Dear libMesh users,
Currently I am with problems when running example fem_system_ex2. MPI_ABORT is
invoked in step 1 right after assembling the system (see attached file).
Below is the setup I am using:
* CPU: Intel i7
* Oracle Virtual Box 5.2.6 r120293
* Host system: Windows 10
* Guest system: Linux Mint 18.3 Mate
* Cloned libMesh master branch as per 01-21-2018
* All libMesh optional libraries installed using apt-get (VTK, openMPI,
PETSc, HDF5, …)
I have also attached the libMesh configuration log and the fem_system_ex2
traceout file.
Thanks in advance
Daniel F. M. Vasconcelos.
Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10
***************************************************************
* Done Running Example fem_system_ex1:
* ./example-dbg
***************************************************************
PASS: run.sh
=============
1 test passed
=============
make[4]: Leaving directory
'/home/daniel/Repo/libmesh/examples/fem_system/fem_system_ex1'
make[3]: Leaving directory
'/home/daniel/Repo/libmesh/examples/fem_system/fem_system_ex1'
make[2]: Leaving directory
'/home/daniel/Repo/libmesh/examples/fem_system/fem_system_ex1'
Making check in fem_system/fem_system_ex2
make[2]: Entering directory
'/home/daniel/Repo/libmesh/examples/fem_system/fem_system_ex2'
make check-am
make[3]: Entering directory
'/home/daniel/Repo/libmesh/examples/fem_system/fem_system_ex2'
make example-dbg run.sh
make[4]: Entering directory
'/home/daniel/Repo/libmesh/examples/fem_system/fem_system_ex2'
CXX example_dbg-fem_system_ex2.o
In file included from /usr/include/c++/5/backward/strstream:50:0,
from /usr/include/vtk-5.10/vtkIOStream.h:108,
from /usr/include/vtk-5.10/vtkSystemIncludes.h:40,
from /usr/include/vtk-5.10/vtkIndent.h:24,
from /usr/include/vtk-5.10/vtkObjectBase.h:43,
from /usr/include/vtk-5.10/vtkSmartPointerBase.h:26,
from /usr/include/vtk-5.10/vtkSmartPointer.h:23,
from ../../../include/libmesh/vtk_io.h:31,
from fem_system_ex2.C:33:
/usr/include/c++/5/backward/backward_warning.h:32:2: warning: #warning This
file includes at least one deprecated or antiquated header which may be removed
without further notice at a future date. Please use a non-deprecated interface
with equivalent functionality instead. For a listing of replacement headers and
interfaces, consult the file backward_warning.h. To disable this warning use
-Wno-deprecated. [-Wcpp]
#warning \
^
CXX example_dbg-solid_system.o
CXX example_dbg-nonlinear_neohooke_cc.o
CXXLD example-dbg
make[4]: Nothing to be done for 'run.sh'.
make[4]: Leaving directory
'/home/daniel/Repo/libmesh/examples/fem_system/fem_system_ex2'
make check-TESTS
make[4]: Entering directory
'/home/daniel/Repo/libmesh/examples/fem_system/fem_system_ex2'
***************************************************************
* Running Example fem_system_ex2:
* ./example-dbg
***************************************************************
*** Warning, This code is untested, experimental, or likely to see future API
changes: ../../../include/libmesh/diff_physics.h, line 592, compiled Jan 22
2018 at 03:11:00 ***
===== Time Step 0 ( 0.00%), time = 0.00 =====
Solving Solid
Assembling the System
Nonlinear Residual: 3691.41
Linear solve starting, tolerance 0.00
Linear solve finished, step 6, residual 0.00
Trying full Newton step
Current Residual: 0.09
Nonlinear solver current_residual 0.09 > 0.00
Nonlinear solver relative residual 0.00 > 0.00
Nonlinear solver converged, step 0, relative step size 0.00 < 0.00
Doing a reinit of the equation systems
Advancing to next step
===== Time Step 1 ( 20.00%), time = 0.00 =====
Solving Solid
Assembling the System
---------------------------------------------------------------------
| Time: Mon Jan 22 03:11:21 2018 |
| OS: Linux |
| HostName: daniel-VirtualBox |
| OS Release: 4.13.0-26-generic |
| OS Version: #29~16.04.2-Ubuntu SMP Tue Jan 9 22:00:44 UTC 2018 |
| Machine: x86_64 |
| Username: daniel |
| Configuration: ./configure '--prefix=/home/daniel/Dev/libmesh' |
| '--enable-everything' |
| '--enable-parmesh' |
| 'METHODS=dbg' |
| 'PETSC_DIR=/usr/lib/petsc' |
| 'HDF5_DIR=/usr/lib/x86_64-linux-gnu/hdf5/openmpi' |
---------------------------------------------------------------------
-----------------------------------------------------------------------------------------------------------------------------
| libMesh Performance: Alive time=7.21674, Active time=6.92119
|
-----------------------------------------------------------------------------------------------------------------------------
| Event nCalls Total Time Avg
Time Total Time Avg Time % of Active Time |
| w/o Sub w/o Sub
With Sub With Sub w/o S With S |
|-----------------------------------------------------------------------------------------------------------------------------|
|
|
|
|
| DefaultCoupling
|
| operator() 136 0.0133
0.000098 0.0133 0.000098 0.19 0.19 |
|
|
| DistributedMesh
|
| renumber_nodes_and_elements() 3 0.0207
0.006886 0.0215 0.007152 0.30 0.31 |
|
|
| DofMap
|
| add_neighbors_to_send_list() 4 0.0046
0.001157 0.0847 0.021176 0.07 1.22 |
| build_sparsity() 2 4.0957
2.047861 4.2557 2.127833 59.18 61.49 |
| create_dof_constraints() 4 0.0062
0.001558 0.0062 0.001561 0.09 0.09 |
| distribute_dofs() 4 0.0465
0.011623 0.2143 0.053577 0.67 3.10 |
| dof_indices() 9031 1.0358
0.000115 1.0358 0.000115 14.97 14.97 |
| old_dof_indices() 1280 0.2271
0.000177 0.2271 0.000177 3.28 3.28 |
| prepare_send_list() 6 0.0002
0.000027 0.0002 0.000027 0.00 0.00 |
| reinit() 4 0.0830
0.020750 0.0830 0.020750 1.20 1.20 |
|
|
| EquationSystems
|
| build_parallel_solution_vector() 1 0.0259
0.025874 0.1048 0.104766 0.37 1.51 |
|
|
| FE
|
| compute_shape_functions() 769 0.0884
0.000115 0.0884 0.000115 1.28 1.28 |
| init_shape_functions() 202 0.0029
0.000014 0.0029 0.000014 0.04 0.04 |
|
|
| FEMSystem
|
| assembly() 2 0.8073
0.403637 1.0030 0.501518 11.66 14.49 |
| assembly(get_residual) 1 0.1622
0.162204 0.3761 0.376147 2.34 5.43 |
|
|
| FEMap
|
| compute_affine_map() 289 0.0101
0.000035 0.0101 0.000035 0.15 0.15 |
| compute_face_map() 192 0.0059
0.000031 0.0059 0.000031 0.09 0.09 |
| compute_map() 480 0.0366
0.000076 0.0366 0.000076 0.53 0.53 |
| init_face_shape_functions() 2 0.0001
0.000040 0.0001 0.000040 0.00 0.00 |
| init_reference_to_physical_map() 202 0.0133
0.000066 0.0133 0.000066 0.19 0.19 |
|
|
| GenericProjector
|
| copy_dofs 768 0.0074
0.000010 0.1781 0.000232 0.11 2.57 |
| operator() 4 0.0220
0.005507 0.3539 0.088467 0.32 5.11 |
|
|
| Mesh
|
| contract() 1 0.0017
0.001653 0.0084 0.008450 0.02 0.12 |
| find_neighbors() 1 0.0178
0.017759 0.0183 0.018338 0.26 0.26 |
|
|
| MeshBase
|
| prepare_for_use() 1 0.0090
0.008985 0.0534 0.053416 0.13 0.77 |
|
|
| MeshCommunication
|
| delete_remote_elements() 1 0.0086
0.008585 0.0088 0.008837 0.12 0.13 |
|
|
| MeshOutput
|
| write_equation_systems() 1 0.0204
0.020444 0.1252 0.125211 0.30 1.81 |
|
|
| MeshRefinement
|
| _coarsen_elements() 1 0.0003
0.000339 0.0003 0.000339 0.00 0.00 |
| _refine_elements() 1 0.0007
0.000732 0.0007 0.000732 0.01 0.01 |
| make_coarsening_compatible() 2 0.0015
0.000770 0.0015 0.000770 0.02 0.02 |
| make_flags_parallel_consistent() 4 0.0030
0.000758 0.0030 0.000758 0.04 0.04 |
| make_refinement_compatible() 2 0.0000
0.000003 0.0000 0.000003 0.00 0.00 |
|
|
| MeshTools
|
| libmesh_assert_parallel_consistent_procids() 8 0.0000
0.000003 0.0000 0.000003 0.00 0.00 |
| libmesh_assert_topology_consistent_procids() 8 0.0000
0.000002 0.0000 0.000002 0.00 0.00 |
| libmesh_assert_valid_amr_interior_parents() 1 0.0002
0.000156 0.0002 0.000156 0.00 0.00 |
| libmesh_assert_valid_boundary_ids() 6 0.0000
0.000002 0.0000 0.000002 0.00 0.00 |
| libmesh_assert_valid_dof_ids() 4 0.0000
0.000003 0.0000 0.000003 0.00 0.00 |
| libmesh_assert_valid_elem_ids() 3 0.0007
0.000247 0.0007 0.000247 0.01 0.01 |
| libmesh_assert_valid_neighbors() 5 0.0022
0.000445 0.0022 0.000445 0.03 0.03 |
| libmesh_assert_valid_refinement_tree() 3 0.0006
0.000199 0.0006 0.000199 0.01 0.01 |
| libmesh_assert_valid_unique_ids() 2 0.0011
0.000545 0.0011 0.000545 0.02 0.02 |
|
|
| MeshTools::Generation
|
| build_cube() 1 0.0108
0.010775 0.0108 0.010775 0.16 0.16 |
|
|
| NewtonSolver
|
| solve() 2 0.1031
0.051563 1.6584 0.829176 1.49 23.96 |
|
|
| OldSolutionBase
|
| check_old_context(c) 768 0.0084
0.000011 0.1646 0.000214 0.12 2.38 |
|
|
| OldSolutionValue
|
| eval_old_dofs() 768 0.0047
0.000006 0.1700 0.000221 0.07 2.46 |
|
|
| Parallel
|
| allgather() 10 0.0001
0.000005 0.0001 0.000005 0.00 0.00 |
|
|
| Partitioner
|
| single_partition_range() 1 0.0003
0.000279 0.0003 0.000279 0.00 0.00 |
|
|
| PetscLinearSolver
|
| solve() 1 0.0011
0.001119 0.0011 0.001119 0.02 0.02 |
|
|
| System
|
| project_vector(old,new) 4 0.0095
0.002371 0.4357 0.108927 0.14 6.30 |
|
|
| TopologyMap
|
| init() 1 0.0002
0.000196 0.0002 0.000196 0.00 0.00 |
-----------------------------------------------------------------------------------------------------------------------------
| Totals: 14997 6.9212
100.00 |
-----------------------------------------------------------------------------------------------------------------------------
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.
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.
--------------------------------------------------------------------------
FAIL: run.sh
====================================================
1 of 1 test failed
Please report to libmesh-users@lists.sourceforge.net
====================================================
Makefile:1146: recipe for target 'check-TESTS' failed
make[4]: *** [check-TESTS] Error 1
make[4]: Leaving directory
'/home/daniel/Repo/libmesh/examples/fem_system/fem_system_ex2'
Makefile:1269: recipe for target 'check-am' failed
make[3]: *** [check-am] Error 2
make[3]: Leaving directory
'/home/daniel/Repo/libmesh/examples/fem_system/fem_system_ex2'
Makefile:1272: recipe for target 'check' failed
make[2]: *** [check] Error 2
make[2]: Leaving directory
'/home/daniel/Repo/libmesh/examples/fem_system/fem_system_ex2'
Makefile:716: recipe for target 'check-recursive' failed
make[1]: *** [check-recursive] Error 1
make[1]: Leaving directory '/home/daniel/Repo/libmesh/examples'
Makefile:29212: recipe for target 'check-recursive' failed
make: *** [check-recursive] Error 1
daniel@daniel-VirtualBox ~/Repo/libmesh $
Stack frames: 22
0: libMesh::print_trace(std::ostream&)
1: libMesh::write_traceout()
2: libMesh::libmesh_terminate_handler()
3: /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x8d6b6) [0x7f3c38dae6b6]
4: /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x8c6a9) [0x7f3c38dad6a9]
5: /usr/lib/x86_64-linux-gnu/libstdc++.so.6(__gxx_personality_v0+0x2e5)
[0x7f3c38dae005]
6: /lib/x86_64-linux-gnu/libgcc_s.so.1(+0xff83) [0x7f3c38844f83]
7: _Unwind_Resume
8: /home/daniel/Repo/libmesh/.libs/libmesh_dbg.so.0(+0x243bcb3) [0x7f3c3b6f9cb3]
9: /home/daniel/Repo/libmesh/.libs/libmesh_dbg.so.0(+0x2444146) [0x7f3c3b702146]
10: /home/daniel/Repo/libmesh/.libs/libmesh_dbg.so.0(+0x2447086)
[0x7f3c3b705086]
11: GOMP_parallel
12: /home/daniel/Repo/libmesh/.libs/libmesh_dbg.so.0(+0x2442a28)
[0x7f3c3b700a28]
13: libMesh::FEMSystem::assembly(bool, bool, bool, bool)
14: libMesh::NewtonSolver::solve()
15: libMesh::TimeSolver::solve()
16: libMesh::DifferentiableSystem::solve()
17: libMesh::FEMSystem::solve()
18:
/home/daniel/Repo/libmesh/examples/fem_system/fem_system_ex2/.libs/example-dbg()
[0x482905]
19:
/home/daniel/Repo/libmesh/examples/fem_system/fem_system_ex2/.libs/example-dbg()
[0x482e7e]
20: __libc_start_main
21:
/home/daniel/Repo/libmesh/examples/fem_system/fem_system_ex2/.libs/example-dbg()
[0x481b49]
------------------------------------------------------------------------------
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