March 2021 - petsc-dev - mailman3.cels.anl.gov

Re: [petsc-dev] Petsc "make test" have more failures for --with-openmp=1
by Barry Smith 02 Mar '21

02 Mar '21

> On Mar 2, 2021, at 9:09 PM, Eric Chamberland <Eric.Chamberland(a)giref.ulaval.ca> wrote: > > Hi Barry, > > My ultimate goal is to compile a single PETSc version that is CUDA aware. That means that I would like a single binary of our FE code (that will be distributed on Compute Canada clusters) so my users can do CPU or GPU computations. > > However, if activating GPU implies activating OpenMP wich implies having many bugs with our code usages (with mumps or Hypre for example), it is a no-go for us right now... or at least, I have to deliver a CUDA only version.. > > > > #1: I always have the feeling that something may go wrong with MKL linking. I know about the link advisor, but... What do you think this is related to? > It could be related to MKL but it could also be due to problems with Scalapack when used with OpenMP. Do you need Scalapack? Maybe you want to use it since it used by MUMPS? > > #2: I can deal with that! :) > > > > #3: I am not sure if this output is due to the way I configure OpenMPI/3.x: > > $ ./configure --prefix=/opt/openmpi-3.x_debug --enable-debug --enable-picky CXXFLAGS=-std=c++14 --with-wrapper-cxxflags=-std=c++14 --with-cma > > or this export: > > export OMPI_MCA_plm_base_verbose=5 > > which I left there to track an intermittent bug at singleton startup (https://www.mail-archive.com/[email protected]/msg19568.html <https://www.mail-archive.com/[email protected]/msg19568.html>).. > > I will remove this now, 4 years later, it does not happen anymore... But I don't think it should be harmful for PETSc tests, is it? > I am guessing that this is just informative information that does not indicate a problem. But I am confused why it appears only occasionally, presumably it is related to the current state of the system. But the PETSc tests have no way of knowing that this type of output to stdout or stderr is "harmless" informative information versus am indication of something being seriously broken. One way of checking PETSc tests in make test is to process the output and look for something that is not "normal" and this is definitely not normal. I think you need to turn off the verbosity when running PETSc tests and then hopefully this particular problem will go away. ok tao_constrained_tutorials-toyf_1 not ok diff-tao_constrained_tutorials-toyf_1 # Error code: 1 # 0a1,17 # > [zorg:09243] [[INVALID],INVALID] plm:rsh_lookup on agent ssh : rsh path NULL # > [zorg:09243] plm:base:set_hnp_name: initial bias 9243 nodename hash 810220270 # > [zorg:09243] plm:base:set_hnp_name: final jobfam 61119 # > [zorg:09243] [[61119,0],0] plm:rsh_setup on agent ssh : rsh path NULL # > [zorg:09243] [[61119,0],0] plm:base:receive start comm # > [zorg:09243] [[61119,0],0] plm:base:setup_job # > [zorg:09243] [[61119,0],0] plm:base:setup_vm # > [zorg:09243] [[61119,0],0] plm:base:setup_vm creating map # > [zorg:09243] [[61119,0],0] setup:vm: working unmanaged allocation # > [zorg:09243] [[61119,0],0] using default hostfile /opt/openmpi-3.x_debug/etc/openmpi-default-hostfile # > [zorg:09243] [[61119,0],0] plm:base:setup_vm only HNP in allocation # > [zorg:09243] [[61119,0],0] plm:base:setting slots for node zorg by cores # > [zorg:09243] [[61119,0],0] complete_setup on job [61119,1] # > [zorg:09243] [[61119,0],0] plm:base:launch_apps for job [61119,1] # > [zorg:09243] [[61119,0],0] plm:base:launch wiring up iof for job [61119,1] # > [zorg:09243] [[61119,0],0] plm:base:launch job [61119,1] is not a dynamic spawn # > [zorg:09243] [[61119,0],0] plm:base:launch [61119,1] registered # 58a76,77 # > [zorg:09243] [[61119,0],0] plm:base:orted_cmd sending orted_exit commands # > [zorg:09243] [[61119,0],0] plm:base:receive stop comm > > #4: I do have a default choice for L2 projections which uses HYPRE BoomerAMG preconditioning...that now ends with KSP_DIVERGED_INDEFINITE_PC, so this is definitely a problem... > > #5: we do sometime use superlu-dist > > I'm afraid for the possibly MUMPS, Superlu_DIST and hypre problems you need to debug them one at a time by running the particular troublesome example in the debugger to determine the problem. It could also be due to the relationship between the MKL and the OpenMP implementation. I don't know exactly how MKL's multi-threaded code runs in relation to OpenML and certainly if the compiler is providing a different OpenMP than MKL is using it will not work. Under most circumstances if you are using MKL with threading and PETSc you likely only want to use one MKL thread since PETSc already handles the maximum parallelism with MPI and there are no "extra" processors available to parallelize the BLAS/LAPACK called from PETSc for more performance inside the MKL. This may not be true if you are using MUMPS which makes things far more complicated. OpenMP is complicated in the context of PETSc and several external packages because different packages may use it in different ways that require different tuning and I won't know the tuning for each. Barry > #6: we do start looking at DD solvers like hpddm... > > So my killer question is: in regard of to the amount of work to have all these external packages fixed, is it possible to activate OpenMP only for the CUDA part? > > Thanks, > > Eric > > On 2021-03-02 3:47 p.m., Barry Smith wrote: >> >> Eric, >> >> Thanks for the detailed information. >> >> I have cc:ed Pierre so he can look at the HPDDM failures. >> >> >>> On Mar 2, 2021, at 2:14 PM, Eric Chamberland <Eric.Chamberland(a)giref.ulaval.ca <mailto:[email protected]>> wrote: >>> >>> Hi, >>> >>> It all started when I wanted to test PETSC/CUDA compatibility for our code. >>> >>> I had to activate --with-openmp to configure with --with-cuda=1 successfully. >>> >>> >> Certain packages like SuperLU_DIST require --with-openmp if using --with-cuda=1 but PETSc's own use of CUDA as well as some other packages do not require the --with-openmp. >> >>> I then saw that PETSC_HAVE_OPENMP is used at least in MUMPS (and some other places). >>> >>> So, I configured and tested petsc with openmp activated, without CUDA. >>> >>> The first thing I see is that our code CI pipelines now fails for many tests. >>> >>> After looking deeper, it seems that PETSc itself fails many tests when I activate openmp! >>> >>> Here are all the configurations I have results for, after/before activating OpenMP for PETSc: >> >> There seem to be several distinct issues >> >> 1) failures inside Scalapack. >> >> 2) possibly slightly different convergence rates for some examples changing the number of iterations slightly in PETSc. >> >> 3) trouble initializing something outside of PETSc, almost for sure not related to PETSc >> >> [zorg:08517] [[INVALID],INVALID] plm:rsh_lookup on agent ssh : rsh path NULL >> # [zorg:08517] plm:base:set_hnp_name: initial bias 8517 nodename hash 810220270 >> # [zorg:08517] plm:base:set_hnp_name: final jobfam 60385 >> # [zorg:08517] [[60385,0],0] plm:rsh_setup on agent ssh : rsh path NULL >> # [zorg:08517] [[60385,0],0] plm:base:receive start comm >> # [zorg:08517] [[60385,0],0] plm:base:setup_job >> # [zorg:08517] [[60385,0],0] plm:base:setup_vm >> 4) problem with a hypre run Linear solve did not converge due to DIVERGED_INDEFINITE_PC iterations 3 , again not likely a PETSc issue but a hypre and OpenMP issue >> >> 5) Different results for initia inside an external package >> >> # 1c1 >> # < MatInertia: nneg: 17, nzero: 0, npos: 83 >> # --- >> # > MatInertia: nneg: 21, nzero: 0, npos: 79 >> TEST arch-linux-c-debug/tests/counts/ksp_ksp_tests-ex33_superlu_dist_2.counts >> ok ksp_ksp_tests-ex33_superlu_dist_2 >> not ok diff-ksp_ksp_tests-ex33_superlu_dist_2 # Error code: 1 >> # 1c1 >> # < MatInertia: nneg: 17, nzero: 0, npos: 83 >> # --- >> # > MatInertia: nneg: 25, nzero: 0, npos: 75 >> >> >> 6) problems with the external package hpddm >> >> not ok snes_tutorials-ex12_quad_hpddm_reuse_baij # Error code: 139 >> # 0 SNES Function norm 21.3344 >> # [0]PETSC ERROR: ------------------------------------------------------------------------ >> # [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range >> # [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger >> # [0]PETSC ERROR: or see https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind <https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind> >> # [0]PETSC ERROR: or try http://valgrind.org <http://valgrind.org/> on GNU/linux and Apple Mac OS X to find memory corruption errors >> # [0]PETSC ERROR: likely location of problem given in stack below >> # [0]PETSC ERROR: --------------------- Stack Frames ------------------------------------ >> # [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available, >> # [0]PETSC ERROR: INSTEAD the line number of the start of the function >> # [0]PETSC ERROR: is given. >> # [0]PETSC ERROR: [0] constructionMatrix line 313 /opt/petsc-main_debug/include/HPDDM_coarse_operator_impl.hpp >> # [0]PETSC ERROR: [0] construction line 256 /opt/petsc-main_debug/include/HPDDM_coarse_operator_impl.hpp >> # [0]PETSC ERROR: [0] buildTwo line 987 /opt/petsc-main_debug/include/HPDDM_schwarz.hpp >> # [0]PETSC ERROR: [0] next line 1130 /opt/petsc-main_debug/include/HPDDM_schwarz.hpp >> # [0]PETSC ERROR: [0] PCSetUp_HPDDM line 746 /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-main-debug/src/ksp/pc/impls/hpddm/hpddm.cxx >> # [0]PETSC ERROR: [0] PCSetUp line 974 /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-main-debug/src/ksp/pc/interface/precon.c >> # [0]PETSC ERROR: [0] KSPSetUp line 319 /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-main-debug/src/ksp/ksp/interface/itfunc.c >> # [0]PETSC ERROR: [0] KSPSolve_Private line 808 /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-main-debug/src/ksp/ksp/interface/itfunc.c >> # [0]PETSC ERROR: [0] KSPSolve line 1080 /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-main-debug/src/ksp/ksp/interface/itfunc.c >> # [0]PETSC ERROR: [0] SNESSolve_NEWTONLS line 144 /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-main-debug/src/snes/impls/ls/ls.c >> # [0]PETSC ERROR: [0] SNESSolve line 4533 /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-main-debug/src/snes/interface/snes.c >> # [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- >> # [0]PETSC ERROR: Signal received >> # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html <https://www.mcs.anl.gov/petsc/documentation/faq.html> for trouble shooting. >> >> PETSc itself does not use OpenMP so turning on OpenMP for pure PETSc should generate no errors except possibly small changes in iteration rates due to the different way the floating point operations in MKL are done. >> >> We don't see much use for OpenMP so rarely turn it on. What is your end goal, to use PETSc on CUDA (for each you can keep OpenMP off) or something else? >> >> >> Barry >> >> >>> ============================================================================== >>> >>> ============================================================================== >>> >>> For petsc/master + OpenMPI 4.0.4 + MKL 2019.4.243: >>> >>> With OpenMP=1 >>> >>> https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.03.02.02h00m02s_m… <https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.03.02.02h00m02s_m…> >>> https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.03.02.02h00m02s_c… <https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.03.02.02h00m02s_c…> >>> # ------------- >>> # Summary >>> # ------------- >>> # FAILED snes_tutorials-ex12_quad_hpddm_reuse_baij diff-ksp_ksp_tests-ex33_superlu_dist_2 diff-ksp_ksp_tests-ex49_superlu_dist+nsize-1herm-0_conv-0 diff-ksp_ksp_tests-ex49_superlu_dist+nsize-1herm-0_conv-1 diff-ksp_ksp_tests-ex49_superlu_dist+nsize-1herm-1_conv-0 diff-ksp_ksp_tests-ex49_superlu_dist+nsize-1herm-1_conv-1 diff-ksp_ksp_tests-ex49_superlu_dist+nsize-4herm-0_conv-0 diff-ksp_ksp_tests-ex49_superlu_dist+nsize-4herm-0_conv-1 diff-ksp_ksp_tests-ex49_superlu_dist+nsize-4herm-1_conv-0 diff-ksp_ksp_tests-ex49_superlu_dist+nsize-4herm-1_conv-1 ksp_ksp_tutorials-ex50_tut_2 diff-ksp_ksp_tests-ex33_superlu_dist diff-snes_tutorials-ex56_hypre snes_tutorials-ex17_3d_q3_trig_elas snes_tutorials-ex12_quad_hpddm_reuse_threshold_baij ksp_ksp_tutorials-ex5_superlu_dist_3 ksp_ksp_tutorials-ex5f_superlu_dist snes_tutorials-ex12_tri_parmetis_hpddm_baij diff-snes_tutorials-ex19_tut_3 mat_tests-ex242_3 snes_tutorials-ex17_3d_q3_trig_vlap ksp_ksp_tutorials-ex5f_superlu_dist_3 snes_tutorials-ex19_superlu_dist diff-snes_tutorials-ex56_attach_mat_nearnullspace-1_bddc_approx_hypre diff-ksp_ksp_tutorials-ex49_hypre_nullspace ts_tutorials-ex18_p1p1_xper_ref ts_tutorials-ex18_p1p1_xyper_ref snes_tutorials-ex19_superlu_dist_2 ksp_ksp_tutorials-ex5_superlu_dist_2 diff-snes_tutorials-ex56_attach_mat_nearnullspace-0_bddc_approx_hypre ksp_ksp_tutorials-ex64_1 ksp_ksp_tutorials-ex5_superlu_dist ksp_ksp_tutorials-ex5f_superlu_dist_2 >>> # success 8275/10003 tests (82.7%) >>> # failed 33/10003 tests (0.3%) >>> With OpenMP=0 >>> >>> https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.02.26.02h00m16s_m… <https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.02.26.02h00m16s_m…> >>> https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.02.26.02h00m16s_c… <https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.02.26.02h00m16s_c…> >>> # ------------- >>> # Summary >>> # ------------- >>> # FAILED tao_constrained_tutorials-tomographyADMM_6 snes_tutorials-ex17_3d_q3_trig_elas mat_tests-ex242_3 snes_tutorials-ex17_3d_q3_trig_vlap tao_leastsquares_tutorials-tomography_1 tao_constrained_tutorials-tomographyADMM_5 >>> # success 8262/9983 tests (82.8%) >>> # failed 6/9983 tests (0.1%) >>> ============================================================================== >>> >>> ============================================================================== >>> >>> For OpenMPI 3.1.x/master: >>> >>> With OpenMP=1: >>> >>> https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.03.01.22h00m01s_make_test.l… <https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.03.01.22h00m01s_make_test.l…> >>> https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.03.01.22h00m01s_configure.l… <https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.03.01.22h00m01s_configure.l…> >>> # ------------- >>> # Summary >>> # ------------- >>> # FAILED mat_tests-ex242_3 mat_tests-ex242_2 diff-mat_tests-ex219f_1 diff-dm_tutorials-ex11f90_1 ksp_ksp_tutorials-ex5_superlu_dist_3 diff-ksp_ksp_tutorials-ex49_hypre_nullspace ksp_ksp_tutorials-ex5f_superlu_dist_3 snes_tutorials-ex17_3d_q3_trig_vlap diff-snes_tutorials-ex56_attach_mat_nearnullspace-1_bddc_approx_hypre diff-snes_tutorials-ex19_tut_3 diff-snes_tutorials-ex56_hypre diff-snes_tutorials-ex56_attach_mat_nearnullspace-0_bddc_approx_hypre tao_leastsquares_tutorials-tomography_1 tao_constrained_tutorials-tomographyADMM_4 tao_constrained_tutorials-tomographyADMM_6 diff-tao_constrained_tutorials-toyf_1 >>> # success 8142/9765 tests (83.4%) >>> # failed 16/9765 tests (0.2%) >>> With OpenMP=0: >>> >>> https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.02.28.22h00m02s_make_test.l… <https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.02.28.22h00m02s_make_test.l…> >>> https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.02.28.22h00m02s_configure.l… <https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.02.28.22h00m02s_configure.l…> >>> # ------------- >>> # Summary >>> # ------------- >>> # FAILED mat_tests-ex242_3 mat_tests-ex242_2 diff-mat_tests-ex219f_1 diff-dm_tutorials-ex11f90_1 ksp_ksp_tutorials-ex56_2 snes_tutorials-ex17_3d_q3_trig_vlap tao_leastsquares_tutorials-tomography_1 tao_constrained_tutorials-tomographyADMM_4 diff-tao_constrained_tutorials-toyf_1 >>> # success 8151/9767 tests (83.5%) >>> # failed 9/9767 tests (0.1%) >>> ============================================================================== >>> >>> ============================================================================== >>> >>> For OpenMPI 4.0.x/master: >>> >>> With OpenMP=1: >>> >>> https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.03.01.20h00m01s_make_test.l… <https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.03.01.20h00m01s_make_test.l…> >>> https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.03.01.20h00m01s_configure.l… <https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.03.01.20h00m01s_configure.l…> >>> # FAILED snes_tutorials-ex17_3d_q3_trig_elas snes_tutorials-ex19_hypre ksp_ksp_tutorials-ex56_2 tao_leastsquares_tutorials-tomography_1 tao_constrained_tutorials-tomographyADMM_5 mat_tests-ex242_3 ksp_ksp_tutorials-ex55_hypre ksp_ksp_tutorials-ex5_superlu_dist_2 tao_constrained_tutorials-tomographyADMM_6 snes_tutorials-ex56_hypre snes_tutorials-ex56_attach_mat_nearnullspace-0_bddc_approx_hypre ksp_ksp_tutorials-ex5f_superlu_dist_3 ksp_ksp_tutorials-ex34_hyprestruct diff-ksp_ksp_tutorials-ex49_hypre_nullspace snes_tutorials-ex56_attach_mat_nearnullspace-1_bddc_approx_hypre ksp_ksp_tutorials-ex5f_superlu_dist ksp_ksp_tutorials-ex5f_superlu_dist_2 ksp_ksp_tutorials-ex5_superlu_dist snes_tutorials-ex19_tut_3 snes_tutorials-ex19_superlu_dist ksp_ksp_tutorials-ex50_tut_2 snes_tutorials-ex17_3d_q3_trig_vlap ksp_ksp_tutorials-ex5_superlu_dist_3 snes_tutorials-ex19_superlu_dist_2 tao_constrained_tutorials-tomographyADMM_4 ts_tutorials-ex26_2 >>> # success 8125/9753 tests (83.3%) >>> # failed 26/9753 tests (0.3%) >>> With OpenMP=0 >>> >>> https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.02.28.20h00m04s_make_test.l… <https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.02.28.20h00m04s_make_test.l…> >>> https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.02.28.20h00m04s_configure.l… <https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.02.28.20h00m04s_configure.l…> >>> # FAILED mat_tests-ex242_3 >>> # success 8174/9777 tests (83.6%) >>> # failed 1/9777 tests (0.0%) >>> >>> ============================================================================== >>> >>> ============================================================================== >>> >>> Is that known and normal? >>> >>> In all cases, I am using MKL and I suspect it may come from there... :/ >>> >>> I also saw a second problem, "make test" fails to compile petsc examples on older versions of MKL (but that's less important for me, I just upgraded to OneAPI to avoid this, but you may want to know): >>> >>> https://giref.ulaval.ca/~cmpgiref/dernier_ompi/2021.03.02.02h16m01s_make_te… <https://giref.ulaval.ca/~cmpgiref/dernier_ompi/2021.03.02.02h16m01s_make_te…> >>> https://giref.ulaval.ca/~cmpgiref/dernier_ompi/2021.03.02.02h16m01s_configu… <https://giref.ulaval.ca/~cmpgiref/dernier_ompi/2021.03.02.02h16m01s_configu…> >>> 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

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Re: [petsc-dev] Commit squashing in MR
by Satish Balay 02 Mar '21

02 Mar '21

On Wed, 3 Mar 2021, Blaise A Bourdin wrote: > Hi, > > This is not technically a petsc question. > It would be great to have a short section in the PETSc integration workflow document explaining how to squash commits in a MR for git-impaired developers like me. > > Anybody wants to pitch in, or explain me how to do this? To squash commits - I use the 'squash' action in 'git rebase -i HASH' and figure out the HASH to use from 'gitk main..branch' [as git rebase requires the commit prior to the first commit of interest] git provides many ways of modifying the branch (and the rebase topic is very generic) so I think its best to rely on proper git docs/tutorials [and its not really specific to petsc workflow] Satish > > Regards, > Blaise > >

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Re: [petsc-dev] Commit squashing in MR
by Mark Adams 02 Mar '21

02 Mar '21

Ah, 'git graph' I will try that next time. I use 'git rebase -i HEAD~N', but you need an N. After you 'git rebase origin/main' you get other commits interspersed in with yours, so I try to rebase -i before rebasing over main. Then rebase over main and you have a clean and updated branch. Pick N to be large enough to cover the commits that you want to clean up. Don't touch the ones that are not yours from main, the last time you rebased over main. On Tue, Mar 2, 2021 at 10:02 PM Junchao Zhang <junchao.zhang(a)gmail.com> wrote: > I am a naive git user, so I use interactive git rebase. Suppose I am on > the branch I want to modify, > > 1) Use git graph to locate an upstream commit to be used as the base > $ git graph > * 0d5433e9 (HEAD -> jczhang/sf-change-api) SF: rename SFCreateEmbeddedSF > to SFCreateEmbeddedRootSF > * e7314fbb SF: add an MPI_Op argument to SFBcast > * 83df288d Replace MPIU_REPLACE with MPI_REPLACE > * b434c516 Merge branch > 'barry/2021-02-02/petscsf-communication-specific' into 'main' > |\ > | * 62152ded (barry/2021-02-02/petscsf-communication-specific) > PetscSFView() never called viewer for the specific type (bug), hence many > output files were incorrect. > * | a4f5d9b4 Merge branch 'jose/upgrade-magma' into 'main' > > 2) Suppose we choose b434c516 as the base. All commits we want to squash > are after it. Do interactive git rebase. It shows a screen for you to > edit. Read the help, which is helpful for new users > $ git rebase -i b434c516 > pick 83df288d Replace MPIU_REPLACE with MPI_REPLACE > pick e7314fbb SF: add an MPI_Op argument to SFBcast > pick 0d5433e9 SF: rename SFCreateEmbeddedSF to SFCreateEmbeddedRootSF > > # Rebase b434c516..0d5433e9 onto b434c516 (3 commands) > # > # Commands: > # p, pick <commit> = use commit > # r, reword <commit> = use commit, but edit the commit message > # e, edit <commit> = use commit, but stop for amending > # s, squash <commit> = use commit, but meld into previous commit > # f, fixup <commit> = like "squash", but discard this commit's log message > # x, exec <command> = run command (the rest of the line) using shell > # b, break = stop here (continue rebase later with 'git rebase --continue') > # d, drop <commit> = remove commit > # l, label <label> = label current HEAD with a name > # t, reset <label> = reset HEAD to a label > # m, merge [-C <commit> | -c <commit>] <label> [# <oneline>] > # . create a merge commit using the original merge commit's > # . message (or the oneline, if no original merge commit was > # . specified). Use -c <commit> to reword the commit message. > # > # These lines can be re-ordered; they are executed from top to bottom. > # > # If you remove a line here THAT COMMIT WILL BE LOST. > # > # However, if you remove everything, the rebase will be aborted. > # > # Note that empty commits are commented out > > 3) Suppose we want to squash the last two commits to 83df288d, replace > their pick with s (or f, see the help for difference), save and exit the > screen > pick 83df288d Replace MPIU_REPLACE with MPI_REPLACE > s e7314fbb SF: add an MPI_Op argument to SFBcast > s 0d5433e9 SF: rename SFCreateEmbeddedSF to SFCreateEmbeddedRootSF > > A new screen shows up > > # This is a combination of 3 commits. > # This is the 1st commit message: > > Replace MPIU_REPLACE with MPI_REPLACE > > Since we believe all MPI implementations support MPI_REPLACE > > # This is the commit message #2: > > SF: add an MPI_Op argument to SFBcast > > # This is the commit message #3: > > SF: rename SFCreateEmbeddedSF to SFCreateEmbeddedRootSF > > # Please enter the commit message for your changes. Lines starting > # with '#' will be ignored, and an empty message aborts the commit. > > 4) Edit the commit message as you want, save and exit, done! > > --Junchao Zhang > > > On Tue, Mar 2, 2021 at 6:19 PM Blaise A Bourdin <bourdin(a)lsu.edu> wrote: > >> Hi, >> >> This is not technically a petsc question. >> It would be great to have a short section in the PETSc integration >> workflow document explaining how to squash commits in a MR for git-impaired >> developers like me. >> >> Anybody wants to pitch in, or explain me how to do this? >> >> Regards, >> Blaise >> >> -- >> A.K. & Shirley Barton Professor of Mathematics >> Adjunct Professor of Mechanical Engineering >> Adjunct of the Center for Computation & Technology >> Louisiana State University, Lockett Hall Room 344, Baton Rouge, LA 70803, >> USA >> Tel. +1 (225) 578 1612, Fax +1 (225) 578 4276 Web >> http://www.math.lsu.edu/~bourdin >> >>

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Re: [petsc-dev] Petsc "make test" have more failures for --with-openmp=1
by Eric Chamberland 02 Mar '21

02 Mar '21

Hi Barry, My ultimate goal is to compile a single PETSc version that is CUDA aware. That means that I would like a single binary of our FE code (that will be distributed on Compute Canada clusters) so my users can do CPU or GPU computations. However, if activating GPU implies activating OpenMP wich implies having many bugs with our code usages (with mumps or Hypre for example), it is a no-go for us right now... or at least, I have to deliver a CUDA only version.. #1: I always have the feeling that something may go wrong with MKL linking. I know about the link advisor, but... What do you think this is related to? #2: I can deal with that! :) #3: I am not sure if this output is due to the way I configure OpenMPI/3.x: $ ./configure --prefix=/opt/openmpi-3.x_debug --enable-debug --enable-picky CXXFLAGS=-std=c++14 --with-wrapper-cxxflags=-std=c++14 --with-cma or this export: export OMPI_MCA_plm_base_verbose=5 which I left there to track an intermittent bug at singleton startup (https://www.mail-archive.com/[email protected]/msg19568.html) I will remove this now, 4 years later, it does not happen anymore... But I don't think it should be harmful for PETSc tests, is it? #4: I do have a default choice for L2 projections which uses HYPRE BoomerAMG preconditioning...that now ends with KSP_DIVERGED_INDEFINITE_PC, so this is definitely a problem... #5: we do sometime use superlu-dist #6: we do start looking at DD solvers like hpddm... So my killer question is: in regard of to the amount of work to have all these external packages fixed, is it possible to activate OpenMP only for the CUDA part? Thanks, Eric On 2021-03-02 3:47 p.m., Barry Smith wrote: > > Eric, > > Thanks for the detailed information. > > I have cc:ed Pierre so he can look at the HPDDM failures. > > >> On Mar 2, 2021, at 2:14 PM, Eric Chamberland >> <Eric.Chamberland(a)giref.ulaval.ca >> <mailto:[email protected]>> wrote: >> >> Hi, >> >> It all started when I wanted to test PETSC/CUDA compatibility for our >> code. >> >> I had to activate --with-openmp to configure with --with-cuda=1 >> successfully. >> >> > Certain packages like SuperLU_DIST require --with-openmp if using > --with-cuda=1 but PETSc's own use of CUDA as well as some other > packages do not require the --with-openmp. > >> I then saw that PETSC_HAVE_OPENMP is used at least in MUMPS (and >> some other places). >> >> So, I configured and tested petsc with openmp activated, without CUDA. >> >> The first thing I see is that our code CI pipelines now fails for >> many tests. >> >> After looking deeper, it seems that PETSc itself fails many tests >> when I activate openmp! >> >> Here are all the configurations I have results for, after/before >> activating OpenMP for PETSc: > > There seem to be several distinct issues > > 1) failures inside Scalapack. > > 2) possibly slightly different convergence rates for some examples > changing the number of iterations slightly in PETSc. > > 3) trouble initializing something outside of PETSc, almost for sure > not related to PETSc > > [zorg:08517] [[INVALID],INVALID] plm:rsh_lookup on agent ssh : rsh path NULL > # [zorg:08517] plm:base:set_hnp_name: initial bias 8517 nodename hash 810220270 > # [zorg:08517] plm:base:set_hnp_name: final jobfam 60385 > # [zorg:08517] [[60385,0],0] plm:rsh_setup on agent ssh : rsh path NULL > # [zorg:08517] [[60385,0],0] plm:base:receive start comm > # [zorg:08517] [[60385,0],0] plm:base:setup_job > # [zorg:08517] [[60385,0],0] plm:base:setup_vm > 4) problem with a hypre run Linear solve did not converge due to > DIVERGED_INDEFINITE_PC iterations 3 , again not likely a PETSc issue > but a hypre and OpenMP issue > 5) Different results for initia inside an external package > # 1c1 > # < MatInertia: nneg: 17, nzero: 0, npos: 83 > # --- > # > MatInertia: nneg: 21, nzero: 0, npos: 79 > TEST arch-linux-c-debug/tests/counts/ksp_ksp_tests-ex33_superlu_dist_2.counts > ok ksp_ksp_tests-ex33_superlu_dist_2 > not ok diff-ksp_ksp_tests-ex33_superlu_dist_2 # Error code: 1 > # 1c1 > # < MatInertia: nneg: 17, nzero: 0, npos: 83 > # --- > # > MatInertia: nneg: 25, nzero: 0, npos: 75 > > > 6) problems with the external package hpddm > > not ok snes_tutorials-ex12_quad_hpddm_reuse_baij # Error code: 139 > # 0 SNES Function norm 21.3344 > # [0]PETSC ERROR: ------------------------------------------------------------------------ > # [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range > # [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > # [0]PETSC ERROR: or seehttps://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind <https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind> > # [0]PETSC ERROR: or tryhttp://valgrind.org <http://valgrind.org> on GNU/linux and Apple Mac OS X to find memory corruption errors > # [0]PETSC ERROR: likely location of problem given in stack below > # [0]PETSC ERROR: --------------------- Stack Frames ------------------------------------ > # [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available, > # [0]PETSC ERROR: INSTEAD the line number of the start of the function > # [0]PETSC ERROR: is given. > # [0]PETSC ERROR: [0] constructionMatrix line 313 /opt/petsc-main_debug/include/HPDDM_coarse_operator_impl.hpp > # [0]PETSC ERROR: [0] construction line 256 /opt/petsc-main_debug/include/HPDDM_coarse_operator_impl.hpp > # [0]PETSC ERROR: [0] buildTwo line 987 /opt/petsc-main_debug/include/HPDDM_schwarz.hpp > # [0]PETSC ERROR: [0] next line 1130 /opt/petsc-main_debug/include/HPDDM_schwarz.hpp > # [0]PETSC ERROR: [0] PCSetUp_HPDDM line 746 /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-main-debug/src/ksp/pc/impls/hpddm/hpddm.cxx > # [0]PETSC ERROR: [0] PCSetUp line 974 /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-main-debug/src/ksp/pc/interface/precon.c > # [0]PETSC ERROR: [0] KSPSetUp line 319 /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-main-debug/src/ksp/ksp/interface/itfunc.c > # [0]PETSC ERROR: [0] KSPSolve_Private line 808 /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-main-debug/src/ksp/ksp/interface/itfunc.c > # [0]PETSC ERROR: [0] KSPSolve line 1080 /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-main-debug/src/ksp/ksp/interface/itfunc.c > # [0]PETSC ERROR: [0] SNESSolve_NEWTONLS line 144 /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-main-debug/src/snes/impls/ls/ls.c > # [0]PETSC ERROR: [0] SNESSolve line 4533 /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-main-debug/src/snes/interface/snes.c > # [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- > # [0]PETSC ERROR: Signal received > # [0]PETSC ERROR: Seehttps://www.mcs.anl.gov/petsc/documentation/faq.html <https://www.mcs.anl.gov/petsc/documentation/faq.html> for trouble shooting. > > PETSc itself does not use OpenMP so turning on OpenMP for pure PETSc > should generate no errors except possibly small changes in iteration > rates due to the different way the floating point operations in MKL > are done. > > We don't see much use for OpenMP so rarely turn it on. What is your > end goal, to use PETSc on CUDA (for each you can keep OpenMP off) or > something else? > > > Barry > > >> ============================================================================== >> >> ============================================================================== >> >> For petsc/master + OpenMPI 4.0.4 + MKL 2019.4.243: >> >> With OpenMP=1 >> >> https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.03.02.02h00m02s_m… >> >> https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.03.02.02h00m02s_c… >> >> # ------------- >> # Summary >> # ------------- >> # FAILED snes_tutorials-ex12_quad_hpddm_reuse_baij diff-ksp_ksp_tests-ex33_superlu_dist_2 diff-ksp_ksp_tests-ex49_superlu_dist+nsize-1herm-0_conv-0 diff-ksp_ksp_tests-ex49_superlu_dist+nsize-1herm-0_conv-1 diff-ksp_ksp_tests-ex49_superlu_dist+nsize-1herm-1_conv-0 diff-ksp_ksp_tests-ex49_superlu_dist+nsize-1herm-1_conv-1 diff-ksp_ksp_tests-ex49_superlu_dist+nsize-4herm-0_conv-0 diff-ksp_ksp_tests-ex49_superlu_dist+nsize-4herm-0_conv-1 diff-ksp_ksp_tests-ex49_superlu_dist+nsize-4herm-1_conv-0 diff-ksp_ksp_tests-ex49_superlu_dist+nsize-4herm-1_conv-1 ksp_ksp_tutorials-ex50_tut_2 diff-ksp_ksp_tests-ex33_superlu_dist diff-snes_tutorials-ex56_hypre snes_tutorials-ex17_3d_q3_trig_elas snes_tutorials-ex12_quad_hpddm_reuse_threshold_baij ksp_ksp_tutorials-ex5_superlu_dist_3 ksp_ksp_tutorials-ex5f_superlu_dist snes_tutorials-ex12_tri_parmetis_hpddm_baij diff-snes_tutorials-ex19_tut_3 mat_tests-ex242_3 snes_tutorials-ex17_3d_q3_trig_vlap ksp_ksp_tutorials-ex5f_superlu_dist_3 snes_tutorials-ex19_superlu_dist diff-snes_tutorials-ex56_attach_mat_nearnullspace-1_bddc_approx_hypre diff-ksp_ksp_tutorials-ex49_hypre_nullspace ts_tutorials-ex18_p1p1_xper_ref ts_tutorials-ex18_p1p1_xyper_ref snes_tutorials-ex19_superlu_dist_2 ksp_ksp_tutorials-ex5_superlu_dist_2 diff-snes_tutorials-ex56_attach_mat_nearnullspace-0_bddc_approx_hypre ksp_ksp_tutorials-ex64_1 ksp_ksp_tutorials-ex5_superlu_dist ksp_ksp_tutorials-ex5f_superlu_dist_2 >> # success 8275/10003 tests (82.7%) >> #*failed 33/10003* tests (0.3%) >> >> With OpenMP=0 >> >> https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.02.26.02h00m16s_m… >> >> https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.02.26.02h00m16s_c… >> >> # ------------- >> # Summary >> # ------------- >> # FAILED tao_constrained_tutorials-tomographyADMM_6 snes_tutorials-ex17_3d_q3_trig_elas mat_tests-ex242_3 snes_tutorials-ex17_3d_q3_trig_vlap tao_leastsquares_tutorials-tomography_1 tao_constrained_tutorials-tomographyADMM_5 >> # success 8262/9983 tests (82.8%) >> #*failed 6/9983* tests (0.1%) >> >> ============================================================================== >> >> ============================================================================== >> >> For OpenMPI 3.1.x/master: >> >> With OpenMP=1: >> >> https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.03.01.22h00m01s_make_test.l… >> >> https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.03.01.22h00m01s_configure.l… >> >> # ------------- >> # Summary >> # ------------- >> # FAILED mat_tests-ex242_3 mat_tests-ex242_2 diff-mat_tests-ex219f_1 diff-dm_tutorials-ex11f90_1 ksp_ksp_tutorials-ex5_superlu_dist_3 diff-ksp_ksp_tutorials-ex49_hypre_nullspace ksp_ksp_tutorials-ex5f_superlu_dist_3 snes_tutorials-ex17_3d_q3_trig_vlap diff-snes_tutorials-ex56_attach_mat_nearnullspace-1_bddc_approx_hypre diff-snes_tutorials-ex19_tut_3 diff-snes_tutorials-ex56_hypre diff-snes_tutorials-ex56_attach_mat_nearnullspace-0_bddc_approx_hypre tao_leastsquares_tutorials-tomography_1 tao_constrained_tutorials-tomographyADMM_4 tao_constrained_tutorials-tomographyADMM_6 diff-tao_constrained_tutorials-toyf_1 >> # success 8142/9765 tests (83.4%) >> #*failed 16/9765* tests (0.2%) >> >> With OpenMP=0: >> >> https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.02.28.22h00m02s_make_test.l… >> >> https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.02.28.22h00m02s_configure.l… >> >> # ------------- >> # Summary >> # ------------- >> # FAILED mat_tests-ex242_3 mat_tests-ex242_2 diff-mat_tests-ex219f_1 diff-dm_tutorials-ex11f90_1 ksp_ksp_tutorials-ex56_2 snes_tutorials-ex17_3d_q3_trig_vlap tao_leastsquares_tutorials-tomography_1 tao_constrained_tutorials-tomographyADMM_4 diff-tao_constrained_tutorials-toyf_1 >> # success 8151/9767 tests (83.5%) >> #*failed 9/9767* tests (0.1%) >> >> ============================================================================== >> >> ============================================================================== >> >> For OpenMPI 4.0.x/master: >> >> With OpenMP=1: >> >> https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.03.01.20h00m01s_make_test.l… >> >> https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.03.01.20h00m01s_configure.l… >> >> # FAILED snes_tutorials-ex17_3d_q3_trig_elas snes_tutorials-ex19_hypre ksp_ksp_tutorials-ex56_2 tao_leastsquares_tutorials-tomography_1 tao_constrained_tutorials-tomographyADMM_5 mat_tests-ex242_3 ksp_ksp_tutorials-ex55_hypre ksp_ksp_tutorials-ex5_superlu_dist_2 tao_constrained_tutorials-tomographyADMM_6 snes_tutorials-ex56_hypre snes_tutorials-ex56_attach_mat_nearnullspace-0_bddc_approx_hypre ksp_ksp_tutorials-ex5f_superlu_dist_3 ksp_ksp_tutorials-ex34_hyprestruct diff-ksp_ksp_tutorials-ex49_hypre_nullspace snes_tutorials-ex56_attach_mat_nearnullspace-1_bddc_approx_hypre ksp_ksp_tutorials-ex5f_superlu_dist ksp_ksp_tutorials-ex5f_superlu_dist_2 ksp_ksp_tutorials-ex5_superlu_dist snes_tutorials-ex19_tut_3 snes_tutorials-ex19_superlu_dist ksp_ksp_tutorials-ex50_tut_2 snes_tutorials-ex17_3d_q3_trig_vlap ksp_ksp_tutorials-ex5_superlu_dist_3 snes_tutorials-ex19_superlu_dist_2 tao_constrained_tutorials-tomographyADMM_4 ts_tutorials-ex26_2 >> # success 8125/9753 tests (83.3%) >> #*failed 26/9753* tests (0.3%) >> >> With OpenMP=0 >> >> https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.02.28.20h00m04s_make_test.l… >> >> https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.02.28.20h00m04s_configure.l… >> >> # FAILED mat_tests-ex242_3 >> # success 8174/9777 tests (83.6%) >> #*failed 1/9777* tests (0.0%) >> >> ============================================================================== >> >> ============================================================================== >> >> Is that known and normal? >> >> In all cases, I am using MKL and I suspect it may come from there... :/ >> >> I also saw a second problem, "make test" fails to compile petsc >> examples on older versions of MKL (but that's less important for me, >> I just upgraded to OneAPI to avoid this, but you may want to know): >> >> https://giref.ulaval.ca/~cmpgiref/dernier_ompi/2021.03.02.02h16m01s_make_te… >> >> https://giref.ulaval.ca/~cmpgiref/dernier_ompi/2021.03.02.02h16m01s_configu… >> >> 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

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Re: [petsc-dev] Commit squashing in MR
by Junchao Zhang 02 Mar '21

02 Mar '21

I am a naive git user, so I use interactive git rebase. Suppose I am on the branch I want to modify, 1) Use git graph to locate an upstream commit to be used as the base $ git graph * 0d5433e9 (HEAD -> jczhang/sf-change-api) SF: rename SFCreateEmbeddedSF to SFCreateEmbeddedRootSF * e7314fbb SF: add an MPI_Op argument to SFBcast * 83df288d Replace MPIU_REPLACE with MPI_REPLACE * b434c516 Merge branch 'barry/2021-02-02/petscsf-communication-specific' into 'main' |\ | * 62152ded (barry/2021-02-02/petscsf-communication-specific) PetscSFView() never called viewer for the specific type (bug), hence many output files were incorrect. * | a4f5d9b4 Merge branch 'jose/upgrade-magma' into 'main' 2) Suppose we choose b434c516 as the base. All commits we want to squash are after it. Do interactive git rebase. It shows a screen for you to edit. Read the help, which is helpful for new users $ git rebase -i b434c516 pick 83df288d Replace MPIU_REPLACE with MPI_REPLACE pick e7314fbb SF: add an MPI_Op argument to SFBcast pick 0d5433e9 SF: rename SFCreateEmbeddedSF to SFCreateEmbeddedRootSF # Rebase b434c516..0d5433e9 onto b434c516 (3 commands) # # Commands: # p, pick <commit> = use commit # r, reword <commit> = use commit, but edit the commit message # e, edit <commit> = use commit, but stop for amending # s, squash <commit> = use commit, but meld into previous commit # f, fixup <commit> = like "squash", but discard this commit's log message # x, exec <command> = run command (the rest of the line) using shell # b, break = stop here (continue rebase later with 'git rebase --continue') # d, drop <commit> = remove commit # l, label <label> = label current HEAD with a name # t, reset <label> = reset HEAD to a label # m, merge [-C <commit> | -c <commit>] <label> [# <oneline>] # . create a merge commit using the original merge commit's # . message (or the oneline, if no original merge commit was # . specified). Use -c <commit> to reword the commit message. # # These lines can be re-ordered; they are executed from top to bottom. # # If you remove a line here THAT COMMIT WILL BE LOST. # # However, if you remove everything, the rebase will be aborted. # # Note that empty commits are commented out 3) Suppose we want to squash the last two commits to 83df288d, replace their pick with s (or f, see the help for difference), save and exit the screen pick 83df288d Replace MPIU_REPLACE with MPI_REPLACE s e7314fbb SF: add an MPI_Op argument to SFBcast s 0d5433e9 SF: rename SFCreateEmbeddedSF to SFCreateEmbeddedRootSF A new screen shows up # This is a combination of 3 commits. # This is the 1st commit message: Replace MPIU_REPLACE with MPI_REPLACE Since we believe all MPI implementations support MPI_REPLACE # This is the commit message #2: SF: add an MPI_Op argument to SFBcast # This is the commit message #3: SF: rename SFCreateEmbeddedSF to SFCreateEmbeddedRootSF # Please enter the commit message for your changes. Lines starting # with '#' will be ignored, and an empty message aborts the commit. 4) Edit the commit message as you want, save and exit, done! --Junchao Zhang On Tue, Mar 2, 2021 at 6:19 PM Blaise A Bourdin <bourdin(a)lsu.edu> wrote: > Hi, > > This is not technically a petsc question. > It would be great to have a short section in the PETSc integration > workflow document explaining how to squash commits in a MR for git-impaired > developers like me. > > Anybody wants to pitch in, or explain me how to do this? > > Regards, > Blaise > > -- > A.K. & Shirley Barton Professor of Mathematics > Adjunct Professor of Mechanical Engineering > Adjunct of the Center for Computation & Technology > Louisiana State University, Lockett Hall Room 344, Baton Rouge, LA 70803, > USA > Tel. +1 (225) 578 1612, Fax +1 (225) 578 4276 Web > http://www.math.lsu.edu/~bourdin > >

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Commit squashing in MR
by Blaise A Bourdin 02 Mar '21

02 Mar '21

Hi, This is not technically a petsc question. It would be great to have a short section in the PETSc integration workflow document explaining how to squash commits in a MR for git-impaired developers like me. Anybody wants to pitch in, or explain me how to do this? Regards, Blaise -- A.K. & Shirley Barton Professor of Mathematics Adjunct Professor of Mechanical Engineering Adjunct of the Center for Computation & Technology Louisiana State University, Lockett Hall Room 344, Baton Rouge, LA 70803, USA Tel. +1 (225) 578 1612, Fax +1 (225) 578 4276 Web http://www.math.lsu.edu/~bourdin

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Re: [petsc-dev] problem registering a new solver
by Matthew Knepley 02 Mar '21

02 Mar '21

Maybe there is a bug in the Register() code. Matt On Tue, Mar 2, 2021 at 4:43 PM Mark Adams <mfadams(a)lbl.gov> wrote: > I see the problem, but not the solution. I put a print statement > in MatSolverTypeDestroy and see: > > MatSolverTypeDestroy seqaij inext->next=0x7fb4a9114c70 inext=0x7fb4a9113c70 > > before it fails. This seqaij node seems to be pointing to itself. If I > remove my registration call and it works and I see this from my print > statement: > > MatSolverTypeDestroy seqaij inext->next=0x7fe811827270 inext=0x7fe811826270 > MatSolverTypeDestroy seqaijperm inext->next=0x7fe811909c70 > inext=0x7fe811827270 > MatSolverTypeDestroy constantdiagonal inext->next=0x7fe81190ac70 > inext=0x7fe811909c70 > .... > > > On Tue, Mar 2, 2021 at 3:42 PM Mark Adams <mfadams(a)lbl.gov> wrote: > >> I am trying to add a band solver to PETSc (later to be moved to Cuda and >> Kokkos) and I have started by adding some types and a copy of the current >> LU as placeholders. I register with: >> >> ierr = MatSolverTypeRegister(MATSOLVERPETSC, MATSEQAIJ, >> MAT_FACTOR_LUBAND,MatGetFactor_seqaij_petsc);CHKERRQ(ierr); >> >> And that is about all that I do that can have any effect at this point. I >> add a switch in MatGetFactor_seqaij_petsc on (ftype == MAT_FACTOR_LUBAND) >> to set the symbolic factorization method (*B)->ops->lufactorsymbolic = >> MatLUBandFactorSymbolic_SeqAIJ; But this is not called (I verified this) >> because I don't know how to get MatGetFactor_seqaij_petsc to receive ftype >> == MAT_FACTOR_LUBAND. (I need help on this to) >> >> Anyway, I would hope that these changes would not do anything but I get >> an error (appended). >> >> It is failing in MatSolverTypeDestroy on this second PetscFree: >> >> while (inext) { >> ierr = PetscFree(inext->mtype);CHKERRQ(ierr); >> iprev = inext; >> inext = inext->next; >> ierr = PetscFree(iprev);CHKERRQ(ierr); >> } >> >> I tried to clone LU here, but I clearly missed something. >> >> Any ideas? >> >> And I just made an MR for this if you want to look at the code. >> >> Thanks, >> Mark >> ... >> Number of SNES iterations = 2 >> [0]PETSC ERROR: PetscTrFreeDefault() called from MatSolverTypeDestroy() >> line 4513 in /Users/markadams/Codes/petsc/src/mat/interface/matrix.c >> [0]PETSC ERROR: Block [id=0(48)] at address 0x7fb7fb8f7620 is corrupted >> (probably write past end of array) >> [0]PETSC ERROR: Block allocated in MatSolverTypeRegister() line 4382 in >> /Users/markadams/Codes/petsc/src/mat/interface/matrix.c >> [0]PETSC ERROR: --------------------- Error Message >> -------------------------------------------------------------- >> [0]PETSC ERROR: Memory corruption: >> https://www.mcs.anl.gov/petsc/documentation/installation.html#valgrind >> [0]PETSC ERROR: Corrupted memory >> [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html >> for trouble shooting. >> [0]PETSC ERROR: Petsc Development GIT revision: v3.14.4-739-g575f931ef8 >> GIT Date: 2021-03-02 13:38:55 -0500 >> [0]PETSC ERROR: ./ex19 on a arch-macosx-gnu-g named MarksMac-302.local by >> markadams Tue Mar 2 15:28:41 2021 >> [0]PETSC ERROR: Configure options >> --with-mpi-dir=/usr/local/Cellar/mpich/3.3.2_1 COPTFLAGS="-g -O0" >> CXXOPTFLAGS="-g -O0" --download-metis=1 --download-parmetis=1 >> --download-kokkos=1 --download-kokkos-kernels=1 --download-p4est=1 >> --with-zlib=1 --download-superlu_dist --download-superlu --with-make-np=4 >> --download-hdf5=1 -with-cuda=0 --with-x=0 --with-debugging=1 >> PETSC_ARCH=arch-macosx-gnu-g --with-64-bit-indices=0 --with-openmp=0 >> --with-ctable=0 >> [0]PETSC ERROR: #1 PetscTrFreeDefault() line 310 in >> /Users/markadams/Codes/petsc/src/sys/memory/mtr.c >> [0]PETSC ERROR: #2 MatSolverTypeDestroy() line 4513 in >> /Users/markadams/Codes/petsc/src/mat/interface/matrix.c >> [0]PETSC ERROR: #3 MatFinalizePackage() line 57 in >> /Users/markadams/Codes/petsc/src/mat/interface/dlregismat.c >> [0]PETSC ERROR: #4 PetscRegisterFinalizeAll() line 389 in >> /Users/markadams/Codes/petsc/src/sys/objects/destroy.c >> [0]PETSC ERROR: #5 PetscFinalize() line 1474 in >> /Users/markadams/Codes/petsc/src/sys/objects/pinit.c >> > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>

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Re: [petsc-dev] problem registering a new solver
by Mark Adams 02 Mar '21

02 Mar '21

I see the problem, but not the solution. I put a print statement in MatSolverTypeDestroy and see: MatSolverTypeDestroy seqaij inext->next=0x7fb4a9114c70 inext=0x7fb4a9113c70 before it fails. This seqaij node seems to be pointing to itself. If I remove my registration call and it works and I see this from my print statement: MatSolverTypeDestroy seqaij inext->next=0x7fe811827270 inext=0x7fe811826270 MatSolverTypeDestroy seqaijperm inext->next=0x7fe811909c70 inext=0x7fe811827270 MatSolverTypeDestroy constantdiagonal inext->next=0x7fe81190ac70 inext=0x7fe811909c70 .... On Tue, Mar 2, 2021 at 3:42 PM Mark Adams <mfadams(a)lbl.gov> wrote: > I am trying to add a band solver to PETSc (later to be moved to Cuda and > Kokkos) and I have started by adding some types and a copy of the current > LU as placeholders. I register with: > > ierr = MatSolverTypeRegister(MATSOLVERPETSC, MATSEQAIJ, > MAT_FACTOR_LUBAND,MatGetFactor_seqaij_petsc);CHKERRQ(ierr); > > And that is about all that I do that can have any effect at this point. I > add a switch in MatGetFactor_seqaij_petsc on (ftype == MAT_FACTOR_LUBAND) > to set the symbolic factorization method (*B)->ops->lufactorsymbolic = > MatLUBandFactorSymbolic_SeqAIJ; But this is not called (I verified this) > because I don't know how to get MatGetFactor_seqaij_petsc to receive ftype > == MAT_FACTOR_LUBAND. (I need help on this to) > > Anyway, I would hope that these changes would not do anything but I get an > error (appended). > > It is failing in MatSolverTypeDestroy on this second PetscFree: > > while (inext) { > ierr = PetscFree(inext->mtype);CHKERRQ(ierr); > iprev = inext; > inext = inext->next; > ierr = PetscFree(iprev);CHKERRQ(ierr); > } > > I tried to clone LU here, but I clearly missed something. > > Any ideas? > > And I just made an MR for this if you want to look at the code. > > Thanks, > Mark > ... > Number of SNES iterations = 2 > [0]PETSC ERROR: PetscTrFreeDefault() called from MatSolverTypeDestroy() > line 4513 in /Users/markadams/Codes/petsc/src/mat/interface/matrix.c > [0]PETSC ERROR: Block [id=0(48)] at address 0x7fb7fb8f7620 is corrupted > (probably write past end of array) > [0]PETSC ERROR: Block allocated in MatSolverTypeRegister() line 4382 in > /Users/markadams/Codes/petsc/src/mat/interface/matrix.c > [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > [0]PETSC ERROR: Memory corruption: > https://www.mcs.anl.gov/petsc/documentation/installation.html#valgrind > [0]PETSC ERROR: Corrupted memory > [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html > for trouble shooting. > [0]PETSC ERROR: Petsc Development GIT revision: v3.14.4-739-g575f931ef8 > GIT Date: 2021-03-02 13:38:55 -0500 > [0]PETSC ERROR: ./ex19 on a arch-macosx-gnu-g named MarksMac-302.local by > markadams Tue Mar 2 15:28:41 2021 > [0]PETSC ERROR: Configure options > --with-mpi-dir=/usr/local/Cellar/mpich/3.3.2_1 COPTFLAGS="-g -O0" > CXXOPTFLAGS="-g -O0" --download-metis=1 --download-parmetis=1 > --download-kokkos=1 --download-kokkos-kernels=1 --download-p4est=1 > --with-zlib=1 --download-superlu_dist --download-superlu --with-make-np=4 > --download-hdf5=1 -with-cuda=0 --with-x=0 --with-debugging=1 > PETSC_ARCH=arch-macosx-gnu-g --with-64-bit-indices=0 --with-openmp=0 > --with-ctable=0 > [0]PETSC ERROR: #1 PetscTrFreeDefault() line 310 in > /Users/markadams/Codes/petsc/src/sys/memory/mtr.c > [0]PETSC ERROR: #2 MatSolverTypeDestroy() line 4513 in > /Users/markadams/Codes/petsc/src/mat/interface/matrix.c > [0]PETSC ERROR: #3 MatFinalizePackage() line 57 in > /Users/markadams/Codes/petsc/src/mat/interface/dlregismat.c > [0]PETSC ERROR: #4 PetscRegisterFinalizeAll() line 389 in > /Users/markadams/Codes/petsc/src/sys/objects/destroy.c > [0]PETSC ERROR: #5 PetscFinalize() line 1474 in > /Users/markadams/Codes/petsc/src/sys/objects/pinit.c >

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Re: [petsc-dev] Petsc "make test" have more failures for --with-openmp=1
by Pierre Jolivet 02 Mar '21

02 Mar '21

Hello Eric, src/mat/tests/ex237.c is a recent test with some code paths that should be disabled for “old” MKL versions. It’s tricky to check directly in the source (we do check in BuildSystem) because there is no such thing as PETSC_PKG_MKL_VERSION_LT, but I guess we can change if defined(PETSC_HAVE_MKL) to if defined(PETSC_HAVE_MKL) && defined(PETSC_HAVE_MKL_SPARSE_OPTIMIZE), I’ll make a MR, thanks for reporting this. For the other issues, I’m sensing this is a problem with gomp + intel_gnu_thread, but this is pure speculation… sorry. I’ll try to reproduce some of these problems if you are not given a more meaningful answer. Thanks, Pierre > On 2 Mar 2021, at 9:14 PM, Eric Chamberland <Eric.Chamberland(a)giref.ulaval.ca> wrote: > > Hi, > > It all started when I wanted to test PETSC/CUDA compatibility for our code. > > I had to activate --with-openmp to configure with --with-cuda=1 successfully. > > I then saw that PETSC_HAVE_OPENMP is used at least in MUMPS (and some other places). > > So, I configured and tested petsc with openmp activated, without CUDA. > > The first thing I see is that our code CI pipelines now fails for many tests. > > After looking deeper, it seems that PETSc itself fails many tests when I activate openmp! > > Here are all the configurations I have results for, after/before activating OpenMP for PETSc: > ============================================================================== > > ============================================================================== > > For petsc/master + OpenMPI 4.0.4 + MKL 2019.4.243: > > With OpenMP=1 > > https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.03.02.02h00m02s_m… <https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.03.02.02h00m02s_m…> > https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.03.02.02h00m02s_c… <https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.03.02.02h00m02s_c…> > # ------------- > # Summary > # ------------- > # FAILED snes_tutorials-ex12_quad_hpddm_reuse_baij diff-ksp_ksp_tests-ex33_superlu_dist_2 diff-ksp_ksp_tests-ex49_superlu_dist+nsize-1herm-0_conv-0 diff-ksp_ksp_tests-ex49_superlu_dist+nsize-1herm-0_conv-1 diff-ksp_ksp_tests-ex49_superlu_dist+nsize-1herm-1_conv-0 diff-ksp_ksp_tests-ex49_superlu_dist+nsize-1herm-1_conv-1 diff-ksp_ksp_tests-ex49_superlu_dist+nsize-4herm-0_conv-0 diff-ksp_ksp_tests-ex49_superlu_dist+nsize-4herm-0_conv-1 diff-ksp_ksp_tests-ex49_superlu_dist+nsize-4herm-1_conv-0 diff-ksp_ksp_tests-ex49_superlu_dist+nsize-4herm-1_conv-1 ksp_ksp_tutorials-ex50_tut_2 diff-ksp_ksp_tests-ex33_superlu_dist diff-snes_tutorials-ex56_hypre snes_tutorials-ex17_3d_q3_trig_elas snes_tutorials-ex12_quad_hpddm_reuse_threshold_baij ksp_ksp_tutorials-ex5_superlu_dist_3 ksp_ksp_tutorials-ex5f_superlu_dist snes_tutorials-ex12_tri_parmetis_hpddm_baij diff-snes_tutorials-ex19_tut_3 mat_tests-ex242_3 snes_tutorials-ex17_3d_q3_trig_vlap ksp_ksp_tutorials-ex5f_superlu_dist_3 snes_tutorials-ex19_superlu_dist diff-snes_tutorials-ex56_attach_mat_nearnullspace-1_bddc_approx_hypre diff-ksp_ksp_tutorials-ex49_hypre_nullspace ts_tutorials-ex18_p1p1_xper_ref ts_tutorials-ex18_p1p1_xyper_ref snes_tutorials-ex19_superlu_dist_2 ksp_ksp_tutorials-ex5_superlu_dist_2 diff-snes_tutorials-ex56_attach_mat_nearnullspace-0_bddc_approx_hypre ksp_ksp_tutorials-ex64_1 ksp_ksp_tutorials-ex5_superlu_dist ksp_ksp_tutorials-ex5f_superlu_dist_2 > # success 8275/10003 tests (82.7%) > # failed 33/10003 tests (0.3%) > With OpenMP=0 > > https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.02.26.02h00m16s_m… <https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.02.26.02h00m16s_m…> > https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.02.26.02h00m16s_c… <https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.02.26.02h00m16s_c…> > # ------------- > # Summary > # ------------- > # FAILED tao_constrained_tutorials-tomographyADMM_6 snes_tutorials-ex17_3d_q3_trig_elas mat_tests-ex242_3 snes_tutorials-ex17_3d_q3_trig_vlap tao_leastsquares_tutorials-tomography_1 tao_constrained_tutorials-tomographyADMM_5 > # success 8262/9983 tests (82.8%) > # failed 6/9983 tests (0.1%) > ============================================================================== > > ============================================================================== > > For OpenMPI 3.1.x/master: > > With OpenMP=1: > > https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.03.01.22h00m01s_make_test.l… <https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.03.01.22h00m01s_make_test.l…> > https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.03.01.22h00m01s_configure.l… <https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.03.01.22h00m01s_configure.l…> > # ------------- > # Summary > # ------------- > # FAILED mat_tests-ex242_3 mat_tests-ex242_2 diff-mat_tests-ex219f_1 diff-dm_tutorials-ex11f90_1 ksp_ksp_tutorials-ex5_superlu_dist_3 diff-ksp_ksp_tutorials-ex49_hypre_nullspace ksp_ksp_tutorials-ex5f_superlu_dist_3 snes_tutorials-ex17_3d_q3_trig_vlap diff-snes_tutorials-ex56_attach_mat_nearnullspace-1_bddc_approx_hypre diff-snes_tutorials-ex19_tut_3 diff-snes_tutorials-ex56_hypre diff-snes_tutorials-ex56_attach_mat_nearnullspace-0_bddc_approx_hypre tao_leastsquares_tutorials-tomography_1 tao_constrained_tutorials-tomographyADMM_4 tao_constrained_tutorials-tomographyADMM_6 diff-tao_constrained_tutorials-toyf_1 > # success 8142/9765 tests (83.4%) > # failed 16/9765 tests (0.2%) > With OpenMP=0: > > https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.02.28.22h00m02s_make_test.l… <https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.02.28.22h00m02s_make_test.l…> > https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.02.28.22h00m02s_configure.l… <https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.02.28.22h00m02s_configure.l…> > # ------------- > # Summary > # ------------- > # FAILED mat_tests-ex242_3 mat_tests-ex242_2 diff-mat_tests-ex219f_1 diff-dm_tutorials-ex11f90_1 ksp_ksp_tutorials-ex56_2 snes_tutorials-ex17_3d_q3_trig_vlap tao_leastsquares_tutorials-tomography_1 tao_constrained_tutorials-tomographyADMM_4 diff-tao_constrained_tutorials-toyf_1 > # success 8151/9767 tests (83.5%) > # failed 9/9767 tests (0.1%) > ============================================================================== > > ============================================================================== > > For OpenMPI 4.0.x/master: > > With OpenMP=1: > > https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.03.01.20h00m01s_make_test.l… <https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.03.01.20h00m01s_make_test.l…> > https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.03.01.20h00m01s_configure.l… <https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.03.01.20h00m01s_configure.l…> > # FAILED snes_tutorials-ex17_3d_q3_trig_elas snes_tutorials-ex19_hypre ksp_ksp_tutorials-ex56_2 tao_leastsquares_tutorials-tomography_1 tao_constrained_tutorials-tomographyADMM_5 mat_tests-ex242_3 ksp_ksp_tutorials-ex55_hypre ksp_ksp_tutorials-ex5_superlu_dist_2 tao_constrained_tutorials-tomographyADMM_6 snes_tutorials-ex56_hypre snes_tutorials-ex56_attach_mat_nearnullspace-0_bddc_approx_hypre ksp_ksp_tutorials-ex5f_superlu_dist_3 ksp_ksp_tutorials-ex34_hyprestruct diff-ksp_ksp_tutorials-ex49_hypre_nullspace snes_tutorials-ex56_attach_mat_nearnullspace-1_bddc_approx_hypre ksp_ksp_tutorials-ex5f_superlu_dist ksp_ksp_tutorials-ex5f_superlu_dist_2 ksp_ksp_tutorials-ex5_superlu_dist snes_tutorials-ex19_tut_3 snes_tutorials-ex19_superlu_dist ksp_ksp_tutorials-ex50_tut_2 snes_tutorials-ex17_3d_q3_trig_vlap ksp_ksp_tutorials-ex5_superlu_dist_3 snes_tutorials-ex19_superlu_dist_2 tao_constrained_tutorials-tomographyADMM_4 ts_tutorials-ex26_2 > # success 8125/9753 tests (83.3%) > # failed 26/9753 tests (0.3%) > With OpenMP=0 > > https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.02.28.20h00m04s_make_test.l… <https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.02.28.20h00m04s_make_test.l…> > https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.02.28.20h00m04s_configure.l… <https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.02.28.20h00m04s_configure.l…> > # FAILED mat_tests-ex242_3 > # success 8174/9777 tests (83.6%) > # failed 1/9777 tests (0.0%) > > ============================================================================== > > ============================================================================== > > Is that known and normal? > > In all cases, I am using MKL and I suspect it may come from there... :/ > > I also saw a second problem, "make test" fails to compile petsc examples on older versions of MKL (but that's less important for me, I just upgraded to OneAPI to avoid this, but you may want to know): > > https://giref.ulaval.ca/~cmpgiref/dernier_ompi/2021.03.02.02h16m01s_make_te… <https://giref.ulaval.ca/~cmpgiref/dernier_ompi/2021.03.02.02h16m01s_make_te…> > https://giref.ulaval.ca/~cmpgiref/dernier_ompi/2021.03.02.02h16m01s_configu… <https://giref.ulaval.ca/~cmpgiref/dernier_ompi/2021.03.02.02h16m01s_configu…> > Thanks, > > Eric > > -- > Eric Chamberland, ing., M. Ing > Professionnel de recherche > GIREF/Université Laval > (418) 656-2131 poste 41 22 42

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Re: [petsc-dev] Petsc "make test" have more failures for --with-openmp=1
by Barry Smith 02 Mar '21

02 Mar '21

Eric, Thanks for the detailed information. I have cc:ed Pierre so he can look at the HPDDM failures. > On Mar 2, 2021, at 2:14 PM, Eric Chamberland <Eric.Chamberland(a)giref.ulaval.ca> wrote: > > Hi, > > It all started when I wanted to test PETSC/CUDA compatibility for our code. > > I had to activate --with-openmp to configure with --with-cuda=1 successfully. > > Certain packages like SuperLU_DIST require --with-openmp if using --with-cuda=1 but PETSc's own use of CUDA as well as some other packages do not require the --with-openmp. > I then saw that PETSC_HAVE_OPENMP is used at least in MUMPS (and some other places). > > So, I configured and tested petsc with openmp activated, without CUDA. > > The first thing I see is that our code CI pipelines now fails for many tests. > > After looking deeper, it seems that PETSc itself fails many tests when I activate openmp! > > Here are all the configurations I have results for, after/before activating OpenMP for PETSc: There seem to be several distinct issues 1) failures inside Scalapack. 2) possibly slightly different convergence rates for some examples changing the number of iterations slightly in PETSc. 3) trouble initializing something outside of PETSc, almost for sure not related to PETSc [zorg:08517] [[INVALID],INVALID] plm:rsh_lookup on agent ssh : rsh path NULL # [zorg:08517] plm:base:set_hnp_name: initial bias 8517 nodename hash 810220270 # [zorg:08517] plm:base:set_hnp_name: final jobfam 60385 # [zorg:08517] [[60385,0],0] plm:rsh_setup on agent ssh : rsh path NULL # [zorg:08517] [[60385,0],0] plm:base:receive start comm # [zorg:08517] [[60385,0],0] plm:base:setup_job # [zorg:08517] [[60385,0],0] plm:base:setup_vm 4) problem with a hypre run Linear solve did not converge due to DIVERGED_INDEFINITE_PC iterations 3 , again not likely a PETSc issue but a hypre and OpenMP issue 5) Different results for initia inside an external package # 1c1 # < MatInertia: nneg: 17, nzero: 0, npos: 83 # --- # > MatInertia: nneg: 21, nzero: 0, npos: 79 TEST arch-linux-c-debug/tests/counts/ksp_ksp_tests-ex33_superlu_dist_2.counts ok ksp_ksp_tests-ex33_superlu_dist_2 not ok diff-ksp_ksp_tests-ex33_superlu_dist_2 # Error code: 1 # 1c1 # < MatInertia: nneg: 17, nzero: 0, npos: 83 # --- # > MatInertia: nneg: 25, nzero: 0, npos: 75 6) problems with the external package hpddm not ok snes_tutorials-ex12_quad_hpddm_reuse_baij # Error code: 139 # 0 SNES Function norm 21.3344 # [0]PETSC ERROR: ------------------------------------------------------------------------ # [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range # [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger # [0]PETSC ERROR: or see https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind # [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors # [0]PETSC ERROR: likely location of problem given in stack below # [0]PETSC ERROR: --------------------- Stack Frames ------------------------------------ # [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available, # [0]PETSC ERROR: INSTEAD the line number of the start of the function # [0]PETSC ERROR: is given. # [0]PETSC ERROR: [0] constructionMatrix line 313 /opt/petsc-main_debug/include/HPDDM_coarse_operator_impl.hpp # [0]PETSC ERROR: [0] construction line 256 /opt/petsc-main_debug/include/HPDDM_coarse_operator_impl.hpp # [0]PETSC ERROR: [0] buildTwo line 987 /opt/petsc-main_debug/include/HPDDM_schwarz.hpp # [0]PETSC ERROR: [0] next line 1130 /opt/petsc-main_debug/include/HPDDM_schwarz.hpp # [0]PETSC ERROR: [0] PCSetUp_HPDDM line 746 /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-main-debug/src/ksp/pc/impls/hpddm/hpddm.cxx # [0]PETSC ERROR: [0] PCSetUp line 974 /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-main-debug/src/ksp/pc/interface/precon.c # [0]PETSC ERROR: [0] KSPSetUp line 319 /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-main-debug/src/ksp/ksp/interface/itfunc.c # [0]PETSC ERROR: [0] KSPSolve_Private line 808 /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-main-debug/src/ksp/ksp/interface/itfunc.c # [0]PETSC ERROR: [0] KSPSolve line 1080 /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-main-debug/src/ksp/ksp/interface/itfunc.c # [0]PETSC ERROR: [0] SNESSolve_NEWTONLS line 144 /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-main-debug/src/snes/impls/ls/ls.c # [0]PETSC ERROR: [0] SNESSolve line 4533 /pmi/cmpbib/compilation_BIB_gcc_redhat_petsc-master_debug/COMPILE_AUTO/petsc-main-debug/src/snes/interface/snes.c # [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- # [0]PETSC ERROR: Signal received # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. PETSc itself does not use OpenMP so turning on OpenMP for pure PETSc should generate no errors except possibly small changes in iteration rates due to the different way the floating point operations in MKL are done. We don't see much use for OpenMP so rarely turn it on. What is your end goal, to use PETSc on CUDA (for each you can keep OpenMP off) or something else? Barry > ============================================================================== > > ============================================================================== > > For petsc/master + OpenMPI 4.0.4 + MKL 2019.4.243: > > With OpenMP=1 > > https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.03.02.02h00m02s_m… <https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.03.02.02h00m02s_m…> > https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.03.02.02h00m02s_c… <https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.03.02.02h00m02s_c…> > # ------------- > # Summary > # ------------- > # FAILED snes_tutorials-ex12_quad_hpddm_reuse_baij diff-ksp_ksp_tests-ex33_superlu_dist_2 diff-ksp_ksp_tests-ex49_superlu_dist+nsize-1herm-0_conv-0 diff-ksp_ksp_tests-ex49_superlu_dist+nsize-1herm-0_conv-1 diff-ksp_ksp_tests-ex49_superlu_dist+nsize-1herm-1_conv-0 diff-ksp_ksp_tests-ex49_superlu_dist+nsize-1herm-1_conv-1 diff-ksp_ksp_tests-ex49_superlu_dist+nsize-4herm-0_conv-0 diff-ksp_ksp_tests-ex49_superlu_dist+nsize-4herm-0_conv-1 diff-ksp_ksp_tests-ex49_superlu_dist+nsize-4herm-1_conv-0 diff-ksp_ksp_tests-ex49_superlu_dist+nsize-4herm-1_conv-1 ksp_ksp_tutorials-ex50_tut_2 diff-ksp_ksp_tests-ex33_superlu_dist diff-snes_tutorials-ex56_hypre snes_tutorials-ex17_3d_q3_trig_elas snes_tutorials-ex12_quad_hpddm_reuse_threshold_baij ksp_ksp_tutorials-ex5_superlu_dist_3 ksp_ksp_tutorials-ex5f_superlu_dist snes_tutorials-ex12_tri_parmetis_hpddm_baij diff-snes_tutorials-ex19_tut_3 mat_tests-ex242_3 snes_tutorials-ex17_3d_q3_trig_vlap ksp_ksp_tutorials-ex5f_superlu_dist_3 snes_tutorials-ex19_superlu_dist diff-snes_tutorials-ex56_attach_mat_nearnullspace-1_bddc_approx_hypre diff-ksp_ksp_tutorials-ex49_hypre_nullspace ts_tutorials-ex18_p1p1_xper_ref ts_tutorials-ex18_p1p1_xyper_ref snes_tutorials-ex19_superlu_dist_2 ksp_ksp_tutorials-ex5_superlu_dist_2 diff-snes_tutorials-ex56_attach_mat_nearnullspace-0_bddc_approx_hypre ksp_ksp_tutorials-ex64_1 ksp_ksp_tutorials-ex5_superlu_dist ksp_ksp_tutorials-ex5f_superlu_dist_2 > # success 8275/10003 tests (82.7%) > # failed 33/10003 tests (0.3%) > With OpenMP=0 > > https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.02.26.02h00m16s_m… <https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.02.26.02h00m16s_m…> > https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.02.26.02h00m16s_c… <https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.02.26.02h00m16s_c…> > # ------------- > # Summary > # ------------- > # FAILED tao_constrained_tutorials-tomographyADMM_6 snes_tutorials-ex17_3d_q3_trig_elas mat_tests-ex242_3 snes_tutorials-ex17_3d_q3_trig_vlap tao_leastsquares_tutorials-tomography_1 tao_constrained_tutorials-tomographyADMM_5 > # success 8262/9983 tests (82.8%) > # failed 6/9983 tests (0.1%) > ============================================================================== > > ============================================================================== > > For OpenMPI 3.1.x/master: > > With OpenMP=1: > > https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.03.01.22h00m01s_make_test.l… <https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.03.01.22h00m01s_make_test.l…> > https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.03.01.22h00m01s_configure.l… <https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.03.01.22h00m01s_configure.l…> > # ------------- > # Summary > # ------------- > # FAILED mat_tests-ex242_3 mat_tests-ex242_2 diff-mat_tests-ex219f_1 diff-dm_tutorials-ex11f90_1 ksp_ksp_tutorials-ex5_superlu_dist_3 diff-ksp_ksp_tutorials-ex49_hypre_nullspace ksp_ksp_tutorials-ex5f_superlu_dist_3 snes_tutorials-ex17_3d_q3_trig_vlap diff-snes_tutorials-ex56_attach_mat_nearnullspace-1_bddc_approx_hypre diff-snes_tutorials-ex19_tut_3 diff-snes_tutorials-ex56_hypre diff-snes_tutorials-ex56_attach_mat_nearnullspace-0_bddc_approx_hypre tao_leastsquares_tutorials-tomography_1 tao_constrained_tutorials-tomographyADMM_4 tao_constrained_tutorials-tomographyADMM_6 diff-tao_constrained_tutorials-toyf_1 > # success 8142/9765 tests (83.4%) > # failed 16/9765 tests (0.2%) > With OpenMP=0: > > https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.02.28.22h00m02s_make_test.l… <https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.02.28.22h00m02s_make_test.l…> > https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.02.28.22h00m02s_configure.l… <https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.02.28.22h00m02s_configure.l…> > # ------------- > # Summary > # ------------- > # FAILED mat_tests-ex242_3 mat_tests-ex242_2 diff-mat_tests-ex219f_1 diff-dm_tutorials-ex11f90_1 ksp_ksp_tutorials-ex56_2 snes_tutorials-ex17_3d_q3_trig_vlap tao_leastsquares_tutorials-tomography_1 tao_constrained_tutorials-tomographyADMM_4 diff-tao_constrained_tutorials-toyf_1 > # success 8151/9767 tests (83.5%) > # failed 9/9767 tests (0.1%) > ============================================================================== > > ============================================================================== > > For OpenMPI 4.0.x/master: > > With OpenMP=1: > > https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.03.01.20h00m01s_make_test.l… <https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.03.01.20h00m01s_make_test.l…> > https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.03.01.20h00m01s_configure.l… <https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.03.01.20h00m01s_configure.l…> > # FAILED snes_tutorials-ex17_3d_q3_trig_elas snes_tutorials-ex19_hypre ksp_ksp_tutorials-ex56_2 tao_leastsquares_tutorials-tomography_1 tao_constrained_tutorials-tomographyADMM_5 mat_tests-ex242_3 ksp_ksp_tutorials-ex55_hypre ksp_ksp_tutorials-ex5_superlu_dist_2 tao_constrained_tutorials-tomographyADMM_6 snes_tutorials-ex56_hypre snes_tutorials-ex56_attach_mat_nearnullspace-0_bddc_approx_hypre ksp_ksp_tutorials-ex5f_superlu_dist_3 ksp_ksp_tutorials-ex34_hyprestruct diff-ksp_ksp_tutorials-ex49_hypre_nullspace snes_tutorials-ex56_attach_mat_nearnullspace-1_bddc_approx_hypre ksp_ksp_tutorials-ex5f_superlu_dist ksp_ksp_tutorials-ex5f_superlu_dist_2 ksp_ksp_tutorials-ex5_superlu_dist snes_tutorials-ex19_tut_3 snes_tutorials-ex19_superlu_dist ksp_ksp_tutorials-ex50_tut_2 snes_tutorials-ex17_3d_q3_trig_vlap ksp_ksp_tutorials-ex5_superlu_dist_3 snes_tutorials-ex19_superlu_dist_2 tao_constrained_tutorials-tomographyADMM_4 ts_tutorials-ex26_2 > # success 8125/9753 tests (83.3%) > # failed 26/9753 tests (0.3%) > With OpenMP=0 > > https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.02.28.20h00m04s_make_test.l… <https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.02.28.20h00m04s_make_test.l…> > https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.02.28.20h00m04s_configure.l… <https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.02.28.20h00m04s_configure.l…> > # FAILED mat_tests-ex242_3 > # success 8174/9777 tests (83.6%) > # failed 1/9777 tests (0.0%) > > ============================================================================== > > ============================================================================== > > Is that known and normal? > > In all cases, I am using MKL and I suspect it may come from there... :/ > > I also saw a second problem, "make test" fails to compile petsc examples on older versions of MKL (but that's less important for me, I just upgraded to OneAPI to avoid this, but you may want to know): > > https://giref.ulaval.ca/~cmpgiref/dernier_ompi/2021.03.02.02h16m01s_make_te… <https://giref.ulaval.ca/~cmpgiref/dernier_ompi/2021.03.02.02h16m01s_make_te…> > https://giref.ulaval.ca/~cmpgiref/dernier_ompi/2021.03.02.02h16m01s_configu… <https://giref.ulaval.ca/~cmpgiref/dernier_ompi/2021.03.02.02h16m01s_configu…> > Thanks, > > Eric > > -- > Eric Chamberland, ing., M. Ing > Professionnel de recherche > GIREF/Université Laval > (418) 656-2131 poste 41 22 42

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