On Sat, Mar 13, 2021 at 8:50 AM Pierre Jolivet <[email protected]> wrote:
> -pc_hypre_boomeramg_relax_type_all Jacobi => > Linear solve did not converge due to DIVERGED_INDEFINITE_PC iterations 3 > FYI, You need to use Chebyshev "KSP" with jacobi. > -pc_hypre_boomeramg_relax_type_all l1scaled-Jacobi => > OK, independently of the architecture it seems (Eric Docker image with 1 > or 2 threads or my macOS), but contraction factor is higher > Linear solve converged due to CONVERGED_RTOL iterations 8 > Linear solve converged due to CONVERGED_RTOL iterations 24 > Linear solve converged due to CONVERGED_RTOL iterations 26 > v. currently > Linear solve converged due to CONVERGED_RTOL iterations 7 > Linear solve converged due to CONVERGED_RTOL iterations 9 > Linear solve converged due to CONVERGED_RTOL iterations 10 > > Do we change this? Or should we force OMP_NUM_THREADS=1 for make test? > The default smoother is pretty good so I'd keep it in the test. Mark > > Thanks, > Pierre > > On 13 Mar 2021, at 2:26 PM, Mark Adams <[email protected]> wrote: > > 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> >> >> >> >> >
