Hypre uses a multiplicative smoother by default. It has a chebyshev smoother. That with a Jacobi PC should be thread invariant. Mark
On Sat, Mar 13, 2021 at 8:18 AM Pierre Jolivet <[email protected]> wrote: > > On 13 Mar 2021, at 9:17 AM, Pierre Jolivet <[email protected]> wrote: > > Hello Eric, > I’ve made an “interesting” discovery, so I’ll put back the list in c/c. > It appears the following snippet of code which uses Allreduce() + lambda > function + MPI_IN_PLACE is: > - Valgrind-clean with MPICH; > - Valgrind-clean with OpenMPI 4.0.5; > - not Valgrind-clean with OpenMPI 4.1.0. > I’m not sure who is to blame here, I’ll need to look at the MPI > specification for what is required by the implementors and users in that > case. > > In the meantime, I’ll do the following: > - update config/BuildSystem/config/packages/OpenMPI.py to use OpenMPI > 4.1.0, see if any other error appears; > - provide a hotfix to bypass the segfaults; > > > I can confirm that splitting the single Allreduce with my own MPI_Op into > two Allreduce with MAX and BAND fixes the segfaults with OpenMPI (*). > > - look at the hypre issue and whether they should be deferred to the hypre > team. > > > I don’t know if there is something wrong in hypre threading or if it’s > just a side effect of threading, but it seems that the number of threads > has a drastic effect on the quality of the PC. > By default, it looks that there are two threads per process with your > Docker image. > If I force OMP_NUM_THREADS=1, then I get the same convergence as in the > output file. > > Thanks, > Pierre > > (*) https://gitlab.com/petsc/petsc/-/merge_requests/3712 > > Thank you for the Docker files, they were really useful. > If you want to avoid oversubscription failures, you can edit the file > /opt/openmpi-4.1.0/etc/openmpi-default-hostfile and append the line: > localhost slots=12 > If you want to increase the timeout limit of PETSc test suite for each > test, you can add the extra flag in your command line TIMEOUT=180 (default > is 60, units are seconds). > > Thanks, I’ll ping you on GitLab when I’ve got something ready for you to > try, > Pierre > > <ompi.cxx> > > On 12 Mar 2021, at 8:54 PM, Eric Chamberland < > [email protected]> wrote: > > Hi Pierre, > > I now have a docker container reproducing the problems here. > > Actually, if I look at snes_tutorials-ex12_quad_singular_hpddm it fails > like this: > > not ok snes_tutorials-ex12_quad_singular_hpddm # Error code: 59 > # Initial guess > # L_2 Error: 0.00803099 > # Initial Residual > # L_2 Residual: 1.09057 > # Au - b = Au + F(0) > # Linear L_2 Residual: 1.09057 > # [d470c54ce086:14127] Read -1, expected 4096, errno = 1 > # [d470c54ce086:14128] Read -1, expected 4096, errno = 1 > # [d470c54ce086:14129] Read -1, expected 4096, errno = 1 > # [3]PETSC ERROR: > ------------------------------------------------------------------------ > # [3]PETSC ERROR: Caught signal number 11 SEGV: Segmentation > Violation, probably memory access out of range > # [3]PETSC ERROR: Try option -start_in_debugger or > -on_error_attach_debugger > # [3]PETSC ERROR: or see > https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind > # [3]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple > Mac OS X to find memory corruption errors > # [3]PETSC ERROR: likely location of problem given in stack below > # [3]PETSC ERROR: --------------------- Stack Frames > ------------------------------------ > # [3]PETSC ERROR: Note: The EXACT line numbers in the stack are not > available, > # [3]PETSC ERROR: INSTEAD the line number of the start of the > function > # [3]PETSC ERROR: is given. > # [3]PETSC ERROR: [3] buildTwo line 987 > /opt/petsc-main/include/HPDDM_schwarz.hpp > # [3]PETSC ERROR: [3] next line 1130 > /opt/petsc-main/include/HPDDM_schwarz.hpp > # [3]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > # [3]PETSC ERROR: Signal received > # [3]PETSC ERROR: [0]PETSC ERROR: > ------------------------------------------------------------------------ > > also ex12_quad_hpddm_reuse_baij fails with a lot more "Read -1, expected > ..." which I don't know where they come from...? > > Hypre (like in diff-snes_tutorials-ex56_hypre) is also having > DIVERGED_INDEFINITE_PC failures... > > Please see the 3 attached docker files: > > 1) fedora_mkl_and_devtools : the DockerFile which install fedore 33 with > gnu compilers and MKL and everything to develop. > > 2) openmpi: the DockerFile to bluid OpenMPI > > 3) petsc: The las DockerFile that build/install and test PETSc > > I build the 3 like this: > > docker build -t fedora_mkl_and_devtools -f fedora_mkl_and_devtools . > > docker build -t openmpi -f openmpi . > > docker build -t petsc -f petsc . > > Disclaimer: I am not a docker expert, so I may do things that are not > docker-stat-of-the-art but I am opened to suggestions... ;) > > I have just ran it on my portable (long) which have not enough cores, so > many more tests failed (should force --oversubscribe but don't know how > to). I will relaunch on my workstation in a few minutes. > > I will now test your branch! (sorry for the delay). > > Thanks, > > Eric > On 2021-03-11 9:03 a.m., Eric Chamberland wrote: > > Hi Pierre, > > ok, that's interesting! > > I will try to build a docker image until tomorrow and give you the exact > recipe to reproduce the bugs. > > Eric > > > On 2021-03-11 2:46 a.m., Pierre Jolivet wrote: > > > > On 11 Mar 2021, at 6:16 AM, Barry Smith <[email protected]> wrote: > > > Eric, > > Sorry about not being more immediate. We still have this in our active > email so you don't need to submit individual issues. We'll try to get to > them as soon as we can. > > > Indeed, I’m still trying to figure this out. > I realized that some of my configure flags were different than yours, > e.g., no --with-memalign. > I’ve also added SuperLU_DIST to my installation. > Still, I can’t reproduce any issue. > I will continue looking into this, it appears I’m seeing some valgrind > errors, but I don’t know if this is some side effect of OpenMPI not being > valgrind-clean (last time I checked, there was no error with MPICH). > > Thank you for your patience, > Pierre > > /usr/bin/gmake -f gmakefile test test-fail=1 > Using MAKEFLAGS: test-fail=1 > TEST > arch-linux2-c-opt-ompi/tests/counts/snes_tutorials-ex12_quad_hpddm_reuse_baij.counts > ok snes_tutorials-ex12_quad_hpddm_reuse_baij > ok diff-snes_tutorials-ex12_quad_hpddm_reuse_baij > TEST > arch-linux2-c-opt-ompi/tests/counts/ksp_ksp_tests-ex33_superlu_dist_2.counts > ok ksp_ksp_tests-ex33_superlu_dist_2 > ok diff-ksp_ksp_tests-ex33_superlu_dist_2 > TEST > arch-linux2-c-opt-ompi/tests/counts/ksp_ksp_tests-ex49_superlu_dist.counts > ok ksp_ksp_tests-ex49_superlu_dist+nsize-1herm-0_conv-0 > ok diff-ksp_ksp_tests-ex49_superlu_dist+nsize-1herm-0_conv-0 > ok ksp_ksp_tests-ex49_superlu_dist+nsize-1herm-0_conv-1 > ok diff-ksp_ksp_tests-ex49_superlu_dist+nsize-1herm-0_conv-1 > ok ksp_ksp_tests-ex49_superlu_dist+nsize-1herm-1_conv-0 > ok diff-ksp_ksp_tests-ex49_superlu_dist+nsize-1herm-1_conv-0 > ok ksp_ksp_tests-ex49_superlu_dist+nsize-1herm-1_conv-1 > ok diff-ksp_ksp_tests-ex49_superlu_dist+nsize-1herm-1_conv-1 > ok ksp_ksp_tests-ex49_superlu_dist+nsize-4herm-0_conv-0 > ok diff-ksp_ksp_tests-ex49_superlu_dist+nsize-4herm-0_conv-0 > ok ksp_ksp_tests-ex49_superlu_dist+nsize-4herm-0_conv-1 > ok diff-ksp_ksp_tests-ex49_superlu_dist+nsize-4herm-0_conv-1 > ok ksp_ksp_tests-ex49_superlu_dist+nsize-4herm-1_conv-0 > ok diff-ksp_ksp_tests-ex49_superlu_dist+nsize-4herm-1_conv-0 > ok ksp_ksp_tests-ex49_superlu_dist+nsize-4herm-1_conv-1 > ok diff-ksp_ksp_tests-ex49_superlu_dist+nsize-4herm-1_conv-1 > TEST > arch-linux2-c-opt-ompi/tests/counts/ksp_ksp_tutorials-ex50_tut_2.counts > ok ksp_ksp_tutorials-ex50_tut_2 > ok diff-ksp_ksp_tutorials-ex50_tut_2 > TEST > arch-linux2-c-opt-ompi/tests/counts/ksp_ksp_tests-ex33_superlu_dist.counts > ok ksp_ksp_tests-ex33_superlu_dist > ok diff-ksp_ksp_tests-ex33_superlu_dist > TEST > arch-linux2-c-opt-ompi/tests/counts/snes_tutorials-ex56_hypre.counts > ok snes_tutorials-ex56_hypre > ok diff-snes_tutorials-ex56_hypre > TEST > arch-linux2-c-opt-ompi/tests/counts/ksp_ksp_tutorials-ex56_2.counts > ok ksp_ksp_tutorials-ex56_2 > ok diff-ksp_ksp_tutorials-ex56_2 > TEST > arch-linux2-c-opt-ompi/tests/counts/snes_tutorials-ex17_3d_q3_trig_elas.counts > ok snes_tutorials-ex17_3d_q3_trig_elas > ok diff-snes_tutorials-ex17_3d_q3_trig_elas > TEST > arch-linux2-c-opt-ompi/tests/counts/snes_tutorials-ex12_quad_hpddm_reuse_threshold_baij.counts > ok snes_tutorials-ex12_quad_hpddm_reuse_threshold_baij > ok diff-snes_tutorials-ex12_quad_hpddm_reuse_threshold_baij > TEST > arch-linux2-c-opt-ompi/tests/counts/ksp_ksp_tutorials-ex5_superlu_dist_3.counts > not ok ksp_ksp_tutorials-ex5_superlu_dist_3 # Error code: 1 > # srun: error: Unable to create step for job 1426755: More processors > requested than permitted > ok ksp_ksp_tutorials-ex5_superlu_dist_3 # SKIP Command failed so no diff > TEST > arch-linux2-c-opt-ompi/tests/counts/ksp_ksp_tutorials-ex5f_superlu_dist.counts > ok ksp_ksp_tutorials-ex5f_superlu_dist # SKIP Fortran required for this > test > TEST > arch-linux2-c-opt-ompi/tests/counts/snes_tutorials-ex12_tri_parmetis_hpddm_baij.counts > ok snes_tutorials-ex12_tri_parmetis_hpddm_baij > ok diff-snes_tutorials-ex12_tri_parmetis_hpddm_baij > TEST > arch-linux2-c-opt-ompi/tests/counts/snes_tutorials-ex19_tut_3.counts > ok snes_tutorials-ex19_tut_3 > ok diff-snes_tutorials-ex19_tut_3 > TEST > arch-linux2-c-opt-ompi/tests/counts/snes_tutorials-ex17_3d_q3_trig_vlap.counts > ok snes_tutorials-ex17_3d_q3_trig_vlap > ok diff-snes_tutorials-ex17_3d_q3_trig_vlap > TEST > arch-linux2-c-opt-ompi/tests/counts/ksp_ksp_tutorials-ex5f_superlu_dist_3.counts > ok ksp_ksp_tutorials-ex5f_superlu_dist_3 # SKIP Fortran required for this > test > TEST > arch-linux2-c-opt-ompi/tests/counts/snes_tutorials-ex19_superlu_dist.counts > ok snes_tutorials-ex19_superlu_dist > ok diff-snes_tutorials-ex19_superlu_dist > TEST > arch-linux2-c-opt-ompi/tests/counts/snes_tutorials-ex56_attach_mat_nearnullspace-1_bddc_approx_hypre.counts > ok snes_tutorials-ex56_attach_mat_nearnullspace-1_bddc_approx_hypre > ok diff-snes_tutorials-ex56_attach_mat_nearnullspace-1_bddc_approx_hypre > TEST > arch-linux2-c-opt-ompi/tests/counts/ksp_ksp_tutorials-ex49_hypre_nullspace.counts > ok ksp_ksp_tutorials-ex49_hypre_nullspace > ok diff-ksp_ksp_tutorials-ex49_hypre_nullspace > TEST > arch-linux2-c-opt-ompi/tests/counts/snes_tutorials-ex19_superlu_dist_2.counts > ok snes_tutorials-ex19_superlu_dist_2 > ok diff-snes_tutorials-ex19_superlu_dist_2 > TEST > arch-linux2-c-opt-ompi/tests/counts/ksp_ksp_tutorials-ex5_superlu_dist_2.counts > not ok ksp_ksp_tutorials-ex5_superlu_dist_2 # Error code: 1 > # srun: error: Unable to create step for job 1426755: More processors > requested than permitted > ok ksp_ksp_tutorials-ex5_superlu_dist_2 # SKIP Command failed so no diff > TEST > arch-linux2-c-opt-ompi/tests/counts/snes_tutorials-ex56_attach_mat_nearnullspace-0_bddc_approx_hypre.counts > ok snes_tutorials-ex56_attach_mat_nearnullspace-0_bddc_approx_hypre > ok diff-snes_tutorials-ex56_attach_mat_nearnullspace-0_bddc_approx_hypre > TEST > arch-linux2-c-opt-ompi/tests/counts/ksp_ksp_tutorials-ex64_1.counts > ok ksp_ksp_tutorials-ex64_1 > ok diff-ksp_ksp_tutorials-ex64_1 > TEST > arch-linux2-c-opt-ompi/tests/counts/ksp_ksp_tutorials-ex5_superlu_dist.counts > not ok ksp_ksp_tutorials-ex5_superlu_dist # Error code: 1 > # srun: error: Unable to create step for job 1426755: More processors > requested than permitted > ok ksp_ksp_tutorials-ex5_superlu_dist # SKIP Command failed so no diff > TEST > arch-linux2-c-opt-ompi/tests/counts/ksp_ksp_tutorials-ex5f_superlu_dist_2.counts > ok ksp_ksp_tutorials-ex5f_superlu_dist_2 # SKIP Fortran required for this > test > > Barry > > > On Mar 10, 2021, at 11:03 PM, Eric Chamberland < > [email protected]> wrote: > > Barry, > > to get a some follow up on --with-openmp=1 failures, shall I open gitlab > issues for: > > a) all hypre failures giving DIVERGED_INDEFINITE_PC > > b) all superlu_dist failures giving different results with initia and > "Exceeded timeout limit of 60 s" > > c) hpddm failures "free(): invalid next size (fast)" and "Segmentation > Violation" > > d) all tao's "Exceeded timeout limit of 60 s" > > I don't see how I could do all these debugging by myself... > > Thanks, > > Eric > > > > -- > Eric Chamberland, ing., M. Ing > Professionnel de recherche > GIREF/Université Laval > (418) 656-2131 poste 41 22 42 > > -- > Eric Chamberland, ing., M. Ing > Professionnel de recherche > GIREF/Université Laval > (418) 656-2131 poste 41 22 42 > > <fedora_mkl_and_devtools.txt><openmpi.txt><petsc.txt> > > > >
