[petsc-dev] Petsc "make test" have more failures for --with-openmp=1

Barry Smith bsmith at petsc.dev
Tue Mar 2 21:59:49 CST 2021 


> On Mar 2, 2021, at 9:09 PM, Eric Chamberland <Eric.Chamberland at 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/devel@lists.open-mpi.org/msg19568.html <https://www.mail-archive.com/devel@lists.open-mpi.org/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 at giref.ulaval.ca <mailto:Eric.Chamberland at 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 <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_make_test.log <https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.03.02.02h00m02s_make_test.log>
>>> https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.03.02.02h00m02s_configure.log <https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.03.02.02h00m02s_configure.log>
>>> # -------------
>>> #   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_make_test.log <https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.02.26.02h00m16s_make_test.log>
>>> https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.02.26.02h00m16s_configure.log <https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.02.26.02h00m16s_configure.log>
>>> # -------------
>>> #   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.log <https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.03.01.22h00m01s_make_test.log>
>>> https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.03.01.22h00m01s_configure.log <https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.03.01.22h00m01s_configure.log>
>>> # -------------
>>> #   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.log <https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.02.28.22h00m02s_make_test.log>
>>> https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.02.28.22h00m02s_configure.log <https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.02.28.22h00m02s_configure.log>
>>> # -------------
>>> #   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.log <https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.03.01.20h00m01s_make_test.log>
>>> https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.03.01.20h00m01s_configure.log <https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.03.01.20h00m01s_configure.log>
>>> # 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.log <https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.02.28.20h00m04s_make_test.log>
>>> https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.02.28.20h00m04s_configure.log <https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.02.28.20h00m04s_configure.log>
>>> # 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_test.log <https://giref.ulaval.ca/~cmpgiref/dernier_ompi/2021.03.02.02h16m01s_make_test.log>
>>> https://giref.ulaval.ca/~cmpgiref/dernier_ompi/2021.03.02.02h16m01s_configure.log <https://giref.ulaval.ca/~cmpgiref/dernier_ompi/2021.03.02.02h16m01s_configure.log>
>>> 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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-dev/attachments/20210302/38988305/attachment-0001.html>

More information about the petsc-dev mailing list