[CIG-SHORT] fault opening with nonzero traction
ozgun.konca at boun.edu.tr
ozgun.konca at boun.edu.tr
Mon Dec 11 09:50:42 PST 2017
Hi Brad,
Thanks for helping our student. I really appricate your effort.
Best wishes
Ozgun
Alinti Yasemin Korkusuz <yaseminkrksz at gmail.com>
> 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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