Hello,
I'm trying to run example 4 under Introduction in parallel. It seems to be
running in serial, but on multiple processors, instead of splitting up the
work.
I've attached the config.log file for my libmesh compilation as well as the
output when I try to run the example using
mpirun -np 2 ./example-opt -d 2 -n 5 > ex4_output.txt
Thanks,
Harriet
Running ./example-opt -d 2 -n 5
Running ./example-opt -d 2 -n 5
*** Warning, This code is deprecated, and likely to be removed in future
library versions! ./include/libmesh/auto_ptr.h, line 270, compiled Apr 7 2016
at 17:40:47 ***
*** Warning, This code is deprecated, and likely to be removed in future
library versions! ./include/libmesh/auto_ptr.h, line 270, compiled Apr 7 2016
at 17:40:47 ***
Mesh Information:
elem_dimensions()={2}
spatial_dimension()=2
n_nodes()=121
n_local_nodes()=121
n_elem()=25
n_local_elem()=25
n_active_elem()=25
n_subdomains()=1
n_partitions()=1
n_processors()=1
n_threads()=1
processor_id()=0
Mesh Information:
elem_dimensions()={2}
spatial_dimension()=2
n_nodes()=121
n_local_nodes()=121
n_elem()=25
n_local_elem()=25
n_active_elem()=25
n_subdomains()=1
n_partitions()=1
n_processors()=1
n_threads()=1
processor_id()=0
EquationSystems
n_systems()=1
System #0, "Poisson"
Type "LinearImplicit"
Variables="u"
Finite Element Types="LAGRANGE", "JACOBI_20_00"
Infinite Element Mapping="CARTESIAN"
Approximation Orders="SECOND", "THIRD"
n_dofs()=121
n_local_dofs()=121
n_constrained_dofs()=40
n_local_constrained_dofs()=40
n_vectors()=1
n_matrices()=1
DofMap Sparsity
Average On-Processor Bandwidth <= 13.8926
Average Off-Processor Bandwidth <= 0
Maximum On-Processor Bandwidth <= 25
Maximum Off-Processor Bandwidth <= 0
DofMap Constraints
Number of DoF Constraints = 40
Number of Heterogenous Constraints= 38
Average DoF Constraint Length= 0
Number of Node Constraints = 0
Mesh Information:
elem_dimensions()={2}
spatial_dimension()=2
n_nodes()=121
n_local_nodes()=121
n_elem()=25
n_local_elem()=25
n_active_elem()=25
n_subdomains()=1
n_partitions()=1
n_processors()=1
n_threads()=1
processor_id()=0
EquationSystems
n_systems()=1
System #0, "Poisson"
Type "LinearImplicit"
Variables="u"
Finite Element Types="LAGRANGE", "JACOBI_20_00"
Infinite Element Mapping="CARTESIAN"
Approximation Orders="SECOND", "THIRD"
n_dofs()=121
n_local_dofs()=121
n_constrained_dofs()=40
n_local_constrained_dofs()=40
n_vectors()=1
n_matrices()=1
DofMap Sparsity
Average On-Processor Bandwidth <= 13.8926
Average Off-Processor Bandwidth <= 0
Maximum On-Processor Bandwidth <= 25
Maximum Off-Processor Bandwidth <= 0
DofMap Constraints
Number of DoF Constraints = 40
Number of Heterogenous Constraints= 38
Average DoF Constraint Length= 0
Number of Node Constraints = 0
Mesh Information:
elem_dimensions()={2}
spatial_dimension()=2
n_nodes()=121
n_local_nodes()=121
n_elem()=25
n_local_elem()=25
n_active_elem()=25
n_subdomains()=1
n_partitions()=1
n_processors()=1
n_threads()=1
processor_id()=0
------------------------------------------------------------------------
| Time: Thu Apr 7 17:48:05 2016 |
| OS: Linux |
| HostName: bassi |
| OS Release: 3.19.0-43-generic |
| OS Version: #49~14.04.1-Ubuntu SMP Thu Dec 31 15:44:49 UTC 2015 |
| Machine: x86_64 |
| Username: kameeko |
| Configuration: ./configure
'prefix=/home/kameeko/software/libmesh_build_petsc_mpidbg'|
| 'PETSC_DIR=/home/kameeko/software/petsc' |
| 'PETSC_ARCH=arch-linux2-c-debug' |
| '--enable-everything' |
| '--enable-cxx11' |
| '--disable-netcdf-4' |
| '--disable-testsets' |
| 'CXX=mpicxx' |
| 'CC=mpicc' |
| 'F77=mpif77' |
| 'FC=mpif90' |
| 'CPPFLAGS=' |
| 'LIBS=' |
------------------------------------------------------------------------
------------------------------------------------------------------------------------------------------------
| Matrix Assembly Performance: Alive time=0.001723, Active time=0.000937
|
------------------------------------------------------------------------------------------------------------
| 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 |
|------------------------------------------------------------------------------------------------------------|
|
|
| Fe 25 0.0002 0.000009 0.0002
0.000009 24.12 24.12 |
| Ke 25 0.0001 0.000004 0.0001
0.000004 10.67 10.67 |
| elem init 25 0.0004 0.000015 0.0004
0.000015 39.70 39.70 |
| matrix insertion 25 0.0002 0.000010 0.0002
0.000010 25.51 25.51 |
------------------------------------------------------------------------------------------------------------
| Totals: 100 0.0009
100.00 |
------------------------------------------------------------------------------------------------------------
------------------------------------------------------------------------
| Time: Thu Apr 7 17:48:05 2016 |
| OS: Linux |
| HostName: bassi |
| OS Release: 3.19.0-43-generic |
| OS Version: #49~14.04.1-Ubuntu SMP Thu Dec 31 15:44:49 UTC 2015 |
| Machine: x86_64 |
| Username: kameeko |
| Configuration: ./configure
'prefix=/home/kameeko/software/libmesh_build_petsc_mpidbg'|
| 'PETSC_DIR=/home/kameeko/software/petsc' |
| 'PETSC_ARCH=arch-linux2-c-debug' |
| '--enable-everything' |
| '--enable-cxx11' |
| '--disable-netcdf-4' |
| '--disable-testsets' |
| 'CXX=mpicxx' |
| 'CC=mpicc' |
| 'F77=mpif77' |
| 'FC=mpif90' |
| 'CPPFLAGS=' |
| 'LIBS=' |
------------------------------------------------------------------------
------------------------------------------------------------------------------------------------------------
| Matrix Assembly Performance: Alive time=0.001723, Active time=0.000931
|
------------------------------------------------------------------------------------------------------------
| 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 |
|------------------------------------------------------------------------------------------------------------|
|
|
| Fe 25 0.0002 0.000009 0.0002
0.000009 23.95 23.95 |
| Ke 25 0.0001 0.000004 0.0001
0.000004 10.42 10.42 |
| elem init 25 0.0004 0.000015 0.0004
0.000015 39.74 39.74 |
| matrix insertion 25 0.0002 0.000010 0.0002
0.000010 25.89 25.89 |
------------------------------------------------------------------------------------------------------------
| Totals: 100 0.0009
100.00 |
------------------------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------------------------------
| libMesh Performance: Alive time=0.01882, Active time=0.010765
|
---------------------------------------------------------------------------------------------------------------------
| 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 |
|---------------------------------------------------------------------------------------------------------------------|
|
|
|
|
| DofMap
|
| add_neighbors_to_send_list() 1 0.0000 0.000028
0.0000 0.000028 0.26 0.26 |
| build_constraint_matrix_and_vector() 25 0.0001 0.000003
0.0001 0.000003 0.71 0.71 |
| build_sparsity() 1 0.0002 0.000191
0.0002 0.000216 1.77 2.01 |
| create_dof_constraints() 1 0.0006 0.000560
0.0011 0.001140 5.20 10.59 |
| distribute_dofs() 1 0.0001 0.000051
0.0002 0.000162 0.47 1.50 |
| dof_indices() 100 0.0001 0.000001
0.0001 0.000001 0.98 0.98 |
| hetero_cnstrn_elem_mat_vec() 25 0.0002 0.000008
0.0002 0.000008 1.82 1.82 |
| prepare_send_list() 2 0.0000 0.000000
0.0000 0.000000 0.01 0.01 |
| reinit() 1 0.0001 0.000109
0.0001 0.000109 1.01 1.01 |
|
|
| EquationSystems
|
| build_solution_vector() 1 0.0006 0.000636
0.0007 0.000660 5.91 6.13 |
|
|
| ExodusII_IO
|
| write_nodal_data() 1 0.0016 0.001552
0.0016 0.001552 14.42 14.42 |
|
|
| FE
|
| compute_shape_functions() 45 0.0002 0.000004
0.0002 0.000004 1.63 1.63 |
| init_shape_functions() 21 0.0000 0.000002
0.0000 0.000002 0.37 0.37 |
| inverse_map() 60 0.0001 0.000002
0.0001 0.000002 1.38 1.38 |
|
|
| FEMap
|
| compute_affine_map() 45 0.0001 0.000002
0.0001 0.000002 0.92 0.92 |
| compute_face_map() 20 0.0001 0.000006
0.0003 0.000014 1.11 2.52 |
| init_face_shape_functions() 20 0.0000 0.000002
0.0000 0.000002 0.28 0.28 |
| init_referenc
---------------------------------------------------------------------------------------------------------------------
| libMesh Performance: Alive time=0.018821, Active time=0.010756
|
---------------------------------------------------------------------------------------------------------------------
| 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 |
|---------------------------------------------------------------------------------------------------------------------|
|
|
|
|
| DofMap
|
| add_neighbors_to_send_list() 1 0.0000 0.000027
0.0000 0.000027 0.25 0.25 |
| build_constraint_matrix_and_vector() 25 0.0001 0.000003
0.0001 0.000003 0.69 0.69 |
| build_sparsity() 1 0.0002 0.000189
0.0002 0.000216 1.76 2.01 |
| create_dof_constraints() 1 0.0006 0.000558
0.0011 0.001142 5.19 10.62 |
| distribute_dofs() 1 0.0001 0.000051
0.0002 0.000164 0.47 1.52 |
| dof_indices() 100 0.0001 0.000001
0.0001 0.000001 1.03 1.03 |
| hetero_cnstrn_elem_mat_vec() 25 0.0002 0.000008
0.0002 0.000008 1.83 1.83 |
| prepare_send_list() 2 0.0000 0.000000
0.0000 0.000000 0.01 0.01 |
| reinit() 1 0.0001 0.000112
0.0001 0.000112 1.04 1.04 |
|
|
| EquationSystems
|
| build_solution_vector() 1 0.0006 0.000636
0.0007 0.000661 5.91 6.15 |
|
|
| ExodusII_IO
|
| write_nodal_data() 1 0.0016 0.001556
0.0016 0.001556 14.47 14.47 |
|
|
| FE
|
| compute_shape_functions() 45 0.0002 0.000004
0.0002 0.000004 1.64 1.64 |
| init_shape_functions() 21 0.0000 0.000002
0.0000 0.000002 0.38 0.38 |
| inverse_map() 60 0.0002 0.000003
0.0002 0.000003 1.43 1.43 |
|
|
| FEMap
|
| compute_affine_map() 45 0.0001 0.000002
0.0001 0.000002 0.91 0.91 |
| compute_face_map() 20 0.0001 0.000006
0.0003 0.000014 1.04 2.52 |
| init_face_shape_functions() 20 0.0000 0.000001
0.0000 0.000001 0.22 0.22 |
| init_reference_to_physical_map() 21 0.0002 0.000008
0.0002 0.000008 1.49 1.49 |
|
|
| Mesh
|
| find_neighbors() 1 0.0001 0.000130
0.0001 0.000130 1.21 1.21 |
| renumber_nodes_and_elem() 2 0.0000 0.000010
0.0000 0.000010 0.20 0.20 |
|
|
| MeshOutput
|
| write_equation_systems() 1 0.0001 0.000051
0.0023 0.002263 0.47 21.02 |
|
|
| MeshTools::Generation
|
| build_cube() 1 0.0001 0.000099
0.0001 0.000099 0.92 0.92 |
|
|
| Parallel
|
| allgather() 1 0.0000 0.000001
0.0000 0.000001 0.01 0.01 |
|
|
| Partitioner
|
| single_partition() 1 0.0000 0.000007
0.0000 0.000007 0.07 0.07 |
|
|
| PetscLinearSolver
|
| solve() 1 0.0049 0.004889
0.0049 0.004889 45.42 45.42 |
|
|
| System
|
| assemble() 1 0.0013 0.001289
0.0018 0.001848 11.97 17.17 |
---------------------------------------------------------------------------------------------------------------------
| Totals: 400 0.0108
100.00 |
---------------------------------------------------------------------------------------------------------------------
e_to_physical_map() 21 0.0002 0.000008 0.0002 0.000008
1.49 1.49 |
|
|
| Mesh
|
| find_neighbors() 1 0.0001 0.000124
0.0001 0.000124 1.15 1.15 |
| renumber_nodes_and_elem() 2 0.0000 0.000011
0.0000 0.000011 0.21 0.21 |
|
|
| MeshOutput
|
| write_equation_systems() 1 0.0001 0.000052
0.0023 0.002269 0.48 21.10 |
|
|
| MeshTools::Generation
|
| build_cube() 1 0.0001 0.000112
0.0001 0.000112 1.04 1.04 |
|
|
| Parallel
|
| allgather() 1 0.0000 0.000001
0.0000 0.000001 0.01 0.01 |
|
|
| Partitioner
|
| single_partition() 1 0.0000 0.000007
0.0000 0.000007 0.07 0.07 |
|
|
| PetscLinearSolver
|
| solve() 1 0.0049 0.004869
0.0049 0.004869 45.27 45.27 |
|
|
| System
|
| assemble() 1 0.0013 0.001291
0.0018 0.001848 12.00 17.18 |
---------------------------------------------------------------------------------------------------------------------
| Totals: 400 0.0108
100.00 |
---------------------------------------------------------------------------------------------------------------------
WARNING! There are options you set that were not used!
WARNING! There are options you set that were not used!
WARNING! could be spelling mistake, etc!
WARNING! could be spelling mistake, etc!
Option left: name:-d value: 2
Option left: name:-n value: 5
Option left: name:-d value: 2
Option left: name:-n value: 5
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