[petsc-dev] [petsc-users] strange segv
Mark Adams
mfadams at lbl.gov
Sat May 29 23:48:36 CDT 2021
On Sun, May 30, 2021 at 12:08 AM Barry Smith <bsmith at 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
[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 <junchao.zhang at gmail.com>
> wrote:
>
> try gcc/6.4.0
> --Junchao Zhang
>
>
> On Sat, May 29, 2021 at 9:50 PM Mark Adams <mfadams at 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 <mfadams at 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
>>> [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 <mfadams at lbl.gov> wrote:
>>>
>>>>
>>>>
>>>> On Sat, May 29, 2021 at 7:48 PM Barry Smith <bsmith at 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:
>>>>> - at echo "Running check examples to verify correct installation"
>>>>> - at echo "Using PETSC_DIR=${PETSC_DIR} and
>>>>> PETSC_ARCH=${PETSC_ARCH}"
>>>>> + at cd src/snes/tutorials >/dev/null; ${OMAKE_SELF}
>>>>> PETSC_ARCH=${PETSC_ARCH} PETSC_DIR=${PETSC_DIR} clean-legacy
>>>>> + at cd src/snes/tutorials >/dev/null; ${OMAKE_SELF}
>>>>> PETSC_ARCH=${PETSC_ARCH} PETSC_DIR=${PETSC_DIR} testex19
>>>>> + at if [ "${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;
>>>>> + at 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;
>>>>> + at 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 <mfadams at 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>
>>>>>
>>>>>
>
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