[petsc-dev] [petsc-users] strange segv
Junchao Zhang
junchao.zhang at gmail.com
Sat May 29 22:46:38 CDT 2021
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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