Hi, OK. So this is clear now. Maybe you will be able to help the answer the question I raised some time ago, why, when submitting a slurm job and setting different number of --cpus-per-task, the execution times of ksp solver (gmres type) vary when max number of iterations set to 100.000 and ksp, when finished, returns ksp.getIterationNumber() (in petsc4py) equal to 900 (for some cases) and 100.000 for other. It looks like number of cpus per task influence the number of steps the solver solves the equation. Is it possible at all?
Best, Damian W liście datowanym 1 lipca 2017 (22:23:19) napisano: >> On Jul 1, 2017, at 3:15 PM, Damian Kaliszan <[email protected]> wrote: >> >> Hi, >> So... - - with-openmp=0/1 configuration option seems to be useless?... > It merely enables the compiler flags for compiling with OpenMP; > for example if your code has OpenMP in it. >> In one of my previous messages I wrote that, when openmp enabled, and >> OMP_NUM_THREADS set, I notice different timings for ksp solver. Strange....? > For the PETSc part yes number of threads shouldn't matter since PETSc > would only use 1. >> >> >> Best, >> Damian >> W dniu 1 lip 2017, o 00:50, użytkownik Barry Smith <[email protected]> >> napisał: >> >> The current version of PETSc does not use OpenMP, you are free to use >> OpenMP in your portions of the code of course. If you want PETSc using >> OpenMP you have to use the old, unsupported version of PETSc. We never found >> any benefit to using OpenMP. >> >> Barry >> >> On Jun 30, 2017, at 5:40 PM, Danyang Su <[email protected]> wrote: >> >> Dear All, >> >> I recalled there was OpenMP available for PETSc for the old development >> version. When google "petsc hybrid mpi openmp", there returned some papers >> about this feature. My code was first parallelized using OpenMP and then >> redeveloped using PETSc, with OpenMP kept but not used together with MPI. >> Before retesting the code using hybrid mpi-openmp, I picked one PETSc >> example ex10 by adding "omp_set_num_threads(max_threads);" under >> PetscInitialize. >> >> The PETSc is the current development version configured as follows >> >> --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --with-debugging=0 >> --CFLAGS=-fopenmp --CXXFLAGS=-fopenmp --FFLAGS=-fopenmp COPTFLAGS="-O3 >> -march=native -mtune=native" CXXOPTFLAGS="-O3 -march=native -mtune=native" >> FOPTFLAGS="-O3 -march=native -mtune=native" --with-large-file-io=1 >> --download-cmake=yes --download-mumps --download-scalapack >> --download-parmetis --download-metis --download-ptscotch >> --download-fblaslapack --download-mpich --download-hypre >> --download-superlu_dist --download-hdf5=yes --with-openmp --with-threadcomm >> --with-pthreadclasses --with-openmpclasses >> >> The code can be successfully compiled. However, when I run the code with >> OpenMP, it does not work, the time shows no change in performance if 1 or 2 >> threads per processor is used. Also, the CPU/Threads usage indicates that no >> thread is used. >> >> I just wonder if OpenMP is still available in the latest version, though it >> is not recommended to use. >> >> mpiexec -n 2 ./ex10 -f0 mat_rhs_pc_nonzero/a_react_in_2.bin -rhs >> mat_rhs_pc_nonzero/b_react_in_2.bin -ksp_rtol 1.0e-20 -ksp_monitor >> -ksp_error_if_not_converged -sub_pc_factor_shift_type nonzero -mat_view >> ascii::ascii_info -log_view -max_threads 1 -threadcomm_type openmp >> -threadcomm_nthreads 1 >> >> KSPSolve 1 1.0 8.9934e-01 1.0 1.03e+09 1.0 7.8e+01 3.6e+04 >> 7.8e+01 69 97 89 6 76 89 97 98 98 96 2290 >> PCSetUp 2 1.0 8.9590e-02 1.0 2.91e+07 1.0 0.0e+00 0.0e+00 >> 0.0e+00 7 3 0 0 0 9 3 0 0 0 648 >> PCSetUpOnBlocks 2 1.0 8.9465e-02 1.0 2.91e+07 1.0 0.0e+00 0.0e+00 >> 0.0e+00 7 3 0 0 0 9 3 0 0 0 649 >> PCApply 40 1.0 3.1993e-01 1.0 2.70e+08 1.0 0.0e+00 0.0e+00 >> 0.0e+00 24 25 0 0 0 32 25 0 0 0 1686 >> >> mpiexec -n 2 ./ex10 -f0 mat_rhs_pc_nonzero/a_react_in_2.bin -rhs >> mat_rhs_pc_nonzero/b_react_in_2.bin -ksp_rtol 1.0e-20 -ksp_monitor >> -ksp_error_if_not_converged -sub_pc_factor_shift_type nonzero -mat_view >> ascii::ascii_info -log_view -max_threads 2 -threadcomm_type openmp >> -threadcomm_nthreads 2 >> >> KSPSolve 1 1.0 8.9701e-01 1.0 1.03e+09 1.0 7.8e+01 3.6e+04 >> 7.8e+01 69 97 89 6 76 89 97 98 98 96 2296 >> PCSetUp 2 1.0 8.7635e-02 1.0 2.91e+07 1.0 0.0e+00 0.0e+00 >> 0.0e+00 7 3 0 0 0 9 3 0 0 0 663 >> PCSetUpOnBlocks 2 1.0 8.7511e-02 1.0 2.91e+07 1.0 0.0e+00 0.0e+00 >> 0.0e+00 7 3 0 0 0 9 3 0 0 0 664 >> PCApply 40 1.0 3.1878e-01 1.0 2.70e+08 1.0 0.0e+00 0.0e+00 >> 0.0e+00 24 25 0 0 0 32 25 0 0 0 1692 >> >> Thanks and regards, >> >> Danyang >> >> >> <ex10.c><makefile.txt> >> ------------------------------------------------------- Damian Kaliszan Poznan Supercomputing and Networking Center HPC and Data Centres Technologies ul. Jana Pawła II 10 61-139 Poznan POLAND phone (+48 61) 858 5109 e-mail [email protected] www - http://www.man.poznan.pl/ -------------------------------------------------------
