Jacob, Great suggestion. https://gitlab.com/petsc/petsc/-/merge_requests/4050 <https://gitlab.com/petsc/petsc/-/merge_requests/4050>
> On May 30, 2021, at 10:53 AM, Jacob Faibussowitsch <jacob....@gmail.com> > wrote: > >> The problem was that I was accessing a device pointer on the host. >> >> Maybe the fact that valgrind did not print a source code line (it was in >> host code) is a hint that you are accessing a device pointer? >> >> ==77820== Invalid read of size 4 >> ==77820== at 0x7E69068: LandauKokkosJacobian (in >> /gpfs/alpine/csc314/scratch/adams/petsc/arch-summit-opt-gnu-kokkos-notpl-cuda10/lib/libpetsc.so.3.015.0) >> ==77820== by 0x7C598AF: LandauFormJacobian_Internal (plexland.c:212) > > When in doubt use cuda-memcheck whenever doing any debugging with gpus, its > the cuda version of valgrind and I cannot recommend it enough. Not directly > related but it also comes with a suite of other useful gpu-related tools that > catch race conditions, uninitialized memory accesses and deadlocks. > > https://docs.nvidia.com/cuda/cuda-memcheck/index.html > <https://docs.nvidia.com/cuda/cuda-memcheck/index.html> > > Best regards, > > Jacob Faibussowitsch > (Jacob Fai - booss - oh - vitch) > >> On May 30, 2021, at 09:06, Mark Adams <mfad...@lbl.gov >> <mailto:mfad...@lbl.gov>> wrote: >> >> The problem was that I was accessing a device pointer on the host. >> >> Maybe the fact that valgrind did not print a source code line (it was in >> host code) is a hint that you are accessing a device pointer? >> >> ==77820== Invalid read of size 4 >> ==77820== at 0x7E69068: LandauKokkosJacobian (in >> /gpfs/alpine/csc314/scratch/adams/petsc/arch-summit-opt-gnu-kokkos-notpl-cuda10/lib/libpetsc.so.3.015.0) >> ==77820== by 0x7C598AF: LandauFormJacobian_Internal (plexland.c:212) >> >> This access is in landau.kokkos.cxx but no source line number. >> >> Thanks, >> >> >> On Sun, May 30, 2021 at 12:48 AM Mark Adams <mfad...@lbl.gov >> <mailto:mfad...@lbl.gov>> wrote: >> >> >> On Sun, May 30, 2021 at 12:08 AM Barry Smith <bsm...@petsc.dev >> <mailto:bsm...@petsc.dev>> wrote: >> >> Try without Valgrind, put a CHKMEMQ; just before the call to >> LandauKokkosJacobian and as its first line. And run with -malloc_debug. This >> is a less optimal way to find memory corruption but may be more useful in >> this case. >> >> I don't seem to get anything with this, but I now see that the segv is on >> the 2nd call to LandauKokkosJacobian, which adds the mass matrix, with >> shift. I am working on the mass matrix part now. Let me try adding print >> statements in LandauKokkosJacobian. (DDT failed to trace into that method, >> but let's see). >> >> Thanks, >> >> CHKMEMQ; >> PetscPrintf(PETSC_COMM_SELF,"call LandauKokkosJacobian\n"); >> ierr = >> LandauKokkosJacobian(ctx->plex,Nq,Eq_m,IPf,N,xdata,ctx->SData_d,ctx->subThreadBlockSize,shift,ctx->events,JacP);CHKERRQ(ierr); >> >> 00:37 adams/landau-mass-opt *= >> /gpfs/alpine/csc314/scratch/adams/petsc/src/ts/utils/dmplexlandau/tutorials$ >> make PETSC_ARCH=arch-summit-opt-gnu-kokkos-notpl-cuda10 -f mymake tiny >> EXTRA='-dm_mat_type aijkokkos -dm_vec_type kokkos -malloc_debug' >> DEVICE=kokkos >> jsrun -n 1 -c 1 -g 1 ./ex2 -dim 2 -ex2_test_type none -dm_landau_Ez 0 >> -petscspace_degree 3 -dm_preallocate_only -dm_landau_type p4est >> -dm_landau_ion_masses 1 -dm_landau_ion_charges 1 -dm_landau_thermal_temps >> 4,4 -dm_landau_n 1,1 -ts_monitorx -snes_rtol 1.e-14 -snes_stol 1.e-14 >> -snes_monitor -snes_converged_reason -snes_max_it 14 -ts_type beuler >> -ts_exact_final_time stepover -ts_max_snes_failures 1 -ts_rtol 5e-1 -ts_dt >> .5 -ts_max_steps 1 -pc_type lu -ksp_type preonly -dm_landau_amr_levels_max >> 13 -dm_landau_device_type kokkos -dm_mat_type aijkokkos -dm_vec_type kokkos >> -malloc_debug >> >> >> [0]FormLandau: 1280 IPs, 80 cells, totDim=32, Nb=16, Nq=16, >> elemMatSize=1024, dim=2, Tab: Nb=16 Nf=2 Np=16 cdim=2 N=1406 shift=0. >> call LandauKokkosJacobian >> 0 SNES Function norm 4.974994975313e-03 >> call LandauKokkosJacobian >> [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: The EXACT line numbers in the error traceback are not >> available. >> [0]PETSC ERROR: instead the line number of the start of the function is >> given. >> [0]PETSC ERROR: #1 LandauKokkosJacobian() at >> /gpfs/alpine/csc314/scratch/adams/petsc/src/ts/utils/dmplexlandau/kokkos/landau.kokkos.cxx:272 >> [0]PETSC ERROR: #2 LandauFormJacobian_Internal() at >> /gpfs/alpine/csc314/scratch/adams/petsc/src/ts/utils/dmplexlandau/plexland.c:66 >> [0]PETSC ERROR: #3 LandauIJacobian() at >> /gpfs/alpine/csc314/scratch/adams/petsc/src/ts/utils/dmplexlandau/plexland.c:2093 >> [0]PETSC ERROR: #4 TS user implicit Jacobian() at >> /gpfs/alpine/csc314/scratch/adams/petsc/src/ts/interface/ts.c:933 >> [0]PETSC ERROR: #5 TSComputeIJacobian() at >> /gpfs/alpine/csc314/scratch/adams/petsc/src/ts/interface/ts.c:916 >> [0]PETSC ERROR: #6 SNESTSFormJacobian_Theta() at >> /gpfs/alpine/csc314/scratch/adams/petsc/src/ts/impls/implicit/theta/theta.c:1000 >> [0]PETSC ERROR: #7 SNESTSFormJacobian() at >> /gpfs/alpine/csc314/scratch/adams/petsc/src/ts/interface/ts.c:4407 >> [0]PETSC ERROR: #8 SNES user Jacobian function() at >> /gpfs/alpine/csc314/scratch/adams/petsc/src/snes/interface/snes.c:2823 >> [0]PETSC ERROR: #9 SNESComputeJacobian() at >> /gpfs/alpine/csc314/scratch/adams/petsc/src/snes/interface/snes.c:2782 >> [0]PETSC ERROR: #10 SNESSolve() at >> /gpfs/alpine/csc314/scratch/adams/petsc/src/snes/interface/snes.c:4653 >> [0]PETSC ERROR: #11 TSTheta_SNESSolve() at >> /gpfs/alpine/csc314/scratch/adams/petsc/src/ts/impls/implicit/theta/theta.c:184 >> [0]PETSC ERROR: #12 TSStep_Theta() at >> /gpfs/alpine/csc314/scratch/adams/petsc/src/ts/impls/implicit/theta/theta.c:200 >> [0]PETSC ERROR: #13 TSStep() at >> /gpfs/alpine/csc314/scratch/adams/petsc/src/ts/interface/ts.c:3548 >> [0]PETSC ERROR: --------------------- Error Message >> -------------------------------------------------------------- >> >> >>> On May 29, 2021, at 10:46 PM, Junchao Zhang <junchao.zh...@gmail.com >>> <mailto:junchao.zh...@gmail.com>> wrote: >>> >>> try gcc/6.4.0 >>> --Junchao Zhang >>> >>> >>> On Sat, May 29, 2021 at 9:50 PM Mark Adams <mfad...@lbl.gov >>> <mailto:mfad...@lbl.gov>> wrote: >>> And I grief using gcc-8.1.1 and get this error: >>> >>> /autofs/nccs-svm1_sw/summit/gcc/8.1.1/include/c++/8.1.1/type_traits(347): >>> error: identifier "__ieee128" is undefined >>> >>> Any ideas? >>> >>> On Sat, May 29, 2021 at 10:39 PM Mark Adams <mfad...@lbl.gov >>> <mailto:mfad...@lbl.gov>> wrote: >>> And valgrind sees this. I think the jump to the function is going to the >>> wrong place. >>> I'm giving up on PGI but can try newer versions of GCC. (what is the deal >>> with the range of major releases, 4-10?) >>> (as I said this looks like an error that a user is getting so I'd like to >>> figure it out). >>> >>> 0 SNES Function norm 4.974994975313e-03 >>> ==77820== Invalid read of size 4 >>> ==77820== at 0x7E69068: LandauKokkosJacobian (in >>> /gpfs/alpine/csc314/scratch/adams/petsc/arch-summit-opt-gnu-kokkos-notpl-cuda10/lib/libpetsc.so.3.015.0) >>> ==77820== by 0x7C598AF: LandauFormJacobian_Internal (plexland.c:212) >>> ==77820== by 0x7C728D3: LandauIJacobian (plexland.c:2107) >>> ==77820== by 0x7C8C26B: TSComputeIJacobian (ts.c:934) >>> ==77820== by 0x7E28337: SNESTSFormJacobian_Theta (theta.c:1007) >>> ==77820== by 0x7CBBFD3: SNESTSFormJacobian (ts.c:4415) >>> ==77820== by 0x7AD84BF: SNESComputeJacobian (snes.c:2824) >>> ==77820== by 0x7BA945B: SNESSolve_NEWTONLS (ls.c:222) >>> ==77820== by 0x7AF336F: SNESSolve (snes.c:4769) >>> ==77820== by 0x7E19D13: TSTheta_SNESSolve (theta.c:185) >>> ==77820== by 0x7E1A8B7: TSStep_Theta (theta.c:223) >>> ==77820== by 0x7CB093F: TSStep (ts.c:3571) >>> ==77820== Address 0x96fff690 is in a --- anonymous segment >>> ==77820== >>> [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: The EXACT line numbers in the error traceback are not >>> available. >>> [0]PETSC ERROR: instead the line number of the start of the function is >>> given. >>> [0]PETSC ERROR: #1 LandauKokkosJacobian() at >>> /gpfs/alpine/csc314/scratch/adams/petsc/src/ts/utils/dmplexlandau/kokkos/landau.kokkos.cxx:272 >>> >>> On Sat, May 29, 2021 at 8:46 PM Mark Adams <mfad...@lbl.gov >>> <mailto:mfad...@lbl.gov>> wrote: >>> >>> >>> On Sat, May 29, 2021 at 7:48 PM Barry Smith <bsm...@petsc.dev >>> <mailto:bsm...@petsc.dev>> wrote: >>> >>> I don't see why it is not running the Kokkos check. Here is the rule >>> right below the CUDA rule that is apparently running. >>> >>> check_build: >>> -@echo "Running check examples to verify correct installation" >>> -@echo "Using PETSC_DIR=${PETSC_DIR} and PETSC_ARCH=${PETSC_ARCH}" >>> +@cd src/snes/tutorials >/dev/null; ${OMAKE_SELF} >>> PETSC_ARCH=${PETSC_ARCH} PETSC_DIR=${PETSC_DIR} clean-legacy >>> +@cd src/snes/tutorials >/dev/null; ${OMAKE_SELF} >>> PETSC_ARCH=${PETSC_ARCH} PETSC_DIR=${PETSC_DIR} testex19 >>> +@if [ "${HYPRE_LIB}" != "" ] && [ "${PETSC_WITH_BATCH}" = "" ] && >>> [ "${PETSC_SCALAR}" = "real" ]; then \ >>> cd src/snes/tutorials >/dev/null; ${OMAKE_SELF} >>> PETSC_ARCH=${PETSC_ARCH} PETSC_DIR=${PETSC_DIR} >>> DIFF=${PETSC_DIR}/lib/petsc/bin/petscdiff runex19_hypre; \ >>> fi; >>> +@if [ "${CUDA_LIB}" != "" ] && [ "${PETSC_WITH_BATCH}" = "" ] && >>> [ "${PETSC_SCALAR}" = "real" ]; then \ >>> cd src/snes/tutorials >/dev/null; ${OMAKE_SELF} >>> PETSC_ARCH=${PETSC_ARCH} PETSC_DIR=${PETSC_DIR} >>> DIFF=${PETSC_DIR}/lib/petsc/bin/petscdiff runex19_cuda; \ >>> fi; >>> +@if [ "${KOKKOS_KERNELS_LIB}" != "" ] && [ "${PETSC_WITH_BATCH}" = >>> "" ] && [ "${PETSC_SCALAR}" = "real" ] && [ "${PETSC_PRECISION}" = >>> "double" ] && [ "${MPI_IS_MPIUNI}" = "0" ]; then \ >>> cd src/snes/tutorials >/dev/null; ${OMAKE_SELF} >>> PETSC_ARCH=${PETSC_ARCH} PETSC_DIR=${PETSC_DIR} >>> DIFF=${PETSC_DIR}/lib/petsc/bin/petscdiff runex3k_kokkos; \ >>> fi; >>> >>> Regarding the debugging, if it is just one MPI rank (or even more) with >>> GDB it will trap the error and show the exact line of source code where the >>> error occurred and you can poke around at variables to see if they look >>> corrupt or wrong (for example crazy address in a pointer), I don't know why >>> your debugger is not giving more useful information. >>> >>> >>> This is what I did (in DDT). It stopped at the function call and the data >>> looked fine. I stepped into the call, but didn't get to it. The signal >>> handler was called and I was dead. >>> Maybe I did something in my branch. Can't see what, but I keep probing, >>> Thanks, >>> >>> Barry >>> >>> >>> > On May 29, 2021, at 2:16 PM, Mark Adams <mfad...@lbl.gov >>> > <mailto:mfad...@lbl.gov>> wrote: >>> > >>> > I am running on Summit with Kokkos-CUDA and I am getting a segv that >>> > looks like some sort of a compile/link mismatch. I also have a user with >>> > a C++ code that is getting strange segvs when calling MatSetValues with >>> > CUDA (I know MatSetValues is not a cupsarse method, but that is the >>> > report that I have). I have no idea if these are related but they both >>> > involve C -- C++ calls ... >>> > >>> > I started with a clean build (attached) and I ran in DDT. DDT stopped at >>> > the call in plexland.c to the KokkosLanau operator. I stepped into this >>> > function and then took this screenshot of the stack, with the Kokkos call >>> > and PETSc signal handler. >>> > >>> > Make check does not seem to be running Kokkos tests: >>> > >>> > 15:02 adams/landau-mass-opt *= /gpfs/alpine/csc314/scratch/adams/petsc$ >>> > make PETSC_DIR=/gpfs/alpine/csc314/scratch/adams/petsc >>> > PETSC_ARCH=arch-summit-opt-gnu-kokkos-notpl-cuda10 check >>> > Running check examples to verify correct installation >>> > Using PETSC_DIR=/gpfs/alpine/csc314/scratch/adams/petsc and >>> > PETSC_ARCH=arch-summit-opt-gnu-kokkos-notpl-cuda10 >>> > C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process >>> > C/C++ example src/snes/tutorials/ex19 run successfully with 2 MPI >>> > processes >>> > C/C++ example src/snes/tutorials/ex19 run successfully with cuda >>> > Completed test examples >>> > >>> > Also, I ran this AM with another branch that had not been rebased with >>> > main as recently as this branch (adams/landau-mass-opt). >>> > >>> > Any ideas? >>> > <make.log><configure.log><Screen Shot 2021-05-29 at 2.51.00 PM.png> >>> >> >