> 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 Best regards, Jacob Faibussowitsch (Jacob Fai - booss - oh - vitch) > On May 30, 2021, at 09:06, Mark Adams <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> >> >
