[petsc-users] CUDA error trying to run a job with two mpi processes and 1 GPU
Junchao Zhang
junchao.zhang at gmail.com
Mon Aug 14 14:24:50 CDT 2023
Yeah, it looks like ex60 was run correctly.
Double check your code again and if you still run into errors, we can try
to reproduce on our end.
Thanks.
--Junchao Zhang
On Mon, Aug 14, 2023 at 1:05 PM Vanella, Marcos (Fed) <
marcos.vanella at nist.gov> wrote:
> Hi Junchao, I compiled and run ex60 through slurm in our Enki system. The
> batch script for slurm submission, ex60.log and gpu stats files are
> attached.
> Nothing stands out as wrong to me but please have a look.
> I'll revisit running the original 2 MPI process + 1 GPU Poisson problem.
> Thanks!
> Marcos
> ------------------------------
> *From:* Junchao Zhang <junchao.zhang at gmail.com>
> *Sent:* Friday, August 11, 2023 5:52 PM
> *To:* Vanella, Marcos (Fed) <marcos.vanella at nist.gov>
> *Cc:* PETSc users list <petsc-users at mcs.anl.gov>; Satish Balay <
> balay at mcs.anl.gov>
> *Subject:* Re: [petsc-users] CUDA error trying to run a job with two mpi
> processes and 1 GPU
>
> Before digging into the details, could you try to run
> src/ksp/ksp/tests/ex60.c to make sure the environment is ok.
>
> The comment at the end shows how to run it
> test:
> requires: cuda
> suffix: 1_cuda
> nsize: 4
> args: -ksp_view -mat_type aijcusparse -sub_pc_factor_mat_solver_type
> cusparse
>
> --Junchao Zhang
>
>
> On Fri, Aug 11, 2023 at 4:36 PM Vanella, Marcos (Fed) <
> marcos.vanella at nist.gov> wrote:
>
> Hi Junchao, thank you for the info. I compiled the main branch of PETSc in
> another machine that has the openmpi/4.1.4/gcc-11.2.1-cuda-11.7 toolchain
> and don't see the fortran compilation error. It might have been related to
> gcc-9.3.
> I tried the case again, 2 CPUs and one GPU and get this error now:
>
> terminate called after throwing an instance of
> 'thrust::system::system_error'
> terminate called after throwing an instance of
> 'thrust::system::system_error'
> what(): parallel_for failed: cudaErrorInvalidConfiguration: invalid
> configuration argument
> what(): parallel_for failed: cudaErrorInvalidConfiguration: invalid
> configuration argument
>
> Program received signal SIGABRT: Process abort signal.
>
> Backtrace for this error:
>
> Program received signal SIGABRT: Process abort signal.
>
> Backtrace for this error:
> #0 0x2000397fcd8f in ???
> #1 0x2000397fb657 in ???
> #0 0x2000397fcd8f in ???
> #1 0x2000397fb657 in ???
> #2 0x2000000604d7 in ???
> #2 0x2000000604d7 in ???
> #3 0x200039cb9628 in ???
> #4 0x200039c93eb3 in ???
> #5 0x200039364a97 in ???
> #6 0x20003935f6d3 in ???
> #7 0x20003935f78f in ???
> #8 0x20003935fc6b in ???
> #3 0x200039cb9628 in ???
> #4 0x200039c93eb3 in ???
> #5 0x200039364a97 in ???
> #6 0x20003935f6d3 in ???
> #7 0x20003935f78f in ???
> #8 0x20003935fc6b in ???
> #9 0x11ec425b in _ZN6thrust8cuda_cub14throw_on_errorE9cudaErrorPKc
> at /usr/local/cuda-11.7/include/thrust/system/cuda/detail/util.h:225
> #10 0x11ec425b in
> _ZN6thrust8cuda_cub20uninitialized_fill_nINS0_3tagENS_10device_ptrIiEEmiEET0_RNS0_16execution_policyIT_EES5_T1_RKT2_
> #9 0x11ec425b in _ZN6thrust8cuda_cub14throw_on_errorE9cudaErrorPKc
> at /usr/local/cuda-11.7/include/thrust/system/cuda/detail/util.h:225
> #10 0x11ec425b in
> _ZN6thrust8cuda_cub20uninitialized_fill_nINS0_3tagENS_10device_ptrIiEEmiEET0_RNS0_16execution_policyIT_EES5_T1_RKT2_
> at
> /usr/local/cuda-11.7/include/thrust/system/cuda/detail/uninitialized_fill.h:88
> #11 0x11efa263 in
> _ZN6thrust20uninitialized_fill_nINS_8cuda_cub3tagENS_10device_ptrIiEEmiEET0_RKNS_6detail21execution_policy_baseIT_EES5_T1_RKT2_
> at
> /usr/local/cuda-11.7/include/thrust/system/cuda/detail/uninitialized_fill.h:88
> #11 0x11efa263 in
> _ZN6thrust20uninitialized_fill_nINS_8cuda_cub3tagENS_10device_ptrIiEEmiEET0_RKNS_6detail21execution_policy_baseIT_EES5_T1_RKT2_
> at /usr/local/cuda-11.7/include/thrust/detail/uninitialized_fill.inl:55
> #12 0x11efa263 in
> _ZN6thrust6detail23allocator_traits_detail23default_construct_rangeINS_16device_allocatorIiEENS_10device_ptrIiEEmEENS0_10disable_ifIXsrNS1_37needs_default_construct_via_allocatorIT_NS0_15pointer_elementIT0_E4typeEEE5valueEvE4typeERS9_SB_T1_
> at
> /usr/local/cuda-11.7/include/thrust/detail/allocator/default_construct_range.inl:93
> #13 0x11efa263 in
> _ZN6thrust6detail23default_construct_rangeINS_16device_allocatorIiEENS_10device_ptrIiEEmEEvRT_T0_T1_
> at
> /usr/local/cuda-11.7/include/thrust/detail/allocator/default_construct_range.inl:104
> at /usr/local/cuda-11.7/include/thrust/detail/uninitialized_fill.inl:55
> #12 0x11efa263 in
> _ZN6thrust6detail23allocator_traits_detail23default_construct_rangeINS_16device_allocatorIiEENS_10device_ptrIiEEmEENS0_10disable_ifIXsrNS1_37needs_default_construct_via_allocatorIT_NS0_15pointer_elementIT0_E4typeEEE5valueEvE4typeERS9_SB_T1_
> at
> /usr/local/cuda-11.7/include/thrust/detail/allocator/default_construct_range.inl:93
> #13 0x11efa263 in
> _ZN6thrust6detail23default_construct_rangeINS_16device_allocatorIiEENS_10device_ptrIiEEmEEvRT_T0_T1_
> at
> /usr/local/cuda-11.7/include/thrust/detail/allocator/default_construct_range.inl:104
> #14 0x11efa263 in
> _ZN6thrust6detail18contiguous_storageIiNS_16device_allocatorIiEEE19default_construct_nENS0_15normal_iteratorINS_10device_ptrIiEEEEm
> at /usr/local/cuda-11.7/include/thrust/detail/contiguous_storage.inl:254
> #15 0x11efa263 in
> _ZN6thrust6detail11vector_baseIiNS_16device_allocatorIiEEE12default_initEm
> at /usr/local/cuda-11.7/include/thrust/detail/vector_base.inl:220
> #14 0x11efa263 in
> _ZN6thrust6detail18contiguous_storageIiNS_16device_allocatorIiEEE19default_construct_nENS0_15normal_iteratorINS_10device_ptrIiEEEEm
> at /usr/local/cuda-11.7/include/thrust/detail/contiguous_storage.inl:254
> #15 0x11efa263 in
> _ZN6thrust6detail11vector_baseIiNS_16device_allocatorIiEEE12default_initEm
> at /usr/local/cuda-11.7/include/thrust/detail/vector_base.inl:220
> #16 0x11efa263 in
> _ZN6thrust6detail11vector_baseIiNS_16device_allocatorIiEEE12default_initEm
> at /usr/local/cuda-11.7/include/thrust/detail/vector_base.inl:213
> #17 0x11efa263 in
> _ZN6thrust6detail11vector_baseIiNS_16device_allocatorIiEEEC2Em
> at /usr/local/cuda-11.7/include/thrust/detail/vector_base.inl:65
> #18 0x11ed7e47 in
> _ZN6thrust13device_vectorIiNS_16device_allocatorIiEEEC4Em
> at /usr/local/cuda-11.7/include/thrust/device_vector.h:88
> #19 0x11ed7e47 in MatSeqAIJCUSPARSECopyToGPU
> at /home/mnv/Software/petsc/src/mat/impls/aij/seq/seqcusparse/
> aijcusparse.cu:2488
> #20 0x11eef623 in MatSeqAIJCUSPARSEMergeMats
> at /home/mnv/Software/petsc/src/mat/impls/aij/seq/seqcusparse/
> aijcusparse.cu:4696
> #16 0x11efa263 in
> _ZN6thrust6detail11vector_baseIiNS_16device_allocatorIiEEE12default_initEm
> at /usr/local/cuda-11.7/include/thrust/detail/vector_base.inl:213
> #17 0x11efa263 in
> _ZN6thrust6detail11vector_baseIiNS_16device_allocatorIiEEEC2Em
> at /usr/local/cuda-11.7/include/thrust/detail/vector_base.inl:65
> #18 0x11ed7e47 in
> _ZN6thrust13device_vectorIiNS_16device_allocatorIiEEEC4Em
> at /usr/local/cuda-11.7/include/thrust/device_vector.h:88
> #19 0x11ed7e47 in MatSeqAIJCUSPARSECopyToGPU
> at /home/mnv/Software/petsc/src/mat/impls/aij/seq/seqcusparse/
> aijcusparse.cu:2488
> #20 0x11eef623 in MatSeqAIJCUSPARSEMergeMats
> at /home/mnv/Software/petsc/src/mat/impls/aij/seq/seqcusparse/
> aijcusparse.cu:4696
> #21 0x11f0682b in MatMPIAIJGetLocalMatMerge_MPIAIJCUSPARSE
> at /home/mnv/Software/petsc/src/mat/impls/aij/mpi/mpicusparse/
> mpiaijcusparse.cu:251
> #21 0x11f0682b in MatMPIAIJGetLocalMatMerge_MPIAIJCUSPARSE
> at /home/mnv/Software/petsc/src/mat/impls/aij/mpi/mpicusparse/
> mpiaijcusparse.cu:251
> #22 0x133f141f in MatMPIAIJGetLocalMatMerge
> at /home/mnv/Software/petsc/src/mat/impls/aij/mpi/mpiaij.c:5342
> #22 0x133f141f in MatMPIAIJGetLocalMatMerge
> at /home/mnv/Software/petsc/src/mat/impls/aij/mpi/mpiaij.c:5342
> #23 0x133fe9cb in MatProductSymbolic_MPIAIJBACKEND
> at /home/mnv/Software/petsc/src/mat/impls/aij/mpi/mpiaij.c:7368
> #23 0x133fe9cb in MatProductSymbolic_MPIAIJBACKEND
> at /home/mnv/Software/petsc/src/mat/impls/aij/mpi/mpiaij.c:7368
> #24 0x1377e1df in MatProductSymbolic
> at /home/mnv/Software/petsc/src/mat/interface/matproduct.c:795
> #24 0x1377e1df in MatProductSymbolic
> at /home/mnv/Software/petsc/src/mat/interface/matproduct.c:795
> #25 0x11e4dd1f in MatPtAP
> at /home/mnv/Software/petsc/src/mat/interface/matrix.c:9934
> #25 0x11e4dd1f in MatPtAP
> at /home/mnv/Software/petsc/src/mat/interface/matrix.c:9934
> #26 0x130d792f in MatCoarsenApply_MISK_private
> at /home/mnv/Software/petsc/src/mat/coarsen/impls/misk/misk.c:283
> #26 0x130d792f in MatCoarsenApply_MISK_private
> at /home/mnv/Software/petsc/src/mat/coarsen/impls/misk/misk.c:283
> #27 0x130db89b in MatCoarsenApply_MISK
> at /home/mnv/Software/petsc/src/mat/coarsen/impls/misk/misk.c:368
> #27 0x130db89b in MatCoarsenApply_MISK
> at /home/mnv/Software/petsc/src/mat/coarsen/impls/misk/misk.c:368
> #28 0x130bf5a3 in MatCoarsenApply
> at /home/mnv/Software/petsc/src/mat/coarsen/coarsen.c:97
> #28 0x130bf5a3 in MatCoarsenApply
> at /home/mnv/Software/petsc/src/mat/coarsen/coarsen.c:97
> #29 0x141518ff in PCGAMGCoarsen_AGG
> at /home/mnv/Software/petsc/src/ksp/pc/impls/gamg/agg.c:524
> #29 0x141518ff in PCGAMGCoarsen_AGG
> at /home/mnv/Software/petsc/src/ksp/pc/impls/gamg/agg.c:524
> #30 0x13b3a43f in PCSetUp_GAMG
> at /home/mnv/Software/petsc/src/ksp/pc/impls/gamg/gamg.c:631
> #30 0x13b3a43f in PCSetUp_GAMG
> at /home/mnv/Software/petsc/src/ksp/pc/impls/gamg/gamg.c:631
> #31 0x1276845b in PCSetUp
> at /home/mnv/Software/petsc/src/ksp/pc/interface/precon.c:1069
> #31 0x1276845b in PCSetUp
> at /home/mnv/Software/petsc/src/ksp/pc/interface/precon.c:1069
> #32 0x127d6cbb in KSPSetUp
> at /home/mnv/Software/petsc/src/ksp/ksp/interface/itfunc.c:415
> #32 0x127d6cbb in KSPSetUp
> at /home/mnv/Software/petsc/src/ksp/ksp/interface/itfunc.c:415
> #33 0x127dddbf in KSPSolve_Private
> at /home/mnv/Software/petsc/src/ksp/ksp/interface/itfunc.c:836
> #33 0x127dddbf in KSPSolve_Private
> at /home/mnv/Software/petsc/src/ksp/ksp/interface/itfunc.c:836
> #34 0x127e4987 in KSPSolve
> at /home/mnv/Software/petsc/src/ksp/ksp/interface/itfunc.c:1082
> #34 0x127e4987 in KSPSolve
> at /home/mnv/Software/petsc/src/ksp/ksp/interface/itfunc.c:1082
> #35 0x1280b18b in kspsolve_
> at
> /home/mnv/Software/petsc/arch-linux-c-dbg/src/ksp/ksp/interface/ftn-auto/itfuncf.c:335
> #35 0x1280b18b in kspsolve_
> at
> /home/mnv/Software/petsc/arch-linux-c-dbg/src/ksp/ksp/interface/ftn-auto/itfuncf.c:335
> #36 0x1140945f in __globmat_solver_MOD_glmat_solver
> at ../../Source/pres.f90:3128
> #36 0x1140945f in __globmat_solver_MOD_glmat_solver
> at ../../Source/pres.f90:3128
> #37 0x119f8853 in pressure_iteration_scheme
> at ../../Source/main.f90:1449
> #37 0x119f8853 in pressure_iteration_scheme
> at ../../Source/main.f90:1449
> #38 0x11969bd3 in fds
> at ../../Source/main.f90:688
> #38 0x11969bd3 in fds
> at ../../Source/main.f90:688
> #39 0x11a10167 in main
> at ../../Source/main.f90:6
> #39 0x11a10167 in main
> at ../../Source/main.f90:6
> srun: error: enki12: tasks 0-1: Aborted (core dumped)
>
>
> This was the slurm submission script in this case:
>
> #!/bin/bash
> # ../../Utilities/Scripts/qfds.sh -p 2 -T db -d test.fds
> #SBATCH -J test
> #SBATCH -e /home/mnv/Firemodels_fork/fds/Issues/PETSc/test.err
> #SBATCH -o /home/mnv/Firemodels_fork/fds/Issues/PETSc/test.log
> #SBATCH --partition=debug
> #SBATCH --ntasks=2
> #SBATCH --nodes=1
> #SBATCH --cpus-per-task=1
> #SBATCH --ntasks-per-node=2
> #SBATCH --time=01:00:00
> #SBATCH --gres=gpu:1
>
> export OMP_NUM_THREADS=1
>
> # PETSc dir and arch:
> export PETSC_DIR=/home/mnv/Software/petsc
> export PETSC_ARCH=arch-linux-c-dbg
>
> # SYSTEM name:
> export MYSYSTEM=enki
>
> # modules
> module load cuda/11.7
> module load gcc/11.2.1/toolset
> module load openmpi/4.1.4/gcc-11.2.1-cuda-11.7
>
> cd /home/mnv/Firemodels_fork/fds/Issues/PETSc
> srun -N 1 -n 2 --ntasks-per-node 2 --mpi=pmi2
> /home/mnv/Firemodels_fork/fds/Build/ompi_gnu_linux_db/fds_ompi_gnu_linux_db
> test.fds -vec_type mpicuda -mat_type mpiaijcusparse -pc_type gamg
>
> The configure.log for the PETSc build is attached. Another clue to what
> is happening is that even setting the matrices/vectors to be mpi (-vec_type
> mpi -mat_type mpiaij) and not requesting a gpu I get a GPU warning :
>
> 0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [1]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [1]PETSC ERROR: GPU error
> [1]PETSC ERROR: Cannot lazily initialize PetscDevice: cuda error 100
> (cudaErrorNoDevice) : no CUDA-capable device is detected
> [1]PETSC ERROR: WARNING! There are unused option(s) set! Could be the
> program crashed before usage or a spelling mistake, etc!
> [0]PETSC ERROR: GPU error
> [0]PETSC ERROR: Cannot lazily initialize PetscDevice: cuda error 100
> (cudaErrorNoDevice) : no CUDA-capable device is detected
> [0]PETSC ERROR: WARNING! There are unused option(s) set! Could be the
> program crashed before usage or a spelling mistake, etc!
> [0]PETSC ERROR: Option left: name:-pc_type value: gamg source: command
> line
> [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
> [1]PETSC ERROR: Option left: name:-pc_type value: gamg source: command
> line
> [1]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
> [1]PETSC ERROR: Petsc Development GIT revision: v3.19.4-946-g590ad0f52ad
> GIT Date: 2023-08-11 15:13:02 +0000
> [0]PETSC ERROR: Petsc Development GIT revision: v3.19.4-946-g590ad0f52ad
> GIT Date: 2023-08-11 15:13:02 +0000
> [0]PETSC ERROR:
> /home/mnv/Firemodels_fork/fds/Build/ompi_gnu_linux_db/fds_ompi_gnu_linux_db
> on a arch-linux-c-dbg named enki11.adlp by mnv Fri Aug 11 17:04:55 2023
> [0]PETSC ERROR: Configure options COPTFLAGS="-g -O2" CXXOPTFLAGS="-g -O2"
> FOPTFLAGS="-g -O2" FCOPTFLAGS="-g -O2" CUDAOPTFLAGS="-g -O2"
> --with-debugging=yes --with-shared-libraries=0 --download-suitesparse
> --download-hypre --download-fblaslapack --with-cuda
> ...
>
> I would have expected not to see GPU errors being printed out, given I did
> not request cuda matrix/vectors. The case run anyways, I assume it
> defaulted to the CPU solver.
> Let me know if you have any ideas as to what is happening. Thanks,
> Marcos
>
>
> ------------------------------
> *From:* Junchao Zhang <junchao.zhang at gmail.com>
> *Sent:* Friday, August 11, 2023 3:35 PM
> *To:* Vanella, Marcos (Fed) <marcos.vanella at nist.gov>; PETSc users list <
> petsc-users at mcs.anl.gov>; Satish Balay <balay at mcs.anl.gov>
> *Subject:* Re: [petsc-users] CUDA error trying to run a job with two mpi
> processes and 1 GPU
>
> Marcos,
> We do not have good petsc/gpu documentation, but see
> https://petsc.org/main/faq/#doc-faq-gpuhowto, and also search "requires:
> cuda" in petsc tests and you will find examples using GPU.
> For the Fortran compile errors, attach your configure.log and Satish
> (Cc'ed) or others should know how to fix them.
>
> Thanks.
> --Junchao Zhang
>
>
> On Fri, Aug 11, 2023 at 2:22 PM Vanella, Marcos (Fed) <
> marcos.vanella at nist.gov> wrote:
>
> Hi Junchao, thanks for the explanation. Is there some development
> documentation on the GPU work? I'm interested learning about it.
> I checked out the main branch and configured petsc. when compiling with
> gcc/gfortran I come across this error:
>
> ....
> CUDAC
> arch-linux-c-opt/obj/src/mat/impls/aij/seq/seqcusparse/aijcusparse.o
> CUDAC.dep
> arch-linux-c-opt/obj/src/mat/impls/aij/seq/seqcusparse/aijcusparse.o
> FC arch-linux-c-opt/obj/src/ksp/f90-mod/petsckspdefmod.o
> FC arch-linux-c-opt/obj/src/ksp/f90-mod/petscpcmod.o
>
> /home/mnv/Software/petsc/include/../src/ksp/f90-mod/ftn-auto-interfaces/petscpc.h90:37:61:
>
> 37 | subroutine PCASMCreateSubdomains2D(a,b,c,d,e,f,g,h,i,z)
> | 1
> *Error: Symbol ‘pcasmcreatesubdomains2d’ at (1) already has an explicit
> interface*
>
> /home/mnv/Software/petsc/include/../src/ksp/f90-mod/ftn-auto-interfaces/petscpc.h90:38:13:
>
> 38 | import tIS
> | 1
> Error: IMPORT statement at (1) only permitted in an INTERFACE body
>
> /home/mnv/Software/petsc/include/../src/ksp/f90-mod/ftn-auto-interfaces/petscpc.h90:39:80:
>
> 39 | PetscInt a ! PetscInt
> |
> 1
> Error: Unexpected data declaration statement in INTERFACE block at (1)
>
> /home/mnv/Software/petsc/include/../src/ksp/f90-mod/ftn-auto-interfaces/petscpc.h90:40:80:
>
> 40 | PetscInt b ! PetscInt
> |
> 1
> Error: Unexpected data declaration statement in INTERFACE block at (1)
>
> /home/mnv/Software/petsc/include/../src/ksp/f90-mod/ftn-auto-interfaces/petscpc.h90:41:80:
>
> 41 | PetscInt c ! PetscInt
> |
> 1
> Error: Unexpected data declaration statement in INTERFACE block at (1)
>
> /home/mnv/Software/petsc/include/../src/ksp/f90-mod/ftn-auto-interfaces/petscpc.h90:42:80:
>
> 42 | PetscInt d ! PetscInt
> |
> 1
> Error: Unexpected data declaration statement in INTERFACE block at (1)
>
> /home/mnv/Software/petsc/include/../src/ksp/f90-mod/ftn-auto-interfaces/petscpc.h90:43:80:
>
> 43 | PetscInt e ! PetscInt
> |
> 1
> Error: Unexpected data declaration statement in INTERFACE block at (1)
>
> /home/mnv/Software/petsc/include/../src/ksp/f90-mod/ftn-auto-interfaces/petscpc.h90:44:80:
>
> 44 | PetscInt f ! PetscInt
> |
> 1
> Error: Unexpected data declaration statement in INTERFACE block at (1)
>
> /home/mnv/Software/petsc/include/../src/ksp/f90-mod/ftn-auto-interfaces/petscpc.h90:45:80:
>
> 45 | PetscInt g ! PetscInt
> |
> 1
> Error: Unexpected data declaration statement in INTERFACE block at (1)
>
> /home/mnv/Software/petsc/include/../src/ksp/f90-mod/ftn-auto-interfaces/petscpc.h90:46:30:
>
> 46 | IS h ! IS
> | 1
> Error: Unexpected data declaration statement in INTERFACE block at (1)
>
> /home/mnv/Software/petsc/include/../src/ksp/f90-mod/ftn-auto-interfaces/petscpc.h90:47:30:
>
> 47 | IS i ! IS
> | 1
> Error: Unexpected data declaration statement in INTERFACE block at (1)
>
> /home/mnv/Software/petsc/include/../src/ksp/f90-mod/ftn-auto-interfaces/petscpc.h90:48:43:
>
> 48 | PetscErrorCode z
> | 1
> Error: Unexpected data declaration statement in INTERFACE block at (1)
>
> /home/mnv/Software/petsc/include/../src/ksp/f90-mod/ftn-auto-interfaces/petscpc.h90:49:10:
>
> 49 | end subroutine PCASMCreateSubdomains2D
> | 1
> Error: Expecting END INTERFACE statement at (1)
> make[3]: *** [gmakefile:225:
> arch-linux-c-opt/obj/src/ksp/f90-mod/petscpcmod.o] Error 1
> make[3]: *** Waiting for unfinished jobs....
> CC
> arch-linux-c-opt/obj/src/tao/leastsquares/impls/pounders/pounders.o
> CC arch-linux-c-opt/obj/src/ksp/pc/impls/bddc/bddcprivate.o
> CUDAC
> arch-linux-c-opt/obj/src/vec/vec/impls/seq/cupm/cuda/vecseqcupm.o
> CUDAC.dep
> arch-linux-c-opt/obj/src/vec/vec/impls/seq/cupm/cuda/vecseqcupm.o
> make[3]: Leaving directory '/home/mnv/Software/petsc'
> make[2]: *** [/home/mnv/Software/petsc/lib/petsc/conf/rules.doc:28: libs]
> Error 2
> make[2]: Leaving directory '/home/mnv/Software/petsc'
> **************************ERROR*************************************
> Error during compile, check arch-linux-c-opt/lib/petsc/conf/make.log
> Send it and arch-linux-c-opt/lib/petsc/conf/configure.log to
> petsc-maint at mcs.anl.gov
> ********************************************************************
> make[1]: *** [makefile:45: all] Error 1
> make: *** [GNUmakefile:9: all] Error 2
> ------------------------------
> *From:* Junchao Zhang <junchao.zhang at gmail.com>
> *Sent:* Friday, August 11, 2023 3:04 PM
> *To:* Vanella, Marcos (Fed) <marcos.vanella at nist.gov>
> *Cc:* petsc-users at mcs.anl.gov <petsc-users at mcs.anl.gov>
> *Subject:* Re: [petsc-users] CUDA error trying to run a job with two mpi
> processes and 1 GPU
>
> Hi, Macros,
> I saw MatSetPreallocationCOO_MPIAIJCUSPARSE_Basic() in the error stack.
> We recently refactored the COO code and got rid of that function. So could
> you try petsc/main?
> We map MPI processes to GPUs in a round-robin fashion. We query the
> number of visible CUDA devices (g), and assign the device (rank%g) to the
> MPI process (rank). In that sense, the work distribution is totally
> determined by your MPI work partition (i.e, yourself).
> On clusters, this MPI process to GPU binding is usually done by the job
> scheduler like slurm. You need to check your cluster's users' guide to see
> how to bind MPI processes to GPUs. If the job scheduler has done that, the
> number of visible CUDA devices to a process might just appear to be 1,
> making petsc's own mapping void.
>
> Thanks.
> --Junchao Zhang
>
>
> On Fri, Aug 11, 2023 at 12:43 PM Vanella, Marcos (Fed) <
> marcos.vanella at nist.gov> wrote:
>
> Hi Junchao, thank you for replying. I compiled petsc in debug mode and
> this is what I get for the case:
>
> terminate called after throwing an instance of
> 'thrust::system::system_error'
> what(): merge_sort: failed to synchronize: cudaErrorIllegalAddress: an
> illegal memory access was encountered
>
> Program received signal SIGABRT: Process abort signal.
>
> Backtrace for this error:
> #0 0x15264731ead0 in ???
> #1 0x15264731dc35 in ???
> #2 0x15264711551f in ???
> #3 0x152647169a7c in ???
> #4 0x152647115475 in ???
> #5 0x1526470fb7f2 in ???
> #6 0x152647678bbd in ???
> #7 0x15264768424b in ???
> #8 0x1526476842b6 in ???
> #9 0x152647684517 in ???
> #10 0x55bb46342ebb in _ZN6thrust8cuda_cub14throw_on_errorE9cudaErrorPKc
> at /usr/local/cuda/include/thrust/system/cuda/detail/util.h:224
> #11 0x55bb46342ebb in
> _ZN6thrust8cuda_cub12__merge_sort10merge_sortINS_6detail17integral_constantIbLb1EEENS4_IbLb0EEENS0_3tagENS_12zip_iteratorINS_5tupleINS_10device_ptrIiEESB_NS_9null_typeESC_SC_SC_SC_SC_SC_SC_EEEENS3_15normal_iteratorISB_EE9IJCompareEEvRNS0_16execution_policyIT1_EET2_SM_T3_T4_
> at /usr/local/cuda/include/thrust/system/cuda/detail/sort.h:1316
> #12 0x55bb46342ebb in
> _ZN6thrust8cuda_cub12__smart_sort10smart_sortINS_6detail17integral_constantIbLb1EEENS4_IbLb0EEENS0_16execution_policyINS0_3tagEEENS_12zip_iteratorINS_5tupleINS_10device_ptrIiEESD_NS_9null_typeESE_SE_SE_SE_SE_SE_SE_EEEENS3_15normal_iteratorISD_EE9IJCompareEENS1_25enable_if_comparison_sortIT2_T4_E4typeERT1_SL_SL_T3_SM_
> at /usr/local/cuda/include/thrust/system/cuda/detail/sort.h:1544
> #13 0x55bb46342ebb in
> _ZN6thrust8cuda_cub11sort_by_keyINS0_3tagENS_12zip_iteratorINS_5tupleINS_10device_ptrIiEES6_NS_9null_typeES7_S7_S7_S7_S7_S7_S7_EEEENS_6detail15normal_iteratorIS6_EE9IJCompareEEvRNS0_16execution_policyIT_EET0_SI_T1_T2_
> at /usr/local/cuda/include/thrust/system/cuda/detail/sort.h:1669
> #14 0x55bb46317bc5 in
> _ZN6thrust11sort_by_keyINS_8cuda_cub3tagENS_12zip_iteratorINS_5tupleINS_10device_ptrIiEES6_NS_9null_typeES7_S7_S7_S7_S7_S7_S7_EEEENS_6detail15normal_iteratorIS6_EE9IJCompareEEvRKNSA_21execution_policy_baseIT_EET0_SJ_T1_T2_
> at /usr/local/cuda/include/thrust/detail/sort.inl:115
> #15 0x55bb46317bc5 in
> _ZN6thrust11sort_by_keyINS_12zip_iteratorINS_5tupleINS_10device_ptrIiEES4_NS_9null_typeES5_S5_S5_S5_S5_S5_S5_EEEENS_6detail15normal_iteratorIS4_EE9IJCompareEEvT_SC_T0_T1_
> at /usr/local/cuda/include/thrust/detail/sort.inl:305
> #16 0x55bb46317bc5 in MatSetPreallocationCOO_SeqAIJCUSPARSE_Basic
> at /home/mnv/Software/petsc/src/mat/impls/aij/seq/seqcusparse/
> aijcusparse.cu:4452
> #17 0x55bb46c5b27c in MatSetPreallocationCOO_MPIAIJCUSPARSE_Basic
> at /home/mnv/Software/petsc/src/mat/impls/aij/mpi/mpicusparse/
> mpiaijcusparse.cu:173
> #18 0x55bb46c5b27c in MatSetPreallocationCOO_MPIAIJCUSPARSE
> at /home/mnv/Software/petsc/src/mat/impls/aij/mpi/mpicusparse/
> mpiaijcusparse.cu:222
> #19 0x55bb468e01cf in MatSetPreallocationCOO
> at /home/mnv/Software/petsc/src/mat/utils/gcreate.c:606
> #20 0x55bb46b39c9b in MatProductSymbolic_MPIAIJBACKEND
> at /home/mnv/Software/petsc/src/mat/impls/aij/mpi/mpiaij.c:7547
> #21 0x55bb469015e5 in MatProductSymbolic
> at /home/mnv/Software/petsc/src/mat/interface/matproduct.c:803
> #22 0x55bb4694ade2 in MatPtAP
> at /home/mnv/Software/petsc/src/mat/interface/matrix.c:9897
> #23 0x55bb4696d3ec in MatCoarsenApply_MISK_private
> at /home/mnv/Software/petsc/src/mat/coarsen/impls/misk/misk.c:283
> #24 0x55bb4696eb67 in MatCoarsenApply_MISK
> at /home/mnv/Software/petsc/src/mat/coarsen/impls/misk/misk.c:368
> #25 0x55bb4695bd91 in MatCoarsenApply
> at /home/mnv/Software/petsc/src/mat/coarsen/coarsen.c:97
> #26 0x55bb478294d8 in PCGAMGCoarsen_AGG
> at /home/mnv/Software/petsc/src/ksp/pc/impls/gamg/agg.c:524
> #27 0x55bb471d1cb4 in PCSetUp_GAMG
> at /home/mnv/Software/petsc/src/ksp/pc/impls/gamg/gamg.c:631
> #28 0x55bb464022cf in PCSetUp
> at /home/mnv/Software/petsc/src/ksp/pc/interface/precon.c:994
> #29 0x55bb4718b8a7 in KSPSetUp
> at /home/mnv/Software/petsc/src/ksp/ksp/interface/itfunc.c:406
> #30 0x55bb4718f22e in KSPSolve_Private
> at /home/mnv/Software/petsc/src/ksp/ksp/interface/itfunc.c:824
> #31 0x55bb47192c0c in KSPSolve
> at /home/mnv/Software/petsc/src/ksp/ksp/interface/itfunc.c:1070
> #32 0x55bb463efd35 in kspsolve_
> at /home/mnv/Software/petsc/src/ksp/ksp/interface/ftn-auto/itfuncf.c:320
> #33 0x55bb45e94b32 in ???
> #34 0x55bb46048044 in ???
> #35 0x55bb46052ea1 in ???
> #36 0x55bb45ac5f8e in ???
> #37 0x1526470fcd8f in ???
> #38 0x1526470fce3f in ???
> #39 0x55bb45aef55d in ???
> #40 0xffffffffffffffff in ???
> --------------------------------------------------------------------------
> Primary job terminated normally, but 1 process returned
> a non-zero exit code. Per user-direction, the job has been aborted.
> --------------------------------------------------------------------------
> --------------------------------------------------------------------------
> mpirun noticed that process rank 0 with PID 1771753 on node dgx02 exited
> on signal 6 (Aborted).
> --------------------------------------------------------------------------
>
> BTW, I'm curious. If I set n MPI processes, each of them building a part
> of the linear system, and g GPUs, how does PETSc distribute those n pieces
> of system matrix and rhs in the g GPUs? Does it do some load balancing
> algorithm? Where can I read about this?
> Thank you and best Regards, I can also point you to my code repo in GitHub
> if you want to take a closer look.
>
> Best Regards,
> Marcos
>
> ------------------------------
> *From:* Junchao Zhang <junchao.zhang at gmail.com>
> *Sent:* Friday, August 11, 2023 10:52 AM
> *To:* Vanella, Marcos (Fed) <marcos.vanella at nist.gov>
> *Cc:* petsc-users at mcs.anl.gov <petsc-users at mcs.anl.gov>
> *Subject:* Re: [petsc-users] CUDA error trying to run a job with two mpi
> processes and 1 GPU
>
> Hi, Marcos,
> Could you build petsc in debug mode and then copy and paste the whole
> error stack message?
>
> Thanks
> --Junchao Zhang
>
>
> On Thu, Aug 10, 2023 at 5:51 PM Vanella, Marcos (Fed) via petsc-users <
> petsc-users at mcs.anl.gov> wrote:
>
> Hi, I'm trying to run a parallel matrix vector build and linear solution
> with PETSc on 2 MPI processes + one V100 GPU. I tested that the matrix
> build and solution is successful in CPUs only. I'm using cuda 11.5 and cuda
> enabled openmpi and gcc 9.3. When I run the job with GPU enabled I get the
> following error:
>
> terminate called after throwing an instance of
> 'thrust::system::system_error'
> *what(): merge_sort: failed to synchronize: cudaErrorIllegalAddress:
> an illegal memory access was encountered*
>
> Program received signal SIGABRT: Process abort signal.
>
> Backtrace for this error:
> terminate called after throwing an instance of
> 'thrust::system::system_error'
> what(): merge_sort: failed to synchronize: cudaErrorIllegalAddress: an
> illegal memory access was encountered
>
> Program received signal SIGABRT: Process abort signal.
>
> I'm new to submitting jobs in slurm that also use GPU resources, so I
> might be doing something wrong in my submission script. This is it:
>
> #!/bin/bash
> #SBATCH -J test
> #SBATCH -e /home/Issues/PETSc/test.err
> #SBATCH -o /home/Issues/PETSc/test.log
> #SBATCH --partition=batch
> #SBATCH --ntasks=2
> #SBATCH --nodes=1
> #SBATCH --cpus-per-task=1
> #SBATCH --ntasks-per-node=2
> #SBATCH --time=01:00:00
> #SBATCH --gres=gpu:1
>
> export OMP_NUM_THREADS=1
> module load cuda/11.5
> module load openmpi/4.1.1
>
> cd /home/Issues/PETSc
> *mpirun -n 2 */home/fds/Build/ompi_gnu_linux/fds_ompi_gnu_linux test.fds *-vec_type
> mpicuda -mat_type mpiaijcusparse -pc_type gamg*
>
> If anyone has any suggestions on how o troubleshoot this please let me
> know.
> Thanks!
> Marcos
>
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20230814/5aa24ceb/attachment-0001.html>
More information about the petsc-users
mailing list