>> /mit/software/python/python-2.7.2/pkg/pylith/pylith-1.6.3-2/lib/python2.7/site-packages/pylith/problems/Formulation.py:489:_initialize -- implicit(info) -- Initializing constraints. >> /mit/software/python/python-2.7.2/pkg/pylith/pylith-1.6.3-2/lib/python2.7/site-packages/pylith/problems/Formulation.py:495:_initialize -- implicit(info) -- Setting up solution output. >> /mit/software/python/python-2.7.2/pkg/pylith/pylith-1.6.3-2/lib/python2.7/site-packages/pylith/problems/Formulation.py:504:_initialize -- implicit(info) -- Creating solution field. >> /mit/software/python/python-2.7.2/pkg/pylith/pylith-1.6.3-2/lib/python2.7/site-packages/pylith/problems/Implicit.py:131:initialize -- implicit(info) -- Creating other fields. >> /mit/software/python/python-2.7.2/pkg/pylith/pylith-1.6.3-2/lib/python2.7/site-packages/pylith/problems/Implicit.py:154:initialize -- implicit(info) -- Creating Jacobian matrix. >> /mit/software/python/python-2.7.2/pkg/pylith/pylith-1.6.3-2/lib/python2.7/site-packages/pylith/problems/Implicit.py:164:initialize -- implicit(info) -- Initializing solver. >> /mit/software/python/python-2.7.2/pkg/pylith/pylith-1.6.3-2/lib/python2.7/site-packages/pylith/problems/TimeDependent.py:128:run -- timedependent(info) -- Solving problem. >> /mit/software/python/python-2.7.2/pkg/pylith/pylith-1.6.3-2/lib/python2.7/site-packages/pylith/problems/TimeDependent.py:138:run -- timedependent(info) -- Main time loop, current time is t=-86.4*s >> /mit/software/python/python-2.7.2/pkg/pylith/pylith-1.6.3-2/lib/python2.7/site-packages/pylith/problems/TimeDependent.py:152:run -- timedependent(info) -- Preparing to advance solution from time t=-86.4*s to t=0*s. >> /mit/software/python/python-2.7.2/pkg/pylith/pylith-1.6.3-2/lib/python2.7/site-packages/pylith/problems/Implicit.py:210:prestep -- implicit(info) -- Setting constraints. >> /mit/software/python/python-2.7.2/pkg/pylith/pylith-1.6.3-2/lib/python2.7/site-packages/pylith/problems/Formulation.py:561:_reformJacobian -- implicit(info) -- Integrating Jacobian operator. >> /mit/software/python/python-2.7.2/pkg/pylith/pylith-1.6.3-2/lib/python2.7/site-packages/pylith/problems/TimeDependent.py:158:run -- timedependent(info) -- Advancing solution from t=-86.4*s to t=0*s. >> /mit/software/python/python-2.7.2/pkg/pylith/pylith-1.6.3-2/lib/python2.7/site-packages/pylith/problems/Formulation.py:589:_reformResidual -- implicit(info) -- Integrating residual term in operator. >> /mit/software/python/python-2.7.2/pkg/pylith/pylith-1.6.3-2/lib/python2.7/site-packages/pylith/problems/Implicit.py:244:step -- implicit(info) -- Solving equations. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/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: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Development HG revision: 4c8ea9bd484535a6b16bda198247a5bf49dea0df HG Date: Thu Mar 08 19:59:42 2012 -0600 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: /mit/software/python/python-2.7.2/pkg/pylith/pylith-1.6.3-2/bin/mpinemesis on a arch-linu named login by bjha Fri Sep 14 02:21:05 2012 [0]PETSC ERROR: Libraries linked from /mit/software/python/python-2.7.2/pkg/pylith/pylith-1.6.3-2/lib [0]PETSC ERROR: Configure run at Fri May 18 10:41:38 2012 [0]PETSC ERROR: Configure options --prefix=/mit/software/python/python-2.7.2/pkg/pylith/pylith-1.6.3-2 --with-c2html=0 --with-x=0 --CXXFLAGS=-DMPICH_IGNORE_CXX_SEEK --with-clanguage=C++ --with-mpicompilers=1 --with-debugging=0 --with-shared-libraries=1 --with-sieve=1 --download-boost=1 --download-chaco=1 --download-ml=1 --download-f-blas-lapack=1 --with-hdf5=1 --with-hdf5-include=/mit/software/python/python-2.7.2/pkg/pylith/pylith-1.6.3-2/include --with-hdf5-lib=/mit/software/python/python-2.7.2/pkg/pylith/pylith-1.6.3-2/lib/libhdf5.dylib --LIBS=-lz CPPFLAGS="-I/mit/software/python/python-2.7.2/pkg/pylith/pylith-1.6.3-2/include " LDFLAGS="-L/mit/software/python/python-2.7.2/pkg/pylith/pylith-1.6.3-2/lib " PETSC_DIR=/mit/software/python/python-2.7.2/pkg/pylith/src/pylith-installer-1.6.3-2/petsc-dev [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 59. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- mpirun has exited due to process rank 0 with PID 2327 on node login exiting without calling "finalize". This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). -------------------------------------------------------------------------- /mit/software/python/python-2.7.2/pkg/pylith/pylith-1.6.3-2/bin/nemesis: mpirun: exit 59 /mit/software/python/python-2.7.2/pkg/pylith/pylith-1.6.3-2/bin/pylith: /mit/software/python/python-2.7.2/pkg/pylith/pylith-1.6.3-2/bin/nemesis: exit 1