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 <[email protected]> wrote: > > > On Sun, May 30, 2021 at 12:08 AM Barry Smith <[email protected]> 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 > [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: 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 <[email protected]> >> wrote: >> >> try gcc/6.4.0 >> --Junchao Zhang >> >> >> On Sat, May 29, 2021 at 9:50 PM Mark Adams <[email protected]> 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 <[email protected]> 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 >>>> [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: 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 <[email protected]> wrote: >>>> >>>>> >>>>> >>>>> On Sat, May 29, 2021 at 7:48 PM Barry Smith <[email protected]> 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 <[email protected]> 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> >>>>>> >>>>>> >>
