Hi Daniel,
here is the report of valgrind. Can you maybe help devising potential
issues? I am afraid to be not sufficiently skilled, yet.
Thank you, I appreciate.
Alberto
albertosalvadori@ubuntu:~/Codes/m4_code/Release$ valgrind --leak-check=yes
mpirun -np 4 ./m4_code_9.1.1 ../input/viscosity_test -mechanics
==15940== Memcheck, a memory error detector
==15940== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
==15940== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info
==15940== Command: mpirun -np 4 ./m4_code_9.1.1 ../input/viscosity_test
-mechanics
==15940==
==15940== Warning: noted but unhandled ioctl 0x5441 with no size/direction
hints.
==15940== This could cause spurious value errors to appear.
==15940== See README_MISSING_SYSCALL_OR_IOCTL for guidance on writing a
proper wrapper.
==15944== Warning: invalid file descriptor 1024 in syscall close()
==15944== Warning: invalid file descriptor 1025 in syscall close()
==15944== Warning: invalid file descriptor 1026 in syscall close()
==15944== Warning: invalid file descriptor 1027 in syscall close()
==15944== Use --log-fd=<number> to select an alternative log fd.
==15944== Warning: invalid file descriptor 1028 in syscall close()
==15944== Warning: invalid file descriptor 1029 in syscall close()
==15945== Warning: invalid file descriptor 1024 in syscall close()
==15945== Warning: invalid file descriptor 1025 in syscall close()
==15945== Warning: invalid file descriptor 1026 in syscall close()
==15945== Warning: invalid file descriptor 1027 in syscall close()
==15945== Use --log-fd=<number> to select an alternative log fd.
==15945== Warning: invalid file descriptor 1028 in syscall close()
==15945== Warning: invalid file descriptor 1029 in syscall close()
==15945== Warning: invalid file descriptor 1030 in syscall close()
==15946== Warning: invalid file descriptor 1024 in syscall close()
==15946== Warning: invalid file descriptor 1025 in syscall close()
==15946== Warning: invalid file descriptor 1026 in syscall close()
==15946== Warning: invalid file descriptor 1027 in syscall close()
==15946== Use --log-fd=<number> to select an alternative log fd.
==15946== Warning: invalid file descriptor 1028 in syscall close()
==15946== Warning: invalid file descriptor 1029 in syscall close()
==15947== Warning: invalid file descriptor 1024 in syscall close()
==15947== Warning: invalid file descriptor 1025 in syscall close()
==15947== Warning: invalid file descriptor 1026 in syscall close()
==15947== Warning: invalid file descriptor 1027 in syscall close()
==15947== Use --log-fd=<number> to select an alternative log fd.
==15947== Warning: invalid file descriptor 1028 in syscall close()
==15947== Warning: invalid file descriptor 1029 in syscall close()
Welcome to m4_code, a multiphysics solver for several class of problems
developed at the m4lab @ UNIBS.
The problem that is going to be solved is: Mechanics for the data set
../input/viscosity_test
Problem LargeStrainMechanicalProblem_OneField defined
Reading material parameters from file ../input/viscosity_test.materials
... done
Reading time discretization parameters from file
../input/viscosity_test.time_discretization ... done
Time = 0.0000, step = 0
Initialization
Reading discretization from file ../input/viscosity_test.msh ... done
Number of active cells: 24 (by partition: 6+6+6+6)
Number of degrees of freedom: 153 (by partition: 63+30+33+27)
Dirichlet faces: 36, Neumann faces (with non-zero tractions): 0, contact
faces: 0
NR it. 0, Assembling..., convergence achieved.
Writing output..., 0.00 s. Elapsed time 0.00 s.
Time = 0.0100, step = 1
Cycle 0:
Number of active cells: 24 (by partition: 6+6+6+6)
Number of degrees of freedom: 153 (by partition: 63+30+33+27)
Dirichlet faces: 36, symmetry faces: 0
Dirichlet faces: 36, Neumann faces (with non-zero tractions): 0, contact
faces: 0
NR it. 0, Assembling..., 0.00 s, norm of residual is
85544.434331779601052
Jacobi - Bicgstab , solver converged in 8 iterations,
0.00 s, updating q. p. data, 0.00 s.
NR it. 1, Assembling..., 0.00 s, norm of residual is
2.878811227221835 residual / initial_residual 0.000033652817389
Jacobi - Bicgstab , solver converged in 7 iterations,
0.00 s, updating q. p. data, 0.00 s.
NR it. 2, Assembling..., 0.00 s, norm of residual is
1.251122517879704 residual / initial_residual 0.000014625411082
Jacobi - Bicgstab , solver converged in 8 iterations,
0.00 s, updating q. p. data, 0.00 s.
NR it. 3, Assembling..., 0.00 s, norm of residual is
0.589683284238633 residual / initial_residual 0.000006893298072
Jacobi - Bicgstab , solver converged in 7 iterations,
0.00 s, updating q. p. data, 0.00 s.
NR it. 4, Assembling..., 0.00 s, norm of residual is
0.286154795390284 residual / initial_residual 0.000003345101264
Jacobi - Bicgstab , solver converged in 7 iterations,
0.00 s, updating q. p. data, 0.00 s.
NR it. 5, Assembling..., 0.00 s, norm of residual is
0.140996840962549 residual / initial_residual 0.000001648229275
Jacobi - Bicgstab , solver converged in 7 iterations,
0.00 s, updating q. p. data, 0.00 s.
NR it. 6, Assembling..., 0.00 s, norm of residual is
0.070130790642500 residual / initial_residual 0.000000819817107,
convergence achieved.
Writing output..., 0.00 s. Elapsed time 0.01 s.
Time = 0.0200, step = 2
NR it. 0, Assembling..., 0.00 s, norm of residual is
85527.166469113071798
Jacobi - Bicgstab , solver converged in 8 iterations,
0.00 s, updating q. p. data, 0.00 s.
NR it. 1, Assembling..., 0.00 s, norm of residual is
2.833292747597304 residual / initial_residual 0.000033127401089
Jacobi - Bicgstab , solver converged in 7 iterations,
0.00 s, updating q. p. data, 0.00 s.
NR it. 2, Assembling..., 0.00 s, norm of residual is
1.237625339847165 residual / initial_residual 0.000014470552351
Jacobi - Bicgstab , solver converged in 8 iterations,
0.00 s, updating q. p. data, 0.00 s.
NR it. 3, Assembling..., 0.00 s, norm of residual is
0.583941014065106 residual / initial_residual 0.000006827550101
Jacobi - Bicgstab , solver converged in 7 iterations,
0.00 s, updating q. p. data, 0.00 s.
NR it. 4, Assembling..., 0.00 s, norm of residual is
0.283285692816626 residual / initial_residual 0.000003312230540
Jacobi - Bicgstab , solver converged in 7 iterations,
0.00 s, updating q. p. data, 0.00 s.
NR it. 5, Assembling..., 0.00 s, norm of residual is
0.139462610870105 residual / initial_residual 0.000001630623539
Jacobi - Bicgstab , solver converged in 7 iterations,
0.00 s, updating q. p. data, 0.00 s.
NR it. 6, Assembling..., 0.00 s, norm of residual is
0.069287951261074 residual / initial_residual 0.000000810127988,
convergence achieved.
Writing output..., 0.00 s. Elapsed time 0.01 s.
Time = 0.0300, step = 3
NR it. 0, Assembling..., 0.00 s, norm of residual is
85508.630080626477138
Jacobi - Bicgstab , solver converged in 8 iterations,
0.00 s, updating q. p. data, 0.00 s.
NR it. 1, Assembling..., 0.00 s, norm of residual is
2.762016583926737 residual / initial_residual 0.000032301027175
Jacobi - Bicgstab , solver converged in 7 iterations,
0.00 s, updating q. p. data, 0.00 s.
NR it. 2, Assembling..., 0.00 s, norm of residual is
1.208785226058421 residual / initial_residual 0.000014136412020
Jacobi - Bicgstab , solver converged in 8 iterations,
0.00 s, updating q. p. data, 0.00 s.
NR it. 3, Assembling..., 0.00 s, norm of residual is
0.570076433206978 residual / initial_residual 0.000006666887689
Jacobi - Bicgstab , solver converged in 7 iterations,
0.00 s, updating q. p. data, 0.00 s.
NR it. 4, Assembling..., 0.00 s, norm of residual is
0.276241018233497 residual / initial_residual 0.000003230563020
Jacobi - Bicgstab , solver converged in 7 iterations,
0.00 s, updating q. p. data, 0.00 s.
NR it. 5, Assembling..., 0.00 s, norm of residual is
0.135804501324608 residual / initial_residual 0.000001588196433
Jacobi - Bicgstab , solver converged in 7 iterations,
0.00 s, updating q. p. data, 0.00 s.
NR it. 6, Assembling..., 0.00 s, norm of residual is
0.067369573885574 residual / initial_residual 0.000000787868708,
convergence achieved.
Writing output..., 0.00 s. Elapsed time 0.01 s.
Time = 0.0400, step = 4
NR it. 0, Assembling..., 0.00 s, norm of residual is
85488.917497585309320
Jacobi - Bicgstab , solver converged in 8 iterations,
0.00 s, updating q. p. data, 0.00 s.
NR it. 1, Assembling..., 0.00 s, norm of residual is
2.695011376135198 residual / initial_residual 0.000031524687118
Jacobi - Bicgstab , solver converged in 7 iterations,
0.00 s, updating q. p. data, 0.00 s.
NR it. 2, Assembling..., 0.00 s, norm of residual is
1.181258398115642 residual / initial_residual 0.000013817678744
Jacobi - Bicgstab , solver converged in 8 iterations,
0.00 s, updating q. p. data, 0.00 s.
NR it. 3, Assembling..., 0.00 s, norm of residual is
0.556795954922090 residual / initial_residual 0.000006513077615
Jacobi - Bicgstab , solver converged in 7 iterations,
0.00 s, updating q. p. data, 0.00 s.
NR it. 4, Assembling..., 0.00 s, norm of residual is
0.269504925293314 residual / initial_residual 0.000003152513018
Jacobi - Bicgstab , solver converged in 7 iterations,
0.00 s, updating q. p. data, 0.00 s.
NR it. 5, Assembling..., 0.00 s, norm of residual is
0.132319587221657 residual / initial_residual 0.000001547798137
Jacobi - Bicgstab , solver converged in 7 iterations,
0.00 s, updating q. p. data, 0.00 s.
NR it. 6, Assembling..., 0.00 s, norm of residual is
0.065549752241302 residual / initial_residual 0.000000766763157,
convergence achieved.
Writing output..., 0.00 s. Elapsed time 0.01 s.
Time = 0.0500, step = 5
NR it. 0, Assembling..., 0.00 s, norm of residual is
85468.116351285294513
Jacobi - Bicgstab , solver converged in 8 iterations,
0.00 s, updating q. p. data, 0.00 s.
NR it. 1, Assembling..., 0.00 s, norm of residual is
2.632626127873656 residual / initial_residual 0.000030802435344
Jacobi - Bicgstab , solver converged in 7 iterations,
0.00 s, updating q. p. data, 0.00 s.
NR it. 2, Assembling..., 0.00 s, norm of residual is
1.155304911256316 residual / initial_residual 0.000013517378884
Jacobi - Bicgstab , solver converged in 8 iterations,
0.00 s, updating q. p. data, 0.00 s.
NR it. 3, Assembling..., 0.00 s, norm of residual is
0.544238373865104 residual / initial_residual 0.000006367735679
Jacobi - Bicgstab , solver converged in 7 iterations,
0.00 s, updating q. p. data, 0.00 s.
NR it. 4, Assembling..., 0.00 s, norm of residual is
0.263146637278587 residual / initial_residual 0.000003078886590
Jacobi - Bicgstab , solver converged in 7 iterations,
0.00 s, updating q. p. data, 0.00 s.
NR it. 5, Assembling..., 0.00 s, norm of residual is
0.129041233945870 residual / initial_residual 0.000001509817221
Jacobi - Bicgstab , solver converged in 7 iterations,
0.00 s, updating q. p. data, 0.00 s.
NR it. 6, Assembling..., 0.00 s, norm of residual is
0.063844231873425 residual / initial_residual 0.000000746994723,
convergence achieved.
Writing output..., 0.00 s. Elapsed time 0.01 s.
Done.
==15940==
==15940== HEAP SUMMARY:
==15940== in use at exit: 702,101 bytes in 9,911 blocks
==15940== total heap usage: 43,195 allocs, 33,284 frees, 1,150,113,471
bytes allocated
==15940==
==15940== 136 bytes in 1 blocks are definitely lost in loss record 30 of 47
==15940== at 0x4C2FB0F: malloc (in
/usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==15940== by 0x4EFA039: orte_rmaps_base_print_mapping (in
/home/dealii/spack/opt/spack/linux-ubuntu18.04-skylake/gcc-7.5.0/openmpi-3.1.5-i73g2jkrcifjgtsishpfwloiu5syp244/lib/libopen-rte.so.40.10.5)
==15940== by 0x4E8BD1A: orte_pmix_server_register_nspace (in
/home/dealii/spack/opt/spack/linux-ubuntu18.04-skylake/gcc-7.5.0/openmpi-3.1.5-i73g2jkrcifjgtsishpfwloiu5syp244/lib/libopen-rte.so.40.10.5)
==15940== by 0x4ECC251: orte_odls_base_default_construct_child_list (in
/home/dealii/spack/opt/spack/linux-ubuntu18.04-skylake/gcc-7.5.0/openmpi-3.1.5-i73g2jkrcifjgtsishpfwloiu5syp244/lib/libopen-rte.so.40.10.5)
==15940== by 0x4ECFA51: orte_odls_default_launch_local_procs (in
/home/dealii/spack/opt/spack/linux-ubuntu18.04-skylake/gcc-7.5.0/openmpi-3.1.5-i73g2jkrcifjgtsishpfwloiu5syp244/lib/libopen-rte.so.40.10.5)
==15940== by 0x4E833A7: orte_daemon_recv (in
/home/dealii/spack/opt/spack/linux-ubuntu18.04-skylake/gcc-7.5.0/openmpi-3.1.5-i73g2jkrcifjgtsishpfwloiu5syp244/lib/libopen-rte.so.40.10.5)
==15940== by 0x4F09B0A: orte_rml_base_process_msg (in
/home/dealii/spack/opt/spack/linux-ubuntu18.04-skylake/gcc-7.5.0/openmpi-3.1.5-i73g2jkrcifjgtsishpfwloiu5syp244/lib/libopen-rte.so.40.10.5)
==15940== by 0x5218CF8: event_process_active_single_queue (event.c:1370)
==15940== by 0x5218CF8: event_process_active (event.c:1440)
==15940== by 0x5218CF8: opal_libevent2022_event_base_loop (event.c:1644)
==15940== by 0x109679: orterun (in
/home/dealii/spack/opt/spack/linux-ubuntu18.04-skylake/gcc-7.5.0/openmpi-3.1.5-i73g2jkrcifjgtsishpfwloiu5syp244/bin/orterun)
==15940== by 0x5602B96: (below main) (libc-start.c:310)
==15940==
==15940== 2,036 (672 direct, 1,364 indirect) bytes in 4 blocks are
definitely lost in loss record 43 of 47
==15940== at 0x4C2FB0F: malloc (in
/usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==15940== by 0x4EF75E0: orte_rmaps_base_setup_proc (in
/home/dealii/spack/opt/spack/linux-ubuntu18.04-skylake/gcc-7.5.0/openmpi-3.1.5-i73g2jkrcifjgtsishpfwloiu5syp244/lib/libopen-rte.so.40.10.5)
==15940== by 0x4EFF1E4: orte_rmaps_rr_byobj (in
/home/dealii/spack/opt/spack/linux-ubuntu18.04-skylake/gcc-7.5.0/openmpi-3.1.5-i73g2jkrcifjgtsishpfwloiu5syp244/lib/libopen-rte.so.40.10.5)
==15940== by 0x4EFE172: orte_rmaps_rr_map (in
/home/dealii/spack/opt/spack/linux-ubuntu18.04-skylake/gcc-7.5.0/openmpi-3.1.5-i73g2jkrcifjgtsishpfwloiu5syp244/lib/libopen-rte.so.40.10.5)
==15940== by 0x4EF4F7F: orte_rmaps_base_map_job (in
/home/dealii/spack/opt/spack/linux-ubuntu18.04-skylake/gcc-7.5.0/openmpi-3.1.5-i73g2jkrcifjgtsishpfwloiu5syp244/lib/libopen-rte.so.40.10.5)
==15940== by 0x5218CF8: event_process_active_single_queue (event.c:1370)
==15940== by 0x5218CF8: event_process_active (event.c:1440)
==15940== by 0x5218CF8: opal_libevent2022_event_base_loop (event.c:1644)
==15940== by 0x109679: orterun (in
/home/dealii/spack/opt/spack/linux-ubuntu18.04-skylake/gcc-7.5.0/openmpi-3.1.5-i73g2jkrcifjgtsishpfwloiu5syp244/bin/orterun)
==15940== by 0x5602B96: (below main) (libc-start.c:310)
==15940==
==15940== LEAK SUMMARY:
==15940== definitely lost: 808 bytes in 5 blocks
==15940== indirectly lost: 1,364 bytes in 16 blocks
==15940== possibly lost: 0 bytes in 0 blocks
==15940== still reachable: 699,929 bytes in 9,890 blocks
==15940== suppressed: 0 bytes in 0 blocks
==15940== Reachable blocks (those to which a pointer was found) are not
shown.
==15940== To see them, rerun with: --leak-check=full --show-leak-kinds=all
==15940==
==15940== For counts of detected and suppressed errors, rerun with: -v
==15940== ERROR SUMMARY: 2 errors from 2 contexts (suppressed: 0 from 0)
albertosalvadori@ubuntu:~/Codes/m4_code/Release$ valgrind --leak-check=yes
./m4_code_9.1.1 ../input/viscosity_test -mechanics
==16016== Memcheck, a memory error detector
==16016== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
==16016== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info
==16016== Command: ./m4_code_9.1.1 ../input/viscosity_test -mechanics
==16016==
Welcome to m4_code, a multiphysics solver for several class of problems
developed at the m4lab @ UNIBS.
The problem that is going to be solved is: Mechanics for the data set
../input/viscosity_test
Problem LargeStrainMechanicalProblem_OneField defined
Reading material parameters from file ../input/viscosity_test.materials
... done
Reading time discretization parameters from file
../input/viscosity_test.time_discretization ... done
Time = 0.0000, step = 0
Initialization
Reading discretization from file ../input/viscosity_test.msh ... done
Number of active cells: 24 (by partition: 24)
Number of degrees of freedom: 153 (by partition: 153)
Dirichlet faces: 36, Neumann faces (with non-zero tractions): 0, contact
faces: 0
NR it. 0, Assembling..., convergence achieved.
Writing output..., 0.13 s. Elapsed time 1.17 s.
Time = 0.0100, step = 1
Cycle 0:
Number of active cells: 24 (by partition: 24)
Number of degrees of freedom: 153 (by partition: 153)
Dirichlet faces: 36, symmetry faces: 0
Dirichlet faces: 36, Neumann faces (with non-zero tractions): 0, contact
faces: 0
NR it. 0, Assembling..., 0.49 s, norm of residual is
91034.225329364344361
Jacobi - Bicgstab , solver converged in 8 iterations,
0.12 s, updating q. p. data, 0.02 s.
NR it. 1, Assembling..., 0.66 s, norm of residual is
2.878811227221786 residual / initial_residual 0.000031623394573
Jacobi - Bicgstab , solver converged in 7 iterations,
0.01 s, updating q. p. data, 0.01 s.
NR it. 2, Assembling..., 0.69 s, norm of residual is
1.251122517853476 residual / initial_residual 0.000013743430159
Jacobi - Bicgstab , solver converged in 8 iterations,
0.01 s, updating q. p. data, 0.01 s.
NR it. 3, Assembling..., 0.85 s, norm of residual is
0.589683284214466 residual / initial_residual 0.000006477599849
Jacobi - Bicgstab , solver converged in 7 iterations,
0.01 s, updating q. p. data, 0.01 s.
NR it. 4, Assembling..., 0.72 s, norm of residual is
0.286154795364823 residual / initial_residual 0.000003143375959
Jacobi - Bicgstab , solver converged in 7 iterations,
0.01 s, updating q. p. data, 0.01 s.
NR it. 5, Assembling..., 0.74 s, norm of residual is
0.140996840961326 residual / initial_residual 0.000001548833315
Jacobi - Bicgstab , solver converged in 7 iterations,
0.01 s, updating q. p. data, 0.01 s.
NR it. 6, Assembling..., 0.73 s, norm of residual is
0.070130790656907 residual / initial_residual 0.000000770378288,
convergence achieved.
Writing output..., 0.02 s. Elapsed time 5.20 s.
Time = 0.0200, step = 2
NR it. 0, Assembling..., 0.76 s, norm of residual is
91019.816765709023457
Jacobi - Bicgstab , solver converged in 8 iterations,
0.01 s, updating q. p. data, 0.01 s.
NR it. 1, Assembling..., 0.83 s, norm of residual is
2.833292747504541 residual / initial_residual 0.000031128306430
Jacobi - Bicgstab , solver converged in 7 iterations,
0.01 s, updating q. p. data, 0.01 s.
NR it. 2, Assembling..., 0.76 s, norm of residual is
1.237625339758325 residual / initial_residual 0.000013597317417
Jacobi - Bicgstab , solver converged in 8 iterations,
0.01 s, updating q. p. data, 0.01 s.
NR it. 3, Assembling..., 0.84 s, norm of residual is
0.583941014051878 residual / initial_residual 0.000006415537130
Jacobi - Bicgstab , solver converged in 7 iterations,
0.01 s, updating q. p. data, 0.01 s.
NR it. 4, Assembling..., 0.76 s, norm of residual is
0.283285692895102 residual / initial_residual 0.000003112351826
Jacobi - Bicgstab , solver converged in 7 iterations,
0.01 s, updating q. p. data, 0.01 s.
NR it. 5, Assembling..., 0.72 s, norm of residual is
0.139462610865597 residual / initial_residual 0.000001532222496
Jacobi - Bicgstab , solver converged in 7 iterations,
0.01 s, updating q. p. data, 0.01 s.
NR it. 6, Assembling..., 0.84 s, norm of residual is
0.069287951197439 residual / initial_residual 0.000000761240284,
convergence achieved.
Writing output..., 0.02 s. Elapsed time 5.67 s.
Time = 0.0300, step = 3
NR it. 0, Assembling..., 0.88 s, norm of residual is
91004.270071844381164
Jacobi - Bicgstab , solver converged in 8 iterations,
0.01 s, updating q. p. data, 0.01 s.
NR it. 1, Assembling..., 0.84 s, norm of residual is
2.762016583840568 residual / initial_residual 0.000030350406433
Jacobi - Bicgstab , solver converged in 7 iterations,
0.01 s, updating q. p. data, 0.01 s.
NR it. 2, Assembling..., 0.86 s, norm of residual is
1.208785225800891 residual / initial_residual 0.000013282730853
Jacobi - Bicgstab , solver converged in 8 iterations,
0.01 s, updating q. p. data, 0.01 s.
NR it. 3, Assembling..., 0.86 s, norm of residual is
0.570076432979952 residual / initial_residual 0.000006264282242
Jacobi - Bicgstab , solver converged in 7 iterations,
0.01 s, updating q. p. data, 0.01 s.
NR it. 4, Assembling..., 0.85 s, norm of residual is
0.276241018094444 residual / initial_residual 0.000003035473147
Jacobi - Bicgstab , solver converged in 7 iterations,
0.01 s, updating q. p. data, 0.01 s.
NR it. 5, Assembling..., 0.85 s, norm of residual is
0.135804501308918 residual / initial_residual 0.000001492287133
Jacobi - Bicgstab , solver converged in 7 iterations,
0.01 s, updating q. p. data, 0.01 s.
NR it. 6, Assembling..., 0.85 s, norm of residual is
0.067369573855780 residual / initial_residual 0.000000740290250,
convergence achieved.
Writing output..., 0.03 s. Elapsed time 6.15 s.
Time = 0.0400, step = 4
NR it. 0, Assembling..., 0.82 s, norm of residual is
90987.672485545655945
Jacobi - Bicgstab , solver converged in 7 iterations,
0.01 s, updating q. p. data, 0.01 s.
NR it. 1, Assembling..., 0.77 s, norm of residual is
11.855541044511227 residual / initial_residual 0.000130298321967
Jacobi - Bicgstab , solver converged in 7 iterations,
0.01 s, updating q. p. data, 0.01 s.
NR it. 2, Assembling..., 0.81 s, norm of residual is
5.024194956080943 residual / initial_residual 0.000055218413867
Jacobi - Bicgstab , solver converged in 7 iterations,
0.01 s, updating q. p. data, 0.01 s.
NR it. 3, Assembling..., 0.73 s, norm of residual is
2.386446299837078 residual / initial_residual 0.000026228237679
Jacobi - Bicgstab , solver converged in 8 iterations,
0.01 s, updating q. p. data, 0.01 s.
NR it. 4, Assembling..., 0.74 s, norm of residual is
1.169642298363859 residual / initial_residual 0.000012854953494
Jacobi - Bicgstab , solver converged in 7 iterations,
0.01 s, updating q. p. data, 0.01 s.
NR it. 5, Assembling..., 0.83 s, norm of residual is
0.580900730478848 residual / initial_residual 0.000006384389386
Jacobi - Bicgstab , solver converged in 7 iterations,
0.01 s, updating q. p. data, 0.01 s.
NR it. 6, Assembling..., 0.83 s, norm of residual is
0.290601814573314 residual / initial_residual 0.000003193859197
Jacobi - Bicgstab , solver converged in 7 iterations,
0.01 s, updating q. p. data, 0.01 s.
NR it. 7, Assembling..., 0.77 s, norm of residual is
0.146033689679270 residual / initial_residual 0.000001604983243
Jacobi - Bicgstab , solver converged in 7 iterations,
0.01 s, updating q. p. data, 0.01 s.
NR it. 8, Assembling..., 0.71 s, norm of residual is
0.073608751294460 residual / initial_residual 0.000000808996969,
convergence achieved.
Writing output..., 0.02 s. Elapsed time 7.20 s.
Time = 0.0500, step = 5
NR it. 0, Assembling..., 0.71 s, norm of residual is
90970.106811760648270
Jacobi - Bicgstab , solver converged in 7 iterations,
0.01 s, updating q. p. data, 0.01 s.
NR it. 1, Assembling..., 0.77 s, norm of residual is
11.664731903434573 residual / initial_residual 0.000128225988869
Jacobi - Bicgstab , solver converged in 7 iterations,
0.01 s, updating q. p. data, 0.01 s.
NR it. 2, Assembling..., 0.84 s, norm of residual is
4.931906111288249 residual / initial_residual 0.000054214579757
Jacobi - Bicgstab , solver converged in 7 iterations,
0.01 s, updating q. p. data, 0.01 s.
NR it. 3, Assembling..., 0.68 s, norm of residual is
2.341475280102340 residual / initial_residual 0.000025738952741
Jacobi - Bicgstab , solver converged in 8 iterations,
0.01 s, updating q. p. data, 0.01 s.
NR it. 4, Assembling..., 0.66 s, norm of residual is
1.146702999151362 residual / initial_residual 0.000012605272648
Jacobi - Bicgstab , solver converged in 7 iterations,
0.01 s, updating q. p. data, 0.01 s.
NR it. 5, Assembling..., 0.69 s, norm of residual is
0.568910548063869 residual / initial_residual 0.000006253818622
Jacobi - Bicgstab , solver converged in 7 iterations,
0.01 s, updating q. p. data, 0.01 s.
NR it. 6, Assembling..., 0.79 s, norm of residual is
0.284260458923041 residual / initial_residual 0.000003124767782
Jacobi - Bicgstab , solver converged in 7 iterations,
0.01 s, updating q. p. data, 0.01 s.
NR it. 7, Assembling..., 0.81 s, norm of residual is
0.142660328891304 residual / initial_residual 0.000001568211074
Jacobi - Bicgstab , solver converged in 7 iterations,
0.01 s, updating q. p. data, 0.01 s.
NR it. 8, Assembling..., 0.77 s, norm of residual is
0.071808965799463 residual / initial_residual 0.000000789368819,
convergence achieved.
Writing output..., 0.02 s. Elapsed time 6.89 s.
Done.
==16016==
==16016== HEAP SUMMARY:
==16016== in use at exit: 128,896 bytes in 78 blocks
==16016== total heap usage: 120,131 allocs, 120,053 frees, 58,222,758
bytes allocated
==16016==
==16016== 79 (64 direct, 15 indirect) bytes in 1 blocks are definitely lost
in loss record 35 of 63
==16016== at 0x4C2FB0F: malloc (in
/usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==16016== by 0x20C6CCC8: mca_mpool_hugepage_open (in
/home/dealii/spack/opt/spack/linux-ubuntu18.04-skylake/gcc-7.5.0/openmpi-3.1.5-i73g2jkrcifjgtsishpfwloiu5syp244/lib/libopen-pal.so.40.10.5)
==16016== by 0x20C176A9: mca_base_framework_components_open (in
/home/dealii/spack/opt/spack/linux-ubuntu18.04-skylake/gcc-7.5.0/openmpi-3.1.5-i73g2jkrcifjgtsishpfwloiu5syp244/lib/libopen-pal.so.40.10.5)
==16016== by 0x20C6B491: mca_mpool_base_open (in
/home/dealii/spack/opt/spack/linux-ubuntu18.04-skylake/gcc-7.5.0/openmpi-3.1.5-i73g2jkrcifjgtsishpfwloiu5syp244/lib/libopen-pal.so.40.10.5)
==16016== by 0x20C23110: mca_base_framework_open (in
/home/dealii/spack/opt/spack/linux-ubuntu18.04-skylake/gcc-7.5.0/openmpi-3.1.5-i73g2jkrcifjgtsishpfwloiu5syp244/lib/libopen-pal.so.40.10.5)
==16016== by 0x11F669F9: ompi_mpi_init (in
/home/dealii/spack/opt/spack/linux-ubuntu18.04-skylake/gcc-7.5.0/openmpi-3.1.5-i73g2jkrcifjgtsishpfwloiu5syp244/lib/libmpi.so.40.10.4)
==16016== by 0x11DF6104: PMPI_Init_thread (in
/home/dealii/spack/opt/spack/linux-ubuntu18.04-skylake/gcc-7.5.0/openmpi-3.1.5-i73g2jkrcifjgtsishpfwloiu5syp244/lib/libmpi.so.40.10.4)
==16016== by 0xCB60C0E:
dealii::Utilities::MPI::MPI_InitFinalize::MPI_InitFinalize(int&, char**&,
unsigned int) (in
/home/dealii/spack/opt/spack/linux-ubuntu18.04-skylake/gcc-7.5.0/dealii-9.1.1-rwy6s7qygaqdwov6gm33spdz5fjaancw/lib/libdeal_II.so.9.1.1)
==16016== by 0x19DBB8: main (in
/home/albertosalvadori/Codes/m4_code/Release/m4_code_9.1.1)
==16016==
==16016== LEAK SUMMARY:
==16016== definitely lost: 64 bytes in 1 blocks
==16016== indirectly lost: 15 bytes in 1 blocks
==16016== possibly lost: 0 bytes in 0 blocks
==16016== still reachable: 128,817 bytes in 76 blocks
==16016== suppressed: 0 bytes in 0 blocks
==16016== Reachable blocks (those to which a pointer was found) are not
shown.
==16016== To see them, rerun with: --leak-check=full --show-leak-kinds=all
==16016==
==16016== For counts of detected and suppressed errors, rerun with: -v
==16016== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 0 from 0)
Il giorno venerdì 24 luglio 2020 alle 21:37:02 UTC+2 d.arnd...@gmail.com ha
scritto:
> Alberto,
>
> Have you tried running valgrind (in parallel) on your code? Admittedly, I
> expect quite a bit of false-positives from the MPI library but it should
> still help.
>
> Best,
> Daniel
>
> Am Fr., 24. Juli 2020 um 12:07 Uhr schrieb Alberto Salvadori <
> alberto....@unibs.it>:
>
>> Dear community,
>>
>> if I am not mistaking my analysis, it turned out that the memory loss is
>> caused by this call:
>>
>> BiCG.solve (this->system_matrix, distributed_incremental_displacement,
>> this->system_rhs, preconditioner);
>>
>> because if I turn it off the top command shows no change in the RES at
>> all.
>>
>> Maybe this is of use. Thanks in advance.
>>
>> Alberto
>>
>> Il giorno venerdì 24 luglio 2020 alle 11:32:13 UTC+2 Alberto Salvadori ha
>> scritto:
>>
>>> Dear community
>>>
>>> I have written the simple code below for solving a system using PETSc,
>>> having defined
>>>
>>> Vector<double> incremental_displacement;
>>> Vector<double> accumulated_displacement;
>>>
>>> in the class LargeStrainMechanicalProblem_OneField<dim>.
>>>
>>> It turns out that this code produces a memory loss, quite significant
>>> since I am solving my system thousands of times, eventually inducing the
>>> run to fail. I am not sure what is causing this issue and how to solve it,
>>> maybe more experienced users than myself can catch the problem with a snap
>>> of fingers.
>>>
>>> I have verified the issue on my mac (Catalina) as well as on linux
>>> ubuntu (4.15.0), using deal.ii 9.1.1.
>>> Apparently the issue reveals only when mpi is invoked with more than one
>>> processor, whereas it does not emerge when running in serial or by mpirun
>>> -np 1.
>>>
>>> Thanks in advance
>>>
>>> Alberto
>>>
>>> =========
>>>
>>>
>>>
>>>
>>> template <int dim>
>>> unsigned int LargeStrainMechanicalProblem_OneField<dim>
>>> ::
>>> solve (
>>> const unsigned penaltyAmplification
>>> )
>>>
>>> //
>>> // this simplified version of solve has been written to find out
>>> // the source of memory leak in parallel
>>> //
>>>
>>> {
>>>
>>> PETScWrappers::MPI::Vector distributed_incremental_displacement
>>> (this>locally_owned_dofs,this->mpi_communicator);
>>>
>>> distributed_incremental_displacement = incremental_displacement;
>>>
>>> size_t
>>> bicgstab_max_iterations = 20000 ;
>>>
>>> double
>>> tolerance = 1e-10 * this->system_rhs.l2_norm() ;
>>>
>>> unsigned solver_control_last_step;
>>>
>>> SolverControl bicgstab_solver_control ( bicgstab_max_iterations ,
>>> tolerance );
>>>
>>> PETScWrappers::PreconditionJacobi preconditioner( this->system_matrix );
>>>
>>> this->pcout << " Bicgstab " << std::flush ;
>>>
>>> PETScWrappers::SolverBicgstab BiCG (bicgstab_solver_control,
>>> this->mpi_communicator);
>>>
>>> BiCG.solve (this->system_matrix, distributed_incremental_displacement,
>>> this->system_rhs, preconditioner);
>>>
>>> solver_control_last_step = bicgstab_solver_control.last_step();
>>>
>>> incremental_displacement = distributed_incremental_displacement;
>>> accumulated_displacement += incremental_displacement;
>>> this->hanging_node_constraints.distribute (accumulated_displacement);
>>>
>>> return solver_control_last_step;
>>>
>>> }
>>>
>>
>>
>> Informativa sulla Privacy: http://www.unibs.it/node/8155
>>
>> --
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>> .
>>
>
--
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<http://www.unibs.it/node/8155>
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