<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Here is a fix for PETSc disregarding what kind of MPI implementation is being used with cluster PARDISO: <a href="https://gitlab.com/petsc/petsc/-/merge_requests/3678" class="">https://gitlab.com/petsc/petsc/-/merge_requests/3678</a><div class="">This doesn’t fix src/mat/tests/ex242, whose backtrace looks suspicious to me…</div><div class=""><div class="">(gdb) #0 0x00002ac152c9c6ed in mkl_trans_avx2_mkl_domatcopy2_t ()</div><div class=""> from /ccc/products/mkl-19.0.5.281/intel--19.0.5.281__openmpi--4.0.1/default/19.0.5.281/mkl/lib/intel64/libmkl_avx2.so</div><div class="">#1 0x00002ba345400dc7 in mkl_trans_avx2_mkl_domatcopy ()</div><div class=""> from /ccc/products/mkl-19.0.5.281/intel--19.0.5.281__openmpi--4.0.1/default/19.0.5.281/mkl/lib/intel64/libmkl_avx2.so</div><div class="">#2 0x00002ba31564fac2 in dmmdatdl_ ()</div><div class=""> from /ccc/products/mkl-19.0.5.281/intel--19.0.5.281__openmpi--4.0.1/default/19.0.5.281/mkl/lib/intel64/libmkl_scalapack_lp64.so</div><div class="">#3 0x00002ba3156d70de in PB_Cptran_DC ()</div><div class=""> from /ccc/products/mkl-19.0.5.281/intel--19.0.5.281__openmpi--4.0.1/default/19.0.5.281/mkl/lib/intel64/libmkl_scalapack_lp64.so</div><div class="">#4 0x00002ba315740062 in pdtran_ ()</div><div class=""> from /ccc/products/mkl-19.0.5.281/intel--19.0.5.281__openmpi--4.0.1/default/19.0.5.281/mkl/lib/intel64/libmkl_scalapack_lp64.so</div><div class="">#5 0x00002ba31370211b in MatTranspose_ScaLAPACK ()</div><div class=""> from /ccc/work/cont003/rndm/rndm/petsc/arch-linux2-c-opt-ompi/lib/libpetsc.so.3.014</div></div><div class=""><div><br class=""></div><div>I’m now realizing that this is also segfaulting with BLACS IntelMPI, so it’s probably unrelated, and simply some Intel mess.</div><div><div>(gdb) #0 0x00002ab818c4f3de in mkl_trans_def_mkl_domatcopy2_t ()</div><div> from /ccc/products/mkl-20.0.4/system/default/20.0.4/mkl/lib/intel64/libmkl_def.so</div><div>#1 0x00002ab818c51247 in mkl_trans_def_mkl_domatcopy ()</div><div> from /ccc/products/mkl-20.0.4/system/default/20.0.4/mkl/lib/intel64/libmkl_def.so</div><div>#2 0x00002ab76e0ba062 in dmmdatdl_ ()</div><div> from /ccc/products/mkl-20.0.4/system/default/20.0.4/mkl/lib/intel64/libmkl_scalapack_lp64.so</div><div>#3 0x00002ab76e14157e in PB_Cptran_DC ()</div><div> from /ccc/products/mkl-20.0.4/system/default/20.0.4/mkl/lib/intel64/libmkl_scalapack_lp64.so</div><div>#4 0x00002ab76e1aa502 in pdtran_ ()</div><div> from /ccc/products/mkl-20.0.4/system/default/20.0.4/mkl/lib/intel64/libmkl_scalapack_lp64.so</div><div>#5 0x00002b7f87c833a1 in MatTranspose_ScaLAPACK ()</div><div> from /ccc/work/cont003/rndm/rndm/petsc/arch-linux2-c-opt-impi/lib/libpetsc.so.3.014</div><div><br class=""></div><div>(Notice the switch from arch-linux2-c-opt-ompi to arch-linux2-c-opt-impi)</div><div><br class=""></div><div>Thanks,</div><div>Pierre</div></div><div><br class=""><blockquote type="cite" class=""><div class="">On 3 Mar 2021, at 8:42 AM, Pierre Jolivet <<a href="mailto:pierre@joliv.et" class="">pierre@joliv.et</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class=""><div class=""><br class="webkit-block-placeholder"></div></div><blockquote type="cite" class=""><div class=""><p class="">If it ends that there is a problem combining MKL + openMP that relies on linking configuration for example, should it be a good thing to have this (--with-openmp=1) tested into the pipelines (with external packages of course)?</p></div></blockquote><div class="">As Barry said, there is not much (if any) OpenMP in PETSc.</div><div class="">There is however some workers with the MKL (+ Intel compilers) turned on, but I don’t think we test MKL + GNU compilers (which I feel like is a very niche combination, hence not really worth testing, IMHO).</div><div class=""><div class=""><br class="webkit-block-placeholder"></div></div><blockquote type="cite" class=""><div class=""><p class="">Does the guys who maintain all these libs are reading petsc-dev? ;)</p></div></blockquote><div class="">I don’t think they are, but don’t worry, we do forward the appropriate messages to them :)</div><div class=""><br class=""></div>About yesterday’s failures…<div class="">1) I cannot reproduce any of the PCHYPRE/PCBDDC/PCHPDDM errors (sorry I didn’t bother putting the SuperLU_DIST tarball on my cluster)</div><div class="">2) I can reproduce the src/mat/tests/ex242.c error (which explicitly uses ScaLAPACK, none of the above PC uses it explicitly, except PCBDDC/PCHPDDM when using MUMPS on “big” problems where root nodes are factorized using ScaLAPACK, see -mat_mumps_icntl_13)</div><div class="">3) I’m seeing that both on your machine and mine, PETSc BuildSystem insist on linking libmkl_blacs_intelmpi_lp64.so even though we supply explicitly libmkl_blacs_openmpi_lp64.so</div><div class="">This for example yields a wrong Makefile.inc for MUMPS:</div><div class="">$ cat arch-linux2-c-opt-ompi/externalpackages/MUMPS_5.3.5/Makefile.inc|grep blacs</div><div class=""><div class="">SCALAP = […] -lmkl_blacs_openmpi_lp64</div><div class="">LIBBLAS = […] -lmkl_blacs_intelmpi_lp64 -lgomp -ldl -lpthread -lm […]</div></div><div class=""><br class=""></div><div class="">Despite what Barry says, I think PETSc is partially to blame as well (why use libmkl_blacs_intelmpi_lp64.so even though BuildSystem is capable of detecting we are using OpenMPI).</div><div class="">I’ll try to fix this to see if it solves 2).</div><div class=""><br class=""></div><div class="">Thanks,</div><div class="">Pierre</div><div class=""><br class=""></div><div class=""><a href="http://joliv.et/irene-rome-configure.log" class="">http://joliv.et/irene-rome-configure.log</a></div><div class=""><div class="">$ /usr/bin/gmake -f gmakefile test test-fail=1</div><div class="">Using MAKEFLAGS: test-fail=1</div><div class=""> TEST arch-linux2-c-opt-ompi/tests/counts/snes_tutorials-ex12_quad_hpddm_reuse_baij.counts</div><div class=""> ok snes_tutorials-ex12_quad_hpddm_reuse_baij</div><div class=""> ok diff-snes_tutorials-ex12_quad_hpddm_reuse_baij</div><div class=""> TEST arch-linux2-c-opt-ompi/tests/counts/ksp_ksp_tutorials-ex50_tut_2.counts</div><div class=""> ok ksp_ksp_tutorials-ex50_tut_2 # SKIP PETSC_HAVE_SUPERLU_DIST requirement not met</div><div class=""> TEST arch-linux2-c-opt-ompi/tests/counts/snes_tutorials-ex56_hypre.counts</div><div class=""> ok snes_tutorials-ex56_hypre</div><div class=""> ok diff-snes_tutorials-ex56_hypre</div><div class=""> TEST arch-linux2-c-opt-ompi/tests/counts/snes_tutorials-ex17_3d_q3_trig_elas.counts</div><div class=""> ok snes_tutorials-ex17_3d_q3_trig_elas</div><div class=""> ok diff-snes_tutorials-ex17_3d_q3_trig_elas</div><div class=""> TEST arch-linux2-c-opt-ompi/tests/counts/snes_tutorials-ex12_quad_hpddm_reuse_threshold_baij.counts</div><div class=""> ok snes_tutorials-ex12_quad_hpddm_reuse_threshold_baij</div><div class=""> ok diff-snes_tutorials-ex12_quad_hpddm_reuse_threshold_baij</div><div class=""> TEST arch-linux2-c-opt-ompi/tests/counts/snes_tutorials-ex12_tri_parmetis_hpddm_baij.counts</div><div class=""> ok snes_tutorials-ex12_tri_parmetis_hpddm_baij</div><div class=""> ok diff-snes_tutorials-ex12_tri_parmetis_hpddm_baij</div><div class=""> TEST arch-linux2-c-opt-ompi/tests/counts/snes_tutorials-ex19_tut_3.counts</div><div class=""> ok snes_tutorials-ex19_tut_3</div><div class=""> ok diff-snes_tutorials-ex19_tut_3</div><div class=""> TEST arch-linux2-c-opt-ompi/tests/counts/mat_tests-ex242_3.counts</div><div class="">not ok mat_tests-ex242_3 # Error code: 137</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>[1]PETSC ERROR: ------------------------------------------------------------------------</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>[1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>[1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>[1]PETSC ERROR: or see <a href="https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind" class="">https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind</a></div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>[1]PETSC ERROR: or try <a href="http://valgrind.org/" class="">http://valgrind.org</a> on GNU/linux and Apple Mac OS X to find memory corruption errors</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>[1]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>[1]PETSC ERROR: to get more information on the crash.</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>[1]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>[1]PETSC ERROR: Signal received</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>[1]PETSC ERROR: See <a href="https://www.mcs.anl.gov/petsc/documentation/faq.html" class="">https://www.mcs.anl.gov/petsc/documentation/faq.html</a> for trouble shooting.</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>[1]PETSC ERROR: Petsc Development GIT revision: v3.14.4-733-g7ab9467ef9 GIT Date: 2021-03-02 16:15:11 +0000</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>[2]PETSC ERROR: ------------------------------------------------------------------------</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>[2]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>[2]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>[2]PETSC ERROR: or see <a href="https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind" class="">https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind</a></div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>[2]PETSC ERROR: or try <a href="http://valgrind.org/" class="">http://valgrind.org</a> on GNU/linux and Apple Mac OS X to find memory corruption errors</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>[2]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>[2]PETSC ERROR: to get more information on the crash.</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>[2]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>[2]PETSC ERROR: Signal received</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>[2]PETSC ERROR: See <a href="https://www.mcs.anl.gov/petsc/documentation/faq.html" class="">https://www.mcs.anl.gov/petsc/documentation/faq.html</a> for trouble shooting.</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>[2]PETSC ERROR: Petsc Development GIT revision: v3.14.4-733-g7ab9467ef9 GIT Date: 2021-03-02 16:15:11 +0000</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>[2]PETSC ERROR: /ccc/work/cont003/rndm/rndm/petsc/arch-linux2-c-opt-ompi/tests/mat/tests/runex242_3/../ex242 on a arch-linux2-c-opt-ompi named irene4047 by jolivetp Wed Mar 3 08:21:20 2021</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>[2]PETSC ERROR: Configure options --download-hpddm --download-hpddm-commit=origin/main --download-hypre --download-metis --download-mumps --download-parmetis --download-ptscotch --download-slepc --download-slepc-commit=origin/main --download-tetgen --known-mpi-c-double-complex --known-mpi-int64_t --known-mpi-long-double --with-avx512-kernels=1 --with-blaslapack-dir=/ccc/products/mkl-19.0.5.281/intel--19.0.5.281__openmpi--4.0.1/default/19.0.5.281/mkl/lib/intel64 --with-cc=mpicc --with-cxx=mpicxx --with-debugging=0 --with-fc=mpifort --with-fortran-bindings=0 --with-make-np=40 --with-mkl_cpardiso-dir=/ccc/products/mkl-19.0.5.281/intel--19.0.5.281__openmpi--4.0.1/default/19.0.5.281 --with-mkl_cpardiso=1 --with-mkl_pardiso-dir=/ccc/products/mkl-19.0.5.281/intel--19.0.5.281__openmpi--4.0.1/default/19.0.5.281/mkl --with-mkl_pardiso=1 --with-mpiexec=ccc_mprun --with-openmp=1 --with-packages-download-dir=/ccc/cont003/home/enseeiht/jolivetp/Dude/externalpackages/ --with-scalapack-include=/ccc/products/mkl-19.0.5.281/intel--19.0.5.281__openmpi--4.0.1/default/19.0.5.281/mkl/include --with-scalapack-lib="[/ccc/products/mkl-19.0.5.281/intel--19.0.5.281__openmpi--4.0.1/default/19.0.5.281/mkl/lib/intel64/libmkl_scalapack_lp64.so,/ccc/products/mkl-19.0.5.281/intel--19.0.5.281__openmpi--4.0.1/default/19.0.5.281/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so]" --with-scalar-type=real --with-x=0 COPTFLAGS="-O3 -fp-model fast -mavx2" CXXOPTFLAGS="-O3 -fp-model fast -mavx2" FOPTFLAGS="-O3 -fp-model fast -mavx2" PETSC_ARCH=arch-linux2-c-opt-ompi</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>[2]PETSC ERROR: #1 User provided function() line 0 in unknown file</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>[2]PETSC ERROR: Run with -malloc_debug to check if memory corruption is causing the crash.</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>[1]PETSC ERROR: /ccc/work/cont003/rndm/rndm/petsc/arch-linux2-c-opt-ompi/tests/mat/tests/runex242_3/../ex242 on a arch-linux2-c-opt-ompi named irene4047 by jolivetp Wed Mar 3 08:21:20 2021</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>[1]PETSC ERROR: Configure options --download-hpddm --download-hpddm-commit=origin/main --download-hypre --download-metis --download-mumps --download-parmetis --download-ptscotch --download-slepc --download-slepc-commit=origin/main --download-tetgen --known-mpi-c-double-complex --known-mpi-int64_t --known-mpi-long-double --with-avx512-kernels=1 --with-blaslapack-dir=/ccc/products/mkl-19.0.5.281/intel--19.0.5.281__openmpi--4.0.1/default/19.0.5.281/mkl/lib/intel64 --with-cc=mpicc --with-cxx=mpicxx --with-debugging=0 --with-fc=mpifort --with-fortran-bindings=0 --with-make-np=40 --with-mkl_cpardiso-dir=/ccc/products/mkl-19.0.5.281/intel--19.0.5.281__openmpi--4.0.1/default/19.0.5.281 --with-mkl_cpardiso=1 --with-mkl_pardiso-dir=/ccc/products/mkl-19.0.5.281/intel--19.0.5.281__openmpi--4.0.1/default/19.0.5.281/mkl --with-mkl_pardiso=1 --with-mpiexec=ccc_mprun --with-openmp=1 --with-packages-download-dir=/ccc/cont003/home/enseeiht/jolivetp/Dude/externalpackages/ --with-scalapack-include=/ccc/products/mkl-19.0.5.281/intel--19.0.5.281__openmpi--4.0.1/default/19.0.5.281/mkl/include --with-scalapack-lib="[/ccc/products/mkl-19.0.5.281/intel--19.0.5.281__openmpi--4.0.1/default/19.0.5.281/mkl/lib/intel64/libmkl_scalapack_lp64.so,/ccc/products/mkl-19.0.5.281/intel--19.0.5.281__openmpi--4.0.1/default/19.0.5.281/mkl/lib/intel64/libmkl_blacs_openmpi_lp64.so]" --with-scalar-type=real --with-x=0 COPTFLAGS="-O3 -fp-model fast -mavx2" CXXOPTFLAGS="-O3 -fp-model fast -mavx2" FOPTFLAGS="-O3 -fp-model fast -mavx2" PETSC_ARCH=arch-linux2-c-opt-ompi</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>[1]PETSC ERROR: #1 User provided function() line 0 in unknown file</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>[1]PETSC ERROR: Run with -malloc_debug to check if memory corruption is causing the crash.</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>--------------------------------------------------------------------------</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>MPI_ABORT was invoked on rank 2 in communicator MPI_COMM_WORLD</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>with errorcode 50176059.</div><div class="">#</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>You may or may not see output from other processes, depending on</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>exactly when Open MPI kills them.</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>--------------------------------------------------------------------------</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>--------------------------------------------------------------------------</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>with errorcode 50176059.</div><div class="">#</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>You may or may not see output from other processes, depending on</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>exactly when Open MPI kills them.</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>--------------------------------------------------------------------------</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>srun: Job step aborted: Waiting up to 302 seconds for job step to finish.</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>slurmstepd-irene4047: error: *** STEP 1374176.36 ON irene4047 CANCELLED AT 2021-03-03T08:21:20 ***</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>srun: error: irene4047: task 0: Killed</div><div class="">#<span class="Apple-tab-span" style="white-space:pre"> </span>srun: error: irene4047: tasks 1-2: Exited with exit code 16</div><div class=""> ok mat_tests-ex242_3 # SKIP Command failed so no diff</div><div class=""> TEST arch-linux2-c-opt-ompi/tests/counts/snes_tutorials-ex17_3d_q3_trig_vlap.counts</div><div class=""> ok snes_tutorials-ex17_3d_q3_trig_vlap</div><div class=""> ok diff-snes_tutorials-ex17_3d_q3_trig_vlap</div><div class=""> TEST arch-linux2-c-opt-ompi/tests/counts/snes_tutorials-ex56_attach_mat_nearnullspace-1_bddc_approx_hypre.counts</div><div class=""> ok snes_tutorials-ex56_attach_mat_nearnullspace-1_bddc_approx_hypre</div><div class=""> ok diff-snes_tutorials-ex56_attach_mat_nearnullspace-1_bddc_approx_hypre</div><div class=""> TEST arch-linux2-c-opt-ompi/tests/counts/ksp_ksp_tutorials-ex49_hypre_nullspace.counts</div><div class=""> ok ksp_ksp_tutorials-ex49_hypre_nullspace</div><div class=""> ok diff-ksp_ksp_tutorials-ex49_hypre_nullspace</div><div class=""> TEST arch-linux2-c-opt-ompi/tests/counts/ts_tutorials-ex18_p1p1_xper_ref.counts</div><div class=""> ok ts_tutorials-ex18_p1p1_xper_ref</div><div class=""> ok diff-ts_tutorials-ex18_p1p1_xper_ref</div><div class=""> TEST arch-linux2-c-opt-ompi/tests/counts/ts_tutorials-ex18_p1p1_xyper_ref.counts</div><div class=""> ok ts_tutorials-ex18_p1p1_xyper_ref</div><div class=""> ok diff-ts_tutorials-ex18_p1p1_xyper_ref</div><div class=""> TEST arch-linux2-c-opt-ompi/tests/counts/snes_tutorials-ex56_attach_mat_nearnullspace-0_bddc_approx_hypre.counts</div><div class=""> ok snes_tutorials-ex56_attach_mat_nearnullspace-0_bddc_approx_hypre</div><div class=""> ok diff-snes_tutorials-ex56_attach_mat_nearnullspace-0_bddc_approx_hypre</div><div class=""> TEST arch-linux2-c-opt-ompi/tests/counts/ksp_ksp_tutorials-ex64_1.counts</div><div class=""> ok ksp_ksp_tutorials-ex64_1 # SKIP PETSC_HAVE_SUPERLU_DIST requirement not met</div><div class=""><br class=""><blockquote type="cite" class=""><div class="">On 3 Mar 2021, at 6:21 AM, Eric Chamberland <<a href="mailto:Eric.Chamberland@giref.ulaval.ca" class="">Eric.Chamberland@giref.ulaval.ca</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" class="">
<div class=""><p class="">Just started a discussion on the side:</p><p class=""><a class="moz-txt-link-freetext" href="https://community.intel.com/t5/Intel-oneAPI-Math-Kernel-Library/Intel-MKL-Link-Line-Advisor-as-external-tool/m-p/1260895#M30974">https://community.intel.com/t5/Intel-oneAPI-Math-Kernel-Library/Intel-MKL-Link-Line-Advisor-as-external-tool/m-p/1260895#M30974</a></p><p class="">Eric<br class="">
</p>
<div class="moz-cite-prefix">On 2021-03-02 3:50 p.m., Pierre Jolivet
wrote:<br class="">
</div>
<blockquote type="cite" cite="mid:FF313618-3465-474B-B13E-A7FDA1FB074D@joliv.et" class="">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" class="">
Hello Eric,
<div class="">
<div class=""><span style="white-space: pre-wrap;" class="">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.</span></div>
<div class="">
<div class=""><span style="white-space: pre-wrap;" class="">
</span></div>
<div class="">
<div class="">For the other issues, I’m sensing this is a
problem with gomp + intel_gnu_thread, but this is pure
speculation… sorry.</div>
<div class="">I’ll try to reproduce some of these problems
if you are not given a more meaningful answer.</div>
</div>
<div class=""><span style="white-space: pre-wrap;" class="">
</span></div>
<div class=""><span style="white-space: pre-wrap;" class="">Thanks,</span></div>
<div class=""><span style="white-space: pre-wrap;" class="">Pierre</span></div>
</div>
<div class="">
<div class=""><span style="white-space: pre-wrap;" class="">
</span></div>
<div class="">
<blockquote type="cite" class="">
<div class="">On 2 Mar 2021, at 9:14 PM, Eric Chamberland
<<a href="mailto:Eric.Chamberland@giref.ulaval.ca" class="" moz-do-not-send="true">Eric.Chamberland@giref.ulaval.ca</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<meta http-equiv="content-type" content="text/html;
charset=UTF-8" class="">
<div class=""><p class="">Hi,</p><p class="">It all started when I wanted to test
PETSC/CUDA compatibility for our code.</p><p class="">I had to activate --with-openmp to
configure with --with-cuda=1 successfully.</p><p class="">I then saw that PETSC_HAVE_OPENMP is used
at least in MUMPS (and some other places).</p><p class="">So, I configured and tested petsc with
openmp activated, without CUDA.<br class="">
</p><p class="">The first thing I see is that our code CI
pipelines now fails for many tests.</p><p class="">After looking deeper, it seems that PETSc
itself fails many tests when I activate openmp!</p>
Here are all the configurations I have results for,
after/before activating OpenMP for PETSc:<br class=""><p class="">==============================================================================</p><p class="">==============================================================================</p><p class="">For petsc/master + OpenMPI 4.0.4 + MKL
2019.4.243:</p><p class="">With OpenMP=1</p><p class=""><a class="moz-txt-link-freetext" href="https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.03.02.02h00m02s_make_test.log" moz-do-not-send="true">https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.03.02.02h00m02s_make_test.log</a></p><p class=""><a class="moz-txt-link-freetext" href="https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.03.02.02h00m02s_configure.log" moz-do-not-send="true">https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.03.02.02h00m02s_configure.log</a></p>
<pre style="font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration-thickness: initial; overflow-wrap: break-word; white-space: pre-wrap;" class=""># -------------
# 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%)
# <b class="">failed 33/10003</b> tests (0.3%)</pre><p class="">With OpenMP=0</p><p class=""><a class="moz-txt-link-freetext" href="https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.02.26.02h00m16s_make_test.log" moz-do-not-send="true">https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.02.26.02h00m16s_make_test.log</a></p><p class=""><a class="moz-txt-link-freetext" href="https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.02.26.02h00m16s_configure.log" moz-do-not-send="true">https://giref.ulaval.ca/~cmpgiref/petsc-master-debug/2021.02.26.02h00m16s_configure.log</a><br class="">
</p>
<pre style="font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration-thickness: initial; overflow-wrap: break-word; white-space: pre-wrap;" class=""># -------------
# 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%)
# <b class="">failed 6/9983</b> tests (0.1%)</pre><p class="">==============================================================================</p><p class="">==============================================================================</p><p class="">For OpenMPI 3.1.x/master:<br class="">
</p><p class="">With OpenMP=1:</p><p class=""><a class="moz-txt-link-freetext" href="https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.03.01.22h00m01s_make_test.log" moz-do-not-send="true">https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.03.01.22h00m01s_make_test.log</a></p><p class=""><a class="moz-txt-link-freetext" href="https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.03.01.22h00m01s_configure.log" moz-do-not-send="true">https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.03.01.22h00m01s_configure.log</a></p>
<pre style="font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration-thickness: initial; overflow-wrap: break-word; white-space: pre-wrap;" class=""># -------------
# 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%)
# <b class="">failed 16/9765</b> tests (0.2%)</pre><p class="">With OpenMP=0:</p><p class=""><a class="moz-txt-link-freetext" href="https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.02.28.22h00m02s_make_test.log" moz-do-not-send="true">https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.02.28.22h00m02s_make_test.log</a></p><p class=""><a class="moz-txt-link-freetext" href="https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.02.28.22h00m02s_configure.log" moz-do-not-send="true">https://giref.ulaval.ca/~cmpgiref/ompi_3.x/2021.02.28.22h00m02s_configure.log</a><br class="">
</p>
<pre style="font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration-thickness: initial; overflow-wrap: break-word; white-space: pre-wrap;" class=""># -------------
# 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%)
# <b class="">failed 9/9767</b> tests (0.1%)
</pre><p class="">==============================================================================</p><p class="">==============================================================================</p><p class="">For OpenMPI 4.0.x/master:</p><p class="">With OpenMP=1:</p><p class=""><a class="moz-txt-link-freetext" href="https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.03.01.20h00m01s_make_test.log" moz-do-not-send="true">https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.03.01.20h00m01s_make_test.log</a></p><p class=""><a class="moz-txt-link-freetext" href="https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.03.01.20h00m01s_configure.log" moz-do-not-send="true">https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.03.01.20h00m01s_configure.log</a><br class="">
</p>
<pre style="font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration-thickness: initial; overflow-wrap: break-word; white-space: pre-wrap;" class=""># 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%)
# <b class="">failed 26/9753</b> tests (0.3%)</pre><p class="">With OpenMP=0</p><p class=""><a class="moz-txt-link-freetext" href="https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.02.28.20h00m04s_make_test.log" moz-do-not-send="true">https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.02.28.20h00m04s_make_test.log</a></p><p class=""><a class="moz-txt-link-freetext" href="https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.02.28.20h00m04s_configure.log" moz-do-not-send="true">https://giref.ulaval.ca/~cmpgiref/ompi_4.x/2021.02.28.20h00m04s_configure.log</a><br class="">
</p>
<pre style="font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration-thickness: initial; overflow-wrap: break-word; white-space: pre-wrap;" class=""># FAILED mat_tests-ex242_3
# success 8174/9777 tests (83.6%)
# <b class="">failed 1/9777</b> tests (0.0%)
</pre><p class="">==============================================================================</p><p class="">==============================================================================</p><p class="">Is that known and normal?</p><p class="">In all cases, I am using MKL and I suspect
it may come from there... :/</p><p class="">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):<br class="">
</p><p class=""><a class="moz-txt-link-freetext" href="https://giref.ulaval.ca/~cmpgiref/dernier_ompi/2021.03.02.02h16m01s_make_test.log" moz-do-not-send="true">https://giref.ulaval.ca/~cmpgiref/dernier_ompi/2021.03.02.02h16m01s_make_test.log</a></p><p class=""><a class="moz-txt-link-freetext" href="https://giref.ulaval.ca/~cmpgiref/dernier_ompi/2021.03.02.02h16m01s_configure.log" moz-do-not-send="true">https://giref.ulaval.ca/~cmpgiref/dernier_ompi/2021.03.02.02h16m01s_configure.log</a><br class="">
</p><p class=""> Thanks,</p><p class="">Eric<br class="">
</p>
<pre class="moz-signature" cols="72">--
Eric Chamberland, ing., M. Ing
Professionnel de recherche
GIREF/Université Laval
(418) 656-2131 poste 41 22 42</pre>
</div>
</div>
</blockquote>
</div>
<br class="">
</div>
</div>
</blockquote>
<pre class="moz-signature" cols="72">--
Eric Chamberland, ing., M. Ing
Professionnel de recherche
GIREF/Université Laval
(418) 656-2131 poste 41 22 42</pre>
</div>
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