR: Configure options --prefix=/home/brad/pylith-binary/dist
>> --with-c2html=0 --with-x=0 --with-clanguage=C --with-mpicompilers=1
>> --with-debugging=0 --with-shared-libraries=1 --with-64-bit-points=1
>> --with-large-file-io=1 --download-chaco=1 --download-ml=1
>> --download-f2cblaslapack=1 --with-hwloc=0 --with-ssl=0 --with-x=0
>> --with-c2html=0 --with-lgrind=0 --with-hdf5=1 --with-hdf5-dir=/home/brad/pylith-binary/dist
>> --LIBS=-lz --with-fc=0 CPPFLAGS="-I/home/brad/pylith-binary/dist/include
>> " LDFLAGS="-L/home/brad/pylith-binary/dist/lib " CFLAGS="-g -O2"
>> CXXFLAGS="-g -O2 -DMPICH_IGNORE_CXX_SEEK" FCFLAGS=
>> PETSC_DIR=/home/brad/pylith-binary/build/petsc-pylith
>> PETSC_ARCH=arch-pylith
>> [2]PETSC ERROR: #1 User provided function() line 0 in unknown file
>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 2
>> /home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/bin/nemesis:
>> mpirun: exit 255
>> /home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/bin/pylith:
>> /home/yasemin/softwares/pylith/pylith-2.1.4-linux-x86_64/bin/nemesis:
>> exit 1
>> fearless#
>>
>>
>>
>
--
*Yasemin Korkusuz Öztürk*
Boğaziçi Üniversitesi
Kandilli Ras. & Dep. Arş. Ens.
Jeofizik Anabilim Dalı
34684, Çengelköy, İstanbul
Ofis: +90 216 516 33 78
Cep: +90 536 942 44 02
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