Launching failed

[François EDF Energy]

Hi,

I tried to launch a crack propagation analysis and obtain immediately this error :

root@a7d15d3974c0:/mofem_build/um/fracture_mechanics/Crack_Propagation/1.2# mpirun -np 4 ./crack_propagation -my_file out.h5m 2>&1 | tee log
read cubit meshset 12682136550675316739 type BLOCKSET UNKNOWNNAME msId 1 name Full_Brick_Slot_Mofem
read cubit meshset 12682136550675316740 type BLOCKSET UNKNOWNNAME msId 2 name Bore
read cubit meshset 12682136550675316741 type BLOCKSET UNKNOWNNAME msId 3 name Crack_Init
read cubit meshset 12682136550675316742 type BLOCKSET UNKNOWNNAME msId 4 name Edges
read cubit meshset 12682136550675316743 type BLOCKSET UNKNOWNNAME msId 5 name Fixed
read cubit meshset 12682136550675316744 type BLOCKSET UNKNOWNNAME msId 6 name Keyway
read cubit meshset 12682136550675316745 type BLOCKSET UNKNOWNNAME msId 7 name Mesh_Refinement
read cubit meshset 12682136550675316746 type BLOCKSET UNKNOWNNAME msId 8 name Vertices
MoFEM version 0.7.9 (MOAB 4.9.3pre Petsc Release Version 3.7.6, unknown )
git commit id GITDIR-NOTFOUND
[0]MoFEM ERROR: --------------------- MoFEM Error Message ---------------------------------------------------
[0]MoFEM ERROR: MoFEM version 0.7.9 (MOAB 4.9.3pre Petsc Release Version 3.7.6, unknown )
[0]MoFEM ERROR: MoFEM git commit id GITDIR-NOTFOUND
[0]MoFEM ERROR: See http://mofem.eng.gla.ac.uk/mofem/html/guidelines_bug_reporting.html for bug reporting.
[0]MoFEM ERROR: See http://mofem.eng.gla.ac.uk/mofem/html/faq_and_bugs.html for trouble shooting.
[0]MoFEM ERROR: msId = 400 is not there
[0]MoFEM ERROR: #1 getEntitiesByDimension() line 501 in /mofem/src/interfaces/impl/MeshsetsManager.cpp
[0]MoFEM ERROR: #2 copySurface() line 136 in /mofem_build/um/users_modules/fracture_mechanics/src/impl/CPMeshCut.cpp
[0]MoFEM ERROR: #3 main() line 210 in /mofem_build/um/users_modules/fracture_mechanics/crack_propagation.cpp
#PETSc Option Table entries:
-adapt_min_smoother_alpha 1e-3
-adapt_step_its_d 8
-adapt_step_max_s 6e-5
-adapt_step_min_s 1e-6
-arc_alpha 1e2
-arc_beta 0
-arc_length_ksp_atol 1e-14
-arc_length_ksp_gmres_restart 500
-arc_length_ksp_max_it 190
-arc_length_ksp_rtol 1e-7
-arc_length_ksp_stol 1e-14
-arc_length_ksp_type fgmres
-arc_s 1e-5
-cut_factor 1
-cut_mesh 1
-cut_surface_side_set 400
-cutting_surf_corner_factor 0.5
-cutting_surf_skin_factor 0.05
-edges_block_set 2
-elastic_ksp_atol 1e-12
-elastic_ksp_max_it 100
-elastic_ksp_monitor
-elastic_ksp_rtol 1e-12
-elastic_ksp_stol 0
-elastic_ksp_type gmres
-elastic_mg_coarse_ksp_type gmres
-elastic_mg_coarse_pc_factor_mat_solver_package mumps
-elastic_mg_coarse_pc_type lu
-elastic_pc_factor_mat_solver_package mumps
-elastic_pc_mg_log
-elastic_pc_mg_smoothdown 1
-elastic_pc_mg_smoothup 1
-elastic_pc_mg_type multiplicative
-elastic_pc_type lu
-elastic_snes_atol 1e-10
-elastic_snes_converged_reason
-elastic_snes_linesearch_type basic
-elastic_snes_max_fail 100
-elastic_snes_max_linear_solve_fail 100
-elastic_snes_monitor
-elastic_snes_rtol 1e-10
-fraction_level 2
-gc_fix_threshold 0.5
-griffith_E 1e4
-griffith_r 1
-ksp_atol 1e-12
-ksp_max_it 10
-ksp_rtol 1e-12
-ksp_type gmres
-load_scale 1
-material HOOKE
-material_ksp_atol 1e-12
-material_ksp_max_it 100
-material_ksp_rtol 1e-12
-material_ksp_stol 0
-material_ksp_type gmres
-material_pc_factor_mat_solver_package mumps
-material_pc_type lu
-material_snes_atol 1e-8
-material_snes_converged_reason
-material_snes_linesearch_damping 1
-material_snes_linesearch_max_it 3
-material_snes_linesearch_minlambda 1e-2
-material_snes_linesearch_type bt
-material_snes_max_fail 100
-material_snes_max_linear_solve_fail 100
-material_snes_rtol 0
-material_snes_stol 0
-mofem_mg_coarse_order 1
-mofem_mg_levels 2
-mofem_mg_verbose 1
-my_add_singularity 1
-my_file out.h5m
-my_gc 1.4e-4
-my_geom_order 1
-my_max_post_proc_ref_level 0
-my_order 1
-my_propagate_crack 1
-my_ref 0
-my_ref_order 1
-nb_cut_steps 100
-nb_load_steps 3
-pc_factor_mat_solver_package mumps
-pc_type lu
-propagation_fieldsplit_0_ksp_type gmres
-propagation_fieldsplit_0_pc_factor_mat_solver_package mumps
-propagation_fieldsplit_0_pc_type lu
-propagation_fieldsplit_1_ksp_type gmres
-propagation_fieldsplit_1_pc_factor_mat_solver_package mumps
-propagation_fieldsplit_1_pc_type lu
-propagation_ksp_atol 1e-10
-propagation_ksp_gmres_restart 500
-propagation_ksp_max_it 100
-propagation_ksp_monitor
-propagation_ksp_rtol 1e-6
-propagation_ksp_stol 0
-propagation_ksp_type fgmres
-propagation_pc_factor_mat_solver_package mumps
-propagation_pc_type lu
-propagation_snes_atol 1e-8
-propagation_snes_converged_reason
-propagation_snes_linesearch_damping 1
-propagation_snes_linesearch_max_it 1
-propagation_snes_linesearch_minlambda 1e-3
-propagation_snes_linesearch_monitor
-propagation_snes_linesearch_type bt
-propagation_snes_max_fail 100
-propagation_snes_max_it 20
-propagation_snes_max_linear_solve_fail 100
-propagation_snes_monitor
-propagation_snes_rtol 1e-6
-propagation_snes_stol 0
-smoother_alpha 1e-2
-smoothing_stabilise 1
-tol_cut 2e-2
-tol_cut_close 2e-1
-tol_trim 1e-1
-tol_trim_close 1e-2
-vertex_block_set 3
-volume_length_type BARRIER_AND_CHANGE_QUALITY_SCALED_BY_VOLUME
#End of PETSc Option Table entries
[0]MoFEM ERROR: -- MoFEM End of Error Message -- send entire error message to mofem-group@googlegroups.com --
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 100.

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.
--------------------------------------------------------------------------
[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: configure using --with-debugging=yes, recompile, link, and run
[3]PETSC ERROR: to get more information on the crash.
[3]MoFEM ERROR: --------------------- MoFEM Error Message ---------------------------------------------------
[3]MoFEM ERROR: MoFEM version 0.7.9 (MOAB 4.9.3pre Petsc Release Version 3.7.6, unknown )
[3]MoFEM ERROR: MoFEM git commit id GITDIR-NOTFOUND
[3]MoFEM ERROR: See http://mofem.eng.gla.ac.uk/mofem/html/guidelines_bug_reporting.html for bug reporting.
[3]MoFEM ERROR: See http://mofem.eng.gla.ac.uk/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 Release Version 3.7.6, unknown
[3]PETSC ERROR: ./crack_propagation on a arch-linux2-c-opt named a7d15d3974c0 by Unknown Fri Apr 13 13:54:57 2018
[3]PETSC ERROR: Configure options --with-debugging=0 --with-mpi=1 --download-metis=1 --download-parmetis=1 --download-hypre=1 --download-mumps=1 --download-blacs=1 --download-hdf5=1 --download-netcdf=/opt/petsc/netcdf-4.3.3.1.tar.gz --download-scalapack=1 --with-shared-libraries=1
[3]PETSC ERROR: #1 User provided function() line 0 in  unknown file
[1]PETSC ERROR: ------------------------------------------------------------------------
[1]PETSC ERROR: Caught signal number 15 Terminate: Some 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/documentation/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]MoFEM ERROR: --------------------- MoFEM Error Message ---------------------------------------------------
[1]MoFEM ERROR: MoFEM version 0.7.9 (MOAB 4.9.3pre Petsc Release Version 3.7.6, unknown )
[1]MoFEM ERROR: MoFEM git commit id GITDIR-NOTFOUND
[1]MoFEM ERROR: See http://mofem.eng.gla.ac.uk/mofem/html/guidelines_bug_reporting.html for bug reporting.
[1]MoFEM ERROR: See http://mofem.eng.gla.ac.uk/mofem/html/faq_and_bugs.html for trouble shooting.
[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 Release Version 3.7.6, unknown
[1]PETSC ERROR: ./crack_propagation on a arch-linux2-c-opt named a7d15d3974c0 by Unknown Fri Apr 13 13:54:57 2018
[1]PETSC ERROR: Configure options --with-debugging=0 --with-mpi=1 --download-metis=1 --download-parmetis=1 --download-hypre=1 --download-mumps=1 --download-blacs=1 --download-hdf5=1 --download-netcdf=/opt/petsc/netcdf-4.3.3.1.tar.gz --download-scalapack=1 --with-shared-libraries=1
[1]PETSC ERROR: #1 User provided function() line 0 in  unknown file
[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: configure using --with-debugging=yes, recompile, link, and run
[2]PETSC ERROR: to get more information on the crash.
[2]MoFEM ERROR: --------------------- MoFEM Error Message ---------------------------------------------------
[2]MoFEM ERROR: MoFEM version 0.7.9 (MOAB 4.9.3pre Petsc Release Version 3.7.6, unknown )
[2]MoFEM ERROR: MoFEM git commit id GITDIR-NOTFOUND
[2]MoFEM ERROR: See http://mofem.eng.gla.ac.uk/mofem/html/guidelines_bug_reporting.html for bug reporting.
[2]MoFEM ERROR: See http://mofem.eng.gla.ac.uk/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 Release Version 3.7.6, unknown
[2]PETSC ERROR: ./crack_propagation on a arch-linux2-c-opt named a7d15d3974c0 by Unknown Fri Apr 13 13:54:57 2018
[2]PETSC ERROR: Configure options --with-debugging=0 --with-mpi=1 --download-metis=1 --download-parmetis=1 --download-hypre=1 --download-mumps=1 --download-blacs=1 --download-hdf5=1 --download-netcdf=/opt/petsc/netcdf-4.3.3.1.tar.gz --download-scalapack=1 --with-shared-libraries=1
[2]PETSC ERROR: #1 User provided function() line 0 in  unknown file
[a7d15d3974c0:00027] 3 more processes have sent help message help-mpi-api.txt / mpi-abort
[a7d15d3974c0:00027] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
root@a7d15d3974c0:/mofem_build/um/fracture_mechanics/Crack_Propagation/1.2# git tag
fatal: Not a git repository (or any parent up to mount point /home/visitor)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
root@a7d15d3974c0:/mofem_build/um/fracture_mechanics/Crack_Propagation/1.2#

I don't know how to interpret it.

Regards,

Francois

[Lukasz Kaczmraczyk]

Look at very top:

[0]MoFEM ERROR: --------------------- MoFEM Error Message ---------------------------------------------------
[0]MoFEM ERROR: MoFEM version 0.7.9 (MOAB 4.9.3pre Petsc Release Version 3.7.6, unknown )
[0]MoFEM ERROR: MoFEM git commit id GITDIR-NOTFOUND
[0]MoFEM ERROR: See http://mofem.eng.gla.ac.uk/mofem/html/guidelines_bug_reporting.html for bug reporting.
[0]MoFEM ERROR: See http://mofem.eng.gla.ac.uk/mofem/html/faq_and_bugs.html for trouble shooting.
[0]MoFEM ERROR: msId = 400 is not there
[0]MoFEM ERROR: #1 getEntitiesByDimension() line 501 in /mofem/src/interfaces/impl/MeshsetsManager.cpp
[0]MoFEM ERROR: #2 copySurface() line 136 in /mofem_build/um/users_modules/fracture_mechanics/src/impl/CPMeshCut.cpp
[0]MoFEM ERROR: #3 main() line 210 in /mofem_build/um/users_modules/fracture_mechanics/crack_propagation.cpp

It says that its can not find side set 400

 [0]MoFEM ERROR: msId = 400 is not there

This is where cutting surface should be.

I see that you have not updated MoFEM, pleas pull recent module, but this is not reason of problems in this case.

Regards,

Lukasz

[François EDF Energy]

Hi Lukasz,

I explored many possibilities to understand and fixed this error but I didn't suceed so far. May you'll have an idea or a solution.


It seems that the link between

-cut_surface_side_set 400

from the param.petsc and

[block_3]        # Applying crack on Crack_Init_Face
id=400          # ID must match -cut_surface_side_set in param file
add=SIDESET

from my .config file is not done.

I ensured that the out.h5m file was created from the correct .config file.
The geometry and the block numbers are checked.
I tried on different problems (Brick_Slice_Slot and Full_Brick_Slot) and I get the same error.

I enclosed the files that I used (those ones are for the Brick_Slice_Slot problem) in case you need to have a look at it.

Kind regards,
Francois

[Lukasz Kaczmraczyk]

Hello, 

You had an error in 1_1.config, see attached corrected, some blocks have duplicated id, in particular, block 3, where I put instead 300. That change needs modification in param_file.pets, where you have to define blocks for edges and vertices

-edges_block_set 200
-vertex_block_set 300

for corresponding set-up in med config file

[block_4] # Indicate edges
id=200 # ID must match -edges_block_set in param file
add=BLOCKSET

[block_8] # Indicate vertices
id=300 # ID must match -vertex_block_set in param file
add=BLOCKSET

You run this with read_mead as follows, 

./read_med -med_file Brick_Slice_Slot_Mofem.med -meshsets_config 1_1.config

However I noticed a different problem, you like to control problem by displacements, 

[block_2] # Applying displacement at Bore
id=1002
add=NODESET    # This is a NODESET but group could be nodes and / or elements
disp_flag1=1 # Activate the dof x
disp_flag2=1 # Activate the dof y
disp_ux=-0.996
disp_uy=-0.087

This is not yet implemented, currently you can solve problem by applying forces on edges instead.

There is other problem, you need to set right young modulus for graphite, the best if it scaled, for example

[block_1] # Applying material block (isotropic elastic material)
id=1001
add=BLOCKSET
name=MAT_ELASTIC
young=9600
poisson=0.2

and this correspond to Griffith energy

gc=1e-4

You can always rescale units, both for dimension, young module and gc. You can do that to have initial residual about 

0 SNES Function norm 3.161621419462e+00

or sometiging one order smaller or bigger than that.

Another is to chose tolerances appropriately, however setting units is faster. 

Kind regards,

Lukasz

[François EDF Energy]

Thank you for this detailed explanations Lukasz. It's working well now :)

I identified the problem. When I created the out.h5m file I was using a corrupted command : -meshset_config instead of -meshsets_config.

Anyway I allso corrected the others problems that you pointed out.

Kind regard,

Francois.