[petsc-users] Performance problem about output mesh in vtk format
Gong Yujie
yc17470 at connect.um.edu.mo
Sun Nov 5 20:54:30 CST 2023
Dear PETSc developers,
I'm trying to output a result data in vtk format and find that it is quite slow. Then I try to check this issue by a simple test code:
PetscCall(PetscInitialize(&argc,&argv,(char*)0,NULL));
DM dm,dmParallel,dmAux;
PetscBool interpolate=PETSC_TRUE;
PetscCall(DMPlexCreateExodusFromFile(PETSC_COMM_WORLD,"artery_plaque.exo",interpolate,&dm));
PetscCall(DMViewFromOptions(dm,NULL,"-dm_view"));
PetscCall(PetscFinalize());
and run with ./dm_test -dm_view vtk:./ksp_data/abc.vtk -log_view
It took about 600s to output the mesh. I'm not sure if there is something wrong in my code or my configuration of PETSc. Could you please give me some advice on this?
Best Regards,
Yujie
P.S. The result for log_view
****************************************************************************************************************************************************************
*** WIDEN YOUR WINDOW TO 160 CHARACTERS. Use 'enscript -r -fCourier9' to print this document ***
****************************************************************************************************************************************************************
------------------------------------------------------------------ PETSc Performance Summary: ------------------------------------------------------------------
./dm_test on a arch-linux-c-opt named DESKTOP-0H8HCOD with 1 processor, by qingfeng Mon Nov 6 10:43:31 2023
Using Petsc Release Version 3.19.5, unknown
Max Max/Min Avg Total
Time (sec): 6.286e+02 1.000 6.286e+02
Objects: 1.400e+02 1.000 1.400e+02
Flops: 0.000e+00 0.000 0.000e+00 0.000e+00
Flops/sec: 0.000e+00 0.000 0.000e+00 0.000e+00
MPI Msg Count: 0.000e+00 0.000 0.000e+00 0.000e+00
MPI Msg Len (bytes): 0.000e+00 0.000 0.000e+00 0.000e+00
MPI Reductions: 0.000e+00 0.000
Flop counting convention: 1 flop = 1 real number operation of type (multiply/divide/add/subtract)
e.g., VecAXPY() for real vectors of length N --> 2N flops
and VecAXPY() for complex vectors of length N --> 8N flops
Summary of Stages: ----- Time ------ ----- Flop ------ --- Messages --- -- Message Lengths -- -- Reductions --
Avg %Total Avg %Total Count %Total Avg %Total Count %Total
0: Main Stage: 6.2859e+02 100.0% 0.0000e+00 0.0% 0.000e+00 0.0% 0.000e+00 0.0% 0.000e+00 0.0%
------------------------------------------------------------------------------------------------------------------------
See the 'Profiling' chapter of the users' manual for details on interpreting output.
Phase summary info:
Count: number of times phase was executed
Time and Flop: Max - maximum over all processors
Ratio - ratio of maximum to minimum over all processors
Mess: number of messages sent
AvgLen: average message length (bytes)
Reduct: number of global reductions
Global: entire computation
Stage: stages of a computation. Set stages with PetscLogStagePush() and PetscLogStagePop().
%T - percent time in this phase %F - percent flop in this phase
%M - percent messages in this phase %L - percent message lengths in this phase
%R - percent reductions in this phase
Total Mflop/s: 10e-6 * (sum of flop over all processors)/(max time over all processors)
------------------------------------------------------------------------------------------------------------------------
Event Count Time (sec) Flop --- Global --- --- Stage ---- Total
Max Ratio Max Ratio Max Ratio Mess AvgLen Reduct %T %F %M %L %R %T %F %M %L %R Mflop/s
------------------------------------------------------------------------------------------------------------------------
--- Event Stage 0: Main Stage
DMPlexInterp 1 1.0 3.1186e+00 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0
DMPlexStratify 3 1.0 4.2802e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0
DMPlexSymmetrize 3 1.0 1.0806e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0
------------------------------------------------------------------------------------------------------------------------
Object Type Creations Destructions. Reports information only for process 0.
--- Event Stage 0: Main Stage
Container 2 1
Distributed Mesh 5 3
DM Label 20 8
Index Set 64 52
Section 17 12
Star Forest Graph 10 7
Discrete System 7 5
Weak Form 7 5
GraphPartitioner 3 2
Matrix 2 1
Vector 1 0
Viewer 2 1
========================================================================================================================
Average time to get PetscTime(): 1.8e-08
#PETSc Option Table entries:
-dm_view vtk:./ksp_data/abc.vtk # (source: command line)
-log_view # (source: command line)
#End of PETSc Option Table entries
Compiled without FORTRAN kernels
Compiled with full precision matrices (default)
sizeof(short) 2 sizeof(int) 4 sizeof(long) 8 sizeof(void*) 8 sizeof(PetscScalar) 8 sizeof(PetscInt) 4
Configure options: --with-debugging=0 --with-strict-petscerrorcode --download-openmpi --download-metis --download-exodusii --download-parmetis --download-netcdf --download-pnetcdf --download-hdf5 --download-zlib --download-superlu --download-superlu_dist --download-triangle --download-cmake --download-fblaslapack --download-slepc
-----------------------------------------
Libraries compiled on 2023-09-15 02:34:25 on DESKTOP-0H8HCOD
Machine characteristics: Linux-5.10.16.3-microsoft-standard-WSL2-x86_64-with-glibc2.29
Using PETSc directory: /home/qingfeng/petsc/optpetsc3-19-5/petsc
Using PETSc arch: arch-linux-c-opt
-----------------------------------------
Using C compiler: /home/qingfeng/petsc/optpetsc3-19-5/petsc/arch-linux-c-opt/bin/mpicc -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -g -O
Using Fortran compiler: /home/qingfeng/petsc/optpetsc3-19-5/petsc/arch-linux-c-opt/bin/mpif90 -fPIC -Wall -ffree-line-length-none -ffree-line-length-0 -Wno-lto-type-mismatch -Wno-unused-dummy-argument -g -O
-----------------------------------------
Using include paths: -I/home/qingfeng/petsc/optpetsc3-19-5/petsc/include -I/home/qingfeng/petsc/optpetsc3-19-5/petsc/arch-linux-c-opt/include
-----------------------------------------
Using C linker: /home/qingfeng/petsc/optpetsc3-19-5/petsc/arch-linux-c-opt/bin/mpicc
Using Fortran linker: /home/qingfeng/petsc/optpetsc3-19-5/petsc/arch-linux-c-opt/bin/mpif90
Using libraries: -Wl,-rpath,/home/qingfeng/petsc/optpetsc3-19-5/petsc/arch-linux-c-opt/lib -L/home/qingfeng/petsc/optpetsc3-19-5/petsc/arch-linux-c-opt/lib -lpetsc -Wl,-rpath,/home/qingfeng/petsc/optpetsc3-19-5/petsc/arch-linux-c-opt/lib -L/home/qingfeng/petsc/optpetsc3-19-5/petsc/arch-linux-c-opt/lib -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9 -lsuperlu -lsuperlu_dist -lflapack -lfblas -lexoIIv2for32 -lexodus -lnetcdf -lpnetcdf -lhdf5_hl -lhdf5 -lparmetis -lmetis -ltriangle -lm -lz -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread -lstdc++ -ldl
-----------------------------------------
The mesh information:
DM Object: Created by ICEMCFD - EXODUS II Interface 1 MPI process
type: plex
Created by ICEMCFD - EXODUS II Interface in 3 dimensions:
Number of 0-cells per rank: 134549
Number of 1-cells per rank: 841756
Number of 2-cells per rank: 1366008
Number of 3-cells per rank: 658801
Labels:
celltype: 4 strata with value/size (0 (134549), 6 (658801), 3 (1366008), 1 (841756))
depth: 4 strata with value/size (0 (134549), 1 (841756), 2 (1366008), 3 (658801))
Cell Sets: 2 strata with value/size (1 (604426), 2 (54375))
Vertex Sets: 5 strata with value/size (3 (481), 4 (27248), 5 (20560), 6 (653), 7 (2370))
Face Sets: 5 strata with value/size (8 (740), 9 (54206), 10 (40857), 11 (999), 12 (4534))
SMALLER: 1 strata with value/size (8 (740))
OUTER: 1 strata with value/size (9 (54206))
INNER: 1 strata with value/size (10 (40857))
BIGGER: 1 strata with value/size (11 (999))
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20231106/39cf5135/attachment-0001.html>
More information about the petsc-users
mailing list