[petsc-users] mac os x, problem with partitioning

Tue May 5 05:18:13 CDT 2015

Hello,

I struggle with problem of matrix partitioning on McOSX for some time, since Maverick. Error is random, it runs ok for couple of times and then it beak. I using the newest version of petsc, for bitbucket repository, however this problem exist for long time for older versions too.

If I load partitioned mesh, f.e. using metis or any other partitioner code work without errors. Moreover, the same code I run on linux, redhat, ubutu, tested with valgrind and no problems like that ever existed. I used as well intel compiler on linux and following problems never existed. 

*) When I use ptscoch,

It is at the point of graph partitioning (random),

(2): ERROR: dgraphCheck: arc data do not match
[2]PETSC ERROR: #1 MatPartitioningApply_PTScotch() line 305 in /opt/petsc/src/mat/partition/impls/scotch/scotch.c
(3): ERROR: dgraphCheck: arc data do not match
[3]PETSC ERROR: #1 MatPartitioningApply_PTScotch() line 305 in /opt/petsc/src/mat/partition/impls/scotch/scotch.c
[3]PETSC ERROR: #2 MatPartitioningApply() line 225 in /opt/petsc/src/mat/partition/partition.c
[3]PETSC ERROR: #3 partition_problem() line 611 in /Users/likask/MyBuild/mofem-cephas/mofem_v0.2/src/interfaces/impl/CreateMat.cpp
(0): ERROR: dgraphCheck: arc data do not match
[0]PETSC ERROR: #1 MatPartitioningApply_PTScotch() line 305 in /opt/petsc/src/mat/partition/impls/scotch/scotch.c
[0]PETSC ERROR: #2 MatPartitioningApply() line 225 in /opt/petsc/src/mat/partition/partition.c
[0]PETSC ERROR: #3 partition_problem() line 611 in /Users/likask/MyBuild/mofem-cephas/mofem_v0.2/src/interfaces/impl/CreateMat.cpp
(1): ERROR: dgraphCheck: arc data do not match
[1]PETSC ERROR: #1 MatPartitioningApply_PTScotch() line 305 in /opt/petsc/src/mat/partition/impls/scotch/scotch.c
[1]PETSC ERROR: #2 MatPartitioningApply() line 225 in /opt/petsc/src/mat/partition/partition.c

*) When I use parmetis

It is random once again, but problem appear later in the code, when matrix is assembled, 

[1]PETSC ERROR: --------------------- MoFEM Error Message---------------------------------------------------------------------------
[1]PETSC ERROR: MoFEM version 0.2.1
[1]PETSC ERROR: MoFEM git commit id 837f38245270d65c22eafb638f023ea3476bc57a
[1]PETSC ERROR: See http://userweb.eng.gla.ac.uk/lukasz.kaczmarczyk/MoFem/html/guidelines_bug_reporting.html for bug reporting.
[1]PETSC ERROR: See http://userweb.eng.gla.ac.uk/lukasz.kaczmarczyk/MoFem/html/faq_and_bugs.html for trouble shooting.
[0]PETSC ERROR: --------------------- MoFEM Error Message---------------------------------------------------------------------------
[0]PETSC ERROR: MoFEM version 0.2.1
[0]PETSC ERROR: MoFEM git commit id 837f38245270d65c22eafb638f023ea3476bc57a
[0]PETSC ERROR: See http://userweb.eng.gla.ac.uk/lukasz.kaczmarczyk/MoFem/html/guidelines_bug_reporting.html for bug reporting.
[0]PETSC ERROR: See http://userweb.eng.gla.ac.uk/lukasz.kaczmarczyk/MoFem/html/faq_and_bugs.html for trouble shooting.
[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[0]PETSC ERROR: Argument out of range
[0]PETSC ERROR: Inserting a new nonzero at global row/column (71, 354) into matrix
[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision: v3.5.3-2812-gc9542f9  GIT Date: 2015-05-03 22:34:15 +0300
[0]PETSC ERROR: /Users/likask/MyBuild/um_debug/nonlinear_elasticity/nonlinear_dynamics on a arch-darwin-c-debug named dh23-181.eng.gla.ac.uk by likask Tue May  5 09:49:38 2015
[0]PETSC ERROR: Configure options --with-mpi=1 --with-debugging=1 --download-fblaslapack=1 --download-superlu_dist=1 --download-metis=1 --download-parmetis=1 --download-hypre=1 --download-mumps=1 --download-scalapack=1 --download-blacs=1 --download-moab=1 --download-hdf5=1 --download-netcdf=/opt/petsc/netcdf-4.3.3.1.tar.gz --download-openmpi=1 --CXXFLAGS=-fno-vectorize -CFLAGS=-fno-vectorize --download-mumps=1 --download-ptscotch=1
[0]PETSC ERROR: #1 MatSetValues_MPIAIJ() line 616 in /opt/petsc/src/mat/impls/aij/mpi/mpiaij.c
[0]PETSC ERROR: #2 MatAssemblyEnd_MPIAIJ() line 731 in /opt/petsc/src/mat/impls/aij/mpi/mpiaij.c
[0]PETSC ERROR: [1]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[1]PETSC ERROR: Argument out of range
[1]PETSC ERROR: Inserting a new nonzero at global row/column (300, 536) into matrix
[1]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
[1]PETSC ERROR: Petsc Development GIT revision: v3.5.3-2812-gc9542f9  GIT Date: 2015-05-03 22:34:15 +0300
[1]PETSC ERROR: /Users/likask/MyBuild/um_debug/nonlinear_elasticity/nonlinear_dynamics on a arch-darwin-c-debug named dh23-181.eng.gla.ac.uk by likask Tue May  5 09:49:38 2015
[1]PETSC ERROR: Configure options --with-mpi=1 --with-debugging=1 --download-fblaslapack=1 --download-superlu_dist=1 --download-metis=1 --download-parmetis=1 --download-hypre=1 --download-mumps=1 --download-scalapack=1 --download-blacs=1 --download-moab=1 --download-hdf5=1 --download-netcdf=/opt/petsc/netcdf-4.3.3.1.tar.gz --download-openmpi=1 --CXXFLAGS=-fno-vectorize -CFLAGS=-fno-vectorize --download-mumps=1 --download-ptscotch=1
[1]PETSC ERROR: #1 MatSetValues_MPIAIJ() line 613 in /opt/petsc/src/mat/impls/aij/mpi/mpiaij.c
[1]PETSC ERROR: #2 MatAssemblyEnd_MPIAIJ() line 731 in /opt/petsc/src/mat/impls/aij/mpi/mpiaij.c
[1]PETSC ERROR: #3 MatAssemblyEnd() line 5097 in /opt/petsc/src/mat/interface/matrix.c
#3 MatAssemblyEnd() line 5097 in /opt/petsc/src/mat/interface/matrix.c
[0]PETSC ERROR: #4 postProcess() line 222 in /Users/likask/MyBuild/mofem-cephas/mofem_v0.2/finite_element_library/impl/DirichletBC.cpp
[0]PETSC ERROR: #5 problem_basic_method_postProcess() line 2636 in /Users/likask/MyBuild/mofem-cephas/mofem_v0.2/src/interfaces/impl/FieldInterfaceCore.cpp
[0]PETSC ERROR: #6 problem_basic_method_postProcess() line 2651 in /Users/likask/MyBuild/mofem-cephas/mofem_v0.2/src/interfaces/impl/FieldInterfaceCore.cpp
[0]PETSC ERROR: #7 preProcess() line 2467 in /Users/likask/MyBuild/mofem-cephas/mofem_v0.2/users_modules/convective_mass_element/src/ConvectiveMassElement.hpp
[0]PETSC ERROR: #8 problem_basic_method_preProcess() line 2615 in /Users/likask/MyBuild/mofem-cephas/mofem_v0.2/src/interfaces/impl/FieldInterfaceCore.cpp
[0]PETSC ERROR: #9 problem_basic_method_preProcess() line 2628 in /Users/likask/MyBuild/mofem-cephas/mofem_v0.2/src/interfaces/impl/FieldInterfaceCore.cpp
[0]PETSC ERROR: #10 f_TSSetIJacobian() line 120 in /Users/likask/MyBuild/mofem-cephas/mofem_v0.2/src/petsc/impl/TsCtx.cpp
[0]PETSC ERROR: #11 TSComputeIJacobian() line 809 in /opt/petsc/src/ts/interface/ts.c
[0]PETSC ERROR: #12 SNESTSFormJacobian_Alpha() line 181 in /opt/petsc/src/ts/impls/implicit/alpha/alpha.c
[0]PETSC ERROR: #13 SNESTSFormJacobian() line 4193 in /opt/petsc/src/ts/interface/ts.c
[0]PETSC ERROR: #14 SNESComputeJacobian() line 2213 in /opt/petsc/src/snes/interface/snes.c
[0]PETSC ERROR: #15 SNESSolve_NEWTONLS() line 242 in /opt/petsc/src/snes/impls/ls/ls.c
[0]PETSC ERROR: #16 SNESSolve() line 3884 in /opt/petsc/src/snes/interface/snes.c
[0]PETSC ERROR: [1]PETSC ERROR: #4 postProcess() line 222 in /Users/likask/MyBuild/mofem-cephas/mofem_v0.2/finite_element_library/impl/DirichletBC.cpp
[1]PETSC ERROR: #5 problem_basic_method_postProcess() line 2636 in /Users/likask/MyBuild/mofem-cephas/mofem_v0.2/src/interfaces/impl/FieldInterfaceCore.cpp
[1]PETSC ERROR: #6 problem_basic_method_postProcess() line 2651 in /Users/likask/MyBuild/mofem-cephas/mofem_v0.2/src/interfaces/impl/FieldInterfaceCore.cpp
[1]PETSC ERROR: #7 preProcess() line 2467 in /Users/likask/MyBuild/mofem-cephas/mofem_v0.2/users_modules/convective_mass_element/src/ConvectiveMassElement.hpp
[1]PETSC ERROR: #8 problem_basic_method_preProcess() line 2615 in /Users/likask/MyBuild/mofem-cephas/mofem_v0.2/src/interfaces/impl/FieldInterfaceCore.cpp
[1]PETSC ERROR: #9 problem_basic_method_preProcess() line 2628 in /Users/likask/MyBuild/mofem-cephas/mofem_v0.2/src/interfaces/impl/FieldInterfaceCore.cpp
[1]PETSC ERROR: #10 f_TSSetIJacobian() line 120 in /Users/likask/MyBuild/mofem-cephas/mofem_v0.2/src/petsc/impl/TsCtx.cpp
[1]PETSC ERROR: #11 TSComputeIJacobian() line 809 in /opt/petsc/src/ts/interface/ts.c
[1]PETSC ERROR: #12 SNESTSFormJacobian_Alpha() line 181 in /opt/petsc/src/ts/impls/implicit/alpha/alpha.c
[1]PETSC ERROR: #13 SNESTSFormJacobian() line 4193 in /opt/petsc/src/ts/interface/ts.c
[1]PETSC ERROR: #14 SNESComputeJacobian() line 2213 in /opt/petsc/src/snes/interface/snes.c
[1]PETSC ERROR: #15 SNESSolve_NEWTONLS() line 242 in /opt/petsc/src/snes/impls/ls/ls.c
[1]PETSC ERROR: #16 SNESSolve() line 3884 in /opt/petsc/src/snes/interface/snes.c
[1]PETSC ERROR: #17 TSStep_Alpha() line 57 in /opt/petsc/src/ts/impls/implicit/alpha/alpha.c
[1]PETSC ERROR: #18 TSStep() line 3100 in /opt/petsc/src/ts/interface/ts.c
[1]PETSC ERROR: #19 TSSolve() line 3290 in /opt/petsc/src/ts/interface/ts.c
[1]PETSC ERROR: #20 main() line 623 in /Users/likask/MyBuild/mofem-cephas/mofem_v0.2/users_modules/nonlinear_elasticity/nonlinear_dynamics.cpp
[1]PETSC ERROR: PETSc Option Table entries:
[1]PETSC ERROR: -ksp_atol 1e-10
[1]PETSC ERROR: -ksp_rtol 1e-10
[1]PETSC ERROR: -ksp_type fgmres
[1]PETSC ERROR: -mat_partitioning_type parmetis
[1]PETSC ERROR: -my_disp_order 3
[1]PETSC ERROR: -my_file LShape.cub
[1]PETSC ERROR: -my_max_post_proc_ref_level 0
[1]PETSC ERROR: -my_output_prt 1
[1]PETSC ERROR: -my_time_data_file data.txt
[1]PETSC ERROR: -my_vel_order 3
[1]PETSC ERROR: -pc_factor_mat_solver_package mumps
[1]PETSC ERROR: -pc_type lu
#17 TSStep_Alpha() line 57 in /opt/petsc/src/ts/impls/implicit/alpha/alpha.c
[0]PETSC ERROR: #18 TSStep() line 3100 in /opt/petsc/src/ts/interface/ts.c
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD 
with errorcode 63.

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.
--------------------------------------------------------------------------
[0]PETSC ERROR: #19 TSSolve() line 3290 in /opt/petsc/src/ts/interface/ts.c
[0]PETSC ERROR: #20 main() line 623 in /Users/likask/MyBuild/mofem-cephas/mofem_v0.2/users_modules/nonlinear_elasticity/nonlinear_dynamics.cpp
[0]PETSC ERROR: PETSc Option Table entries:
[0]PETSC ERROR: -ksp_atol 1e-10
[0]PETSC ERROR: -ksp_rtol 1e-10
[0]PETSC ERROR: -ksp_type fgmres
[0]PETSC ERROR: -mat_partitioning_type parmetis
[0]PETSC ERROR: -my_disp_order 3
[0]PETSC ERROR: -my_file LShape.cub
[0]PETSC ERROR: -my_max_post_proc_ref_level 0
[0]PETSC ERROR: -my_output_prt 1
[0]PETSC ERROR: -my_time_data_file data.txt
[0]PETSC ERROR: -my_vel_order 3
[0]PETSC ERROR: -pc_factor_mat_solver_package mumps
[0]PETSC ERROR: -pc_type lu
[0]PETSC ERROR: -snes_atol 1e-7
[0]PETSC ERROR: -snes_linesearch_type basic
[0]PETSC ERROR: -snes_max_it 100
[0]PETSC ERROR: -snes_monitor
[0]PETSC ERROR: -snes_rtol 1e-7
[0]PETSC ERROR: -snes_type newtonls
[0]PETSC ERROR: -ts_dt 0.001
[0]PETSC ERROR: -ts_final_time 0.002
[0]PETSC ERROR: -ts_monitor
[0]PETSC ERROR: -ts_type alpha
[0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov----------
[0]PETSC ERROR: ----------MoFEM End of Error Message -------send entire error message to CMatGU <cmatgu at googlegroups.com> ----------
[1]PETSC ERROR: -snes_atol 1e-7
[1]PETSC ERROR: -snes_linesearch_type basic
[1]PETSC ERROR: -snes_max_it 100
[1]PETSC ERROR: -snes_monitor
[1]PETSC ERROR: -snes_rtol 1e-7
[1]PETSC ERROR: -snes_type newtonls
[1]PETSC ERROR: -ts_dt 0.001
[1]PETSC ERROR: -ts_final_time 0.002
[1]PETSC ERROR: -ts_monitor
[1]PETSC ERROR: -ts_type alpha
[1]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov----------
[1]PETSC ERROR: ----------MoFEM End of Error Message -------send entire error message to CMatGU <cmatgu at googlegroups.com> ----------
[2]PETSC ERROR: ------------------------------------------------------------------------
[2]PETSC ERROR: Caught signal number 15 Terminate: Some 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/documentation/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: likely location of problem given in stack below
[2]PETSC ERROR: ---------------------  Stack Frames ------------------------------------
[2]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
[2]PETSC ERROR:       INSTEAD the line number of the start of the function
[2]PETSC ERROR:       is given.
[2]PETSC ERROR: [2] MatStashScatterGetMesg_Private line 615 /opt/petsc/src/mat/utils/matstash.c
[2]PETSC ERROR: [2] MatAssemblyEnd_MPIAIJ line 717 /opt/petsc/src/mat/impls/aij/mpi/mpiaij.c
[2]PETSC ERROR: [2] MatAssemblyEnd line 5088 /opt/petsc/src/mat/interface/matrix.c
[2]PETSC ERROR: [2] postProcess line 164 /Users/likask/MyBuild/mofem-cephas/mofem_v0.2/finite_element_library/impl/DirichletBC.cpp
[2]PETSC ERROR: [2] problem_basic_method_postProcess line 2632 /Users/likask/MyBuild/mofem-cephas/mofem_v0.2/src/interfaces/impl/FieldInterfaceCore.cpp
[2]PETSC ERROR: [2] problem_basic_method_postProcess line 2642 /Users/likask/MyBuild/mofem-cephas/mofem_v0.2/src/interfaces/impl/FieldInterfaceCore.cpp
[2]PETSC ERROR: [2] preProcess line 2441 /Users/likask/MyBuild/mofem-cephas/mofem_v0.2/users_modules/convective_mass_element/src/ConvectiveMassElement.hpp
[2]PETSC ERROR: [2] problem_basic_method_preProcess line 2610 /Users/likask/MyBuild/mofem-cephas/mofem_v0.2/src/interfaces/impl/FieldInterfaceCore.cpp
[2]PETSC ERROR: [2] problem_basic_method_preProcess line 2621 /Users/likask/MyBuild/mofem-cephas/mofem_v0.2/src/interfaces/impl/FieldInterfaceCore.cpp
[2]PETSC ERROR: [2] f_TSSetIJacobian line 94 /Users/likask/MyBuild/mofem-cephas/mofem_v0.2/src/petsc/impl/TsCtx.cpp
[2]PETSC ERROR: [2] TS user implicit Jacobian line 808 /opt/petsc/src/ts/interface/ts.c
[2]PETSC ERROR: [2] TSComputeIJacobian line 791 /opt/petsc/src/ts/interface/ts.c
[2]PETSC ERROR: [2] SNESTSFormJacobian_Alpha line 179 /opt/petsc/src/ts/impls/implicit/alpha/alpha.c
[2]PETSC ERROR: [2] SNESTSFormJacobian line 4185 /opt/petsc/src/ts/interface/ts.c
[2]PETSC ERROR: [2] SNES user Jacobian function line 2212 /opt/petsc/src/snes/interface/snes.c
[2]PETSC ERROR: [2] SNESComputeJacobian line 2171 /opt/petsc/src/snes/interface/snes.c
[2]PETSC ERROR: [2] SNESSolve_NEWTONLS line 152 /opt/petsc/src/snes/impls/ls/ls.c
[2]PETSC ERROR: [2] SNESSolve line 3837 /opt/petsc/src/snes/interface/snes.c
[2]PETSC ERROR: [2] TSStep_Alpha line 40 /opt/petsc/src/ts/impls/implicit/alpha/alpha.c
[2]PETSC ERROR: [2] TSStep line 3081 /opt/petsc/src/ts/interface/ts.c
[2]PETSC ERROR: [2] TSSolve line 3246 /opt/petsc/src/ts/interface/ts.c
[2]PETSC ERROR: --------------------- MoFEM Error Message---------------------------------------------------------------------------
[2]PETSC ERROR: MoFEM version 0.2.1
[2]PETSC ERROR: MoFEM git commit id 837f38245270d65c22eafb638f023ea3476bc57a
[2]PETSC ERROR: See http://userweb.eng.gla.ac.uk/lukasz.kaczmarczyk/MoFem/html/guidelines_bug_reporting.html for bug reporting.
[2]PETSC ERROR: See http://userweb.eng.gla.ac.uk/lukasz.kaczmarczyk/MoFem/html/faq_and_bugs.html for trouble shooting.
[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: v3.5.3-2812-gc9542f9  GIT Date: 2015-05-03 22:34:15 +0300
[2]PETSC ERROR: /Users/likask/MyBuild/um_debug/nonlinear_elasticity/nonlinear_dynamics on a arch-darwin-c-debug named dh23-181.eng.gla.ac.uk by likask Tue May  5 09:49:38 2015
[2]PETSC ERROR: Configure options --with-mpi=1 --with-debugging=1 --do[3]PETSC ERROR: ------------------------------------------------------------------------
[3]PETSC ERROR: Caught signal number 15 Terminate: Some 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/documentation/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: likely location of problem given in stack below
[3]PETSC ERROR: ---------------------  Stack Frames ------------------------------------
[3]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
[3]PETSC ERROR:       INSTEAD the line number of the start of the function
[3]PETSC ERROR:       is given.
[3]PETSC ERROR: [3] MatStashScatterGetMesg_Private line 615 /opt/petsc/src/mat/utils/matstash.c
[3]PETSC ERROR: [3] MatAssemblyEnd_MPIAIJ line 717 /opt/petsc/src/mat/impls/aij/mpi/mpiaij.c
[3]PETSC ERROR: [3] MatAssemblyEnd line 5088 /opt/petsc/src/mat/interface/matrix.c
[3]PETSC ERROR: [3] postProcess line 164 /Users/likask/MyBuild/mofem-cephas/mofem_v0.2/finite_element_library/impl/DirichletBC.cpp
[3]PETSC ERROR: [3] problem_basic_method_postProcess line 2632 /Users/likask/MyBuild/mofem-cephas/mofem_v0.2/src/interfaces/impl/FieldInterfaceCore.cpp
[3]PETSC ERROR: [3] problem_basic_method_postProcess line 2642 /Users/likask/MyBuild/mofem-cephas/mofem_v0.2/src/interfaces/impl/FieldInterfaceCore.cpp
[3]PETSC ERROR: [3] preProcess line 2441 /Users/likask/MyBuild/mofem-cephas/mofem_v0.2/users_modules/convective_mass_element/src/ConvectiveMassElement.hpp
[3]PETSC ERROR: [3] problem_basic_method_preProcess line 2610 /Users/likask/MyBuild/mofem-cephas/mofem_v0.2/src/interfaces/impl/FieldInterfaceCore.cpp
[3]PETSC ERROR: [3] problem_basic_method_preProcess line 2621 /Users/likask/MyBuild/mofem-cephas/mofem_v0.2/src/interfaces/impl/FieldInterfaceCore.cpp
[3]PETSC ERROR: [3] f_TSSetIJacobian line 94 /Users/likask/MyBuild/mofem-cephas/mofem_v0.2/src/petsc/impl/TsCtx.cpp
[3]PETSC ERROR: [3] TS user implicit Jacobian line 808 /opt/petsc/src/ts/interface/ts.c
[3]PETSC ERROR: [3] TSComputeIJacobian line 791 /opt/petsc/src/ts/interface/ts.c
[3]PETSC ERROR: [3] SNESTSFormJacobian_Alpha line 179 /opt/petsc/src/ts/impls/implicit/alpha/alpha.c
[3]PETSC ERROR: [3] SNESTSFormJacobian line 4185 /opt/petsc/src/ts/interface/ts.c
[3]PETSC ERROR: [3] SNES user Jacobian function line 2212 /opt/petsc/src/snes/interface/snes.c
[3]PETSC ERROR: [3] SNESComputeJacobian line 2171 /opt/petsc/src/snes/interface/snes.c
[3]PETSC ERROR: [3] SNESSolve_NEWTONLS line 152 /opt/petsc/src/snes/impls/ls/ls.c
[3]PETSC ERROR: [3] SNESSolve line 3837 /opt/petsc/src/snes/interface/snes.c
[3]PETSC ERROR: [3] TSStep_Alpha line 40 /opt/petsc/src/ts/impls/implicit/alpha/alpha.c
[3]PETSC ERROR: [3] TSStep line 3081 /opt/petsc/src/ts/interface/ts.c
[3]PETSC ERROR: [3] TSSolve line 3246 /opt/petsc/src/ts/interface/ts.c
[3]PETSC ERROR: --------------------- MoFEM Error Message---------------------------------------------------------------------------
[3]PETSC ERROR: MoFEM version 0.2.1
[3]PETSC ERROR: MoFEM git commit id 837f38245270d65c22eafb638f023ea3476bc57a
[3]PETSC ERROR: See http://userweb.eng.gla.ac.uk/lukasz.kaczmarczyk/MoFem/html/guidelines_bug_reporting.html for bug reporting.
[3]PETSC ERROR: See http://userweb.eng.gla.ac.uk/lukasz.kaczmarczyk/MoFem/html/faq_and_bugs.html for trouble shooting.
[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: v3.5.3-2812-gc9542f9  GIT Date: 2015-05-03 22:34:15 +0300
[3]PETSC ERROR: /Users/likask/MyBuild/um_debug/nonlinear_elasticity/nonlinear_dynamics on a arch-darwin-c-debug named dh23-181.eng.gla.ac.uk by likask Tue May  5 09:49:38 2015
[3]PETSC ERROR: Configure options --with-mpi=1 --with-debugging=1 --download-fblaslapack=1 --download-superlu_dist=1 --download-metis=1 --download-parmetis=1 --download-hypre=1 --download-mumps=1 --download-scalapack=1 --download-blacs=1 --download-moab=1 --download-hdf5=1 --download-netcdf=/opt/petsc/netcdf-4.3.3.1.tar.gz --download-openmpi=1 --CXXFLAGS=-fno-vectorize -CFLAGS=-fno-vectorize --download-mumps=1 --download-ptscotch=1
[2]PETSC ERROR: #1 User provided function() line 0 in  unknown file
wnload-fblaslapack=1 --download-superlu_dist=1 --download-metis=1 --download-parmetis=1 --download-hypre=1 --download-mumps=1 --download-scalapack=1 --download-blacs=1 --download-moab=1 --download-hdf5=1 --download-netcdf=/opt/petsc/netcdf-4.3.3.1.tar.gz --download-openmpi=1 --CXXFLAGS=-fno-vectorize -CFLAGS=-fno-vectorize --download-mumps=1 --download-ptscotch=1
[3]PETSC ERROR: #1 User provided function() line 0 in  unknown file
[dh23-181.eng.gla.ac.uk:06691] 3 more processes have sent help message help-mpi-api.txt / mpi-abort
[dh23-181.eng.gla.ac.uk:06691] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
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