[petsc-users] CUDA error trying to run a job with two mpi processes and 1 GPU
Vanella, Marcos (Fed)
marcos.vanella at nist.gov
Mon Aug 14 16:45:00 CDT 2023
All right Junchao, thank you for looking at this!
So, I checked out the /dir_to_petsc/petsc/main branch, setup the petsc env variables:
# PETSc dir and arch, set MYSYS to nisaba dor FDS:
export PETSC_DIR=/dir_to_petsc/petsc
export PETSC_ARCH=arch-linux-c-dbg
export MYSYSTEM=nisaba
and configured the library with:
$ ./Configure 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
Then made and checked the PETSc build.
Then for FDS:
1. Clone my fds repo in a ~/fds_dir you make, and checkout the FireX branch:
$ cd ~/fds_dir
$ git clone https://github.com/marcosvanella/fds.git
$ cd fds
$ git checkout FireX
1. With PETSC_DIR, PETSC_ARCH and MYSYSTEM=nisaba defined, compile a debug target for fds (this is with cuda enabled openmpi compiled with gcc, in my case gcc-11.2 + PETSc):
$ cd Build/ompi_gnu_linux_db
$./make_fds.sh
You should see compilation lines like this, with the WITH_PETSC Preprocessor variable being defined:
Building ompi_gnu_linux_db
mpifort -c -m64 -O0 -std=f2018 -ggdb -Wall -Wunused-parameter -Wcharacter-truncation -Wno-target-lifetime -fcheck=all -fbacktrace -ffpe-trap=invalid,zero,overflow -frecursive -ffpe-summary=none -fall-intrinsics -fbounds-check -cpp -DGITHASH_PP=\"FDS-6.8.0-556-g04d5df7-dirty-FireX\" -DGITDATE_PP=\""Mon Aug 14 17:07:20 2023 -0400\"" -DBUILDDATE_PP=\""Aug 14, 2023 17:34:36\"" -DCOMPVER_PP=\""Gnu gfortran 11.2.1"\" -DWITH_PETSC -I"/home/mnv/Software/petsc/include/" -I"/home/mnv/Software/petsc/arch-linux-c-dbg/include" ../../Source/prec.f90
mpifort -c -m64 -O0 -std=f2018 -ggdb -Wall -Wunused-parameter -Wcharacter-truncation -Wno-target-lifetime -fcheck=all -fbacktrace -ffpe-trap=invalid,zero,overflow -frecursive -ffpe-summary=none -fall-intrinsics -fbounds-check -cpp -DGITHASH_PP=\"FDS-6.8.0-556-g04d5df7-dirty-FireX\" -DGITDATE_PP=\""Mon Aug 14 17:07:20 2023 -0400\"" -DBUILDDATE_PP=\""Aug 14, 2023 17:34:36\"" -DCOMPVER_PP=\""Gnu gfortran 11.2.1"\" -DWITH_PETSC -I"/home/mnv/Software/petsc/include/" -I"/home/mnv/Software/petsc/arch-linux-c-dbg/include" ../../Source/cons.f90
mpifort -c -m64 -O0 -std=f2018 -ggdb -Wall -Wunused-parameter -Wcharacter-truncation -Wno-target-lifetime -fcheck=all -fbacktrace -ffpe-trap=invalid,zero,overflow -frecursive -ffpe-summary=none -fall-intrinsics -fbounds-check -cpp -DGITHASH_PP=\"FDS-6.8.0-556-g04d5df7-dirty-FireX\" -DGITDATE_PP=\""Mon Aug 14 17:07:20 2023 -0400\"" -DBUILDDATE_PP=\""Aug 14, 2023 17:34:36\"" -DCOMPVER_PP=\""Gnu gfortran 11.2.1"\" -DWITH_PETSC -I"/home/mnv/Software/petsc/include/" -I"/home/mnv/Software/petsc/arch-linux-c-dbg/include" ../../Source/prop.f90
mpifort -c -m64 -O0 -std=f2018 -ggdb -Wall -Wunused-parameter -Wcharacter-truncation -Wno-target-lifetime -fcheck=all -fbacktrace -ffpe-trap=invalid,zero,overflow -frecursive -ffpe-summary=none -fall-intrinsics -fbounds-check -cpp -DGITHASH_PP=\"FDS-6.8.0-556-g04d5df7-dirty-FireX\" -DGITDATE_PP=\""Mon Aug 14 17:07:20 2023 -0400\"" -DBUILDDATE_PP=\""Aug 14, 2023 17:34:36\"" -DCOMPVER_PP=\""Gnu gfortran 11.2.1"\" -DWITH_PETSC -I"/home/mnv/Software/petsc/include/" -I"/home/mnv/Software/petsc/arch-linux-c-dbg/include" ../../Source/devc.f90
...
...
If you are compiling on a Power9 node you might come across this error right off the bat:
../../Source/prec.f90:34:8:
34 | REAL(QB), PARAMETER :: TWO_EPSILON_QB=2._QB*EPSILON(1._QB) !< A very small number 16 byte accuracy
| 1
Error: Kind -3 not supported for type REAL at (1)
which means for some reason gcc in the Power9 does not like quad precision definition in this manner. A way around it is to add the intrinsic Fortran2008 module iso_fortran_env:
use, intrinsic :: iso_fortran_env
in the fds/Source/prec.f90 file and change the quad precision denominator to:
INTEGER, PARAMETER :: QB = REAL128
in there. We are investigating the reason why this is happening. This is not related to Petsc in the code, everything related to PETSc calls is integers and double precision reals.
After the code compiles you get the executable in ~/fds_dir/fds/Build/ompi_gnu_linux_db/fds_ompi_gnu_linux_db
With which you can run the attached 2 mesh case as:
$ mpirun -n 2 ~/fds_dir/fds/Build/ompi_gnu_linux_db/fds_ompi_gnu_linux_db test.fds -log_view
and change PETSc ksp, pc runtime flags, etc. The default is PCG + HYPRE which is what I was testing in CPU. This is the result I get from the previous submission in an interactive job in Enki (similar with batch submissions, gmres ksp, gamg pc):
Starting FDS ...
MPI Process 1 started on enki11.adlp
MPI Process 0 started on enki11.adlp
Reading FDS input file ...
WARNING: SPEC REAC_FUEL is not in the table of pre-defined species. Any unassigned SPEC variables in the input were assigned the properties of nitrogen.
At line 3014 of file ../../Source/read.f90
Fortran runtime warning: An array temporary was created
At line 3014 of file ../../Source/read.f90
Fortran runtime warning: An array temporary was created
At line 3461 of file ../../Source/read.f90
Fortran runtime warning: An array temporary was created
At line 3461 of file ../../Source/read.f90
Fortran runtime warning: An array temporary was created
WARNING: DEVC Device is not within any mesh.
Fire Dynamics Simulator
Current Date : August 14, 2023 17:26:22
Revision : FDS6.7.0-11263-g04d5df7-dirty-FireX
Revision Date : Mon Aug 14 17:07:20 2023 -0400
Compiler : Gnu gfortran 11.2.1
Compilation Date : Aug 14, 2023 17:11:05
MPI Enabled; Number of MPI Processes: 2
OpenMP Enabled; Number of OpenMP Threads: 1
MPI version: 3.1
MPI library version: Open MPI v4.1.4, package: Open MPI xng4 at enki01.adlp Distribution, ident: 4.1.4, repo rev: v4.1.4, May 26, 2022
Job TITLE :
Job ID string : test
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 ???
#2 0x2000000604d7 in ???
#3 0x200039cb9628 in ???
#0 0x2000397fcd8f in ???
#1 0x2000397fb657 in ???
#2 0x2000000604d7 in ???
#3 0x200039cb9628 in ???
#4 0x200039c93eb3 in ???
#5 0x200039364a97 in ???
#4 0x200039c93eb3 in ???
#5 0x200039364a97 in ???
#6 0x20003935f6d3 in ???
#7 0x20003935f78f in ???
#8 0x20003935fc6b in ???
#6 0x20003935f6d3 in ???
#7 0x20003935f78f in ???
#8 0x20003935fc6b in ???
#9 0x11ec67db in _ZN6thrust8cuda_cub14throw_on_errorE9cudaErrorPKc
at /usr/local/cuda-11.7/include/thrust/system/cuda/detail/util.h:225
#10 0x11ec67db 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 0x11efc7e3 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
#9 0x11ec67db in _ZN6thrust8cuda_cub14throw_on_errorE9cudaErrorPKc
at /usr/local/cuda-11.7/include/thrust/system/cuda/detail/util.h:225
#10 0x11ec67db 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 0x11efc7e3 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 0x11efc7e3 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
#12 0x11efc7e3 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 0x11efc7e3 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 0x11efc7e3 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 0x11efc7e3 in _ZN6thrust6detail11vector_baseIiNS_16device_allocatorIiEEE12default_initEm
at /usr/local/cuda-11.7/include/thrust/detail/vector_base.inl:220
#16 0x11efc7e3 in _ZN6thrust6detail11vector_baseIiNS_16device_allocatorIiEEE12default_initEm
at /usr/local/cuda-11.7/include/thrust/detail/vector_base.inl:213
#17 0x11efc7e3 in _ZN6thrust6detail11vector_baseIiNS_16device_allocatorIiEEEC2Em
at /usr/local/cuda-11.7/include/thrust/detail/vector_base.inl:65
#13 0x11efc7e3 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 0x11efc7e3 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 0x11efc7e3 in _ZN6thrust6detail11vector_baseIiNS_16device_allocatorIiEEE12default_initEm
at /usr/local/cuda-11.7/include/thrust/detail/vector_base.inl:220
#16 0x11efc7e3 in _ZN6thrust6detail11vector_baseIiNS_16device_allocatorIiEEE12default_initEm
at /usr/local/cuda-11.7/include/thrust/detail/vector_base.inl:213
#17 0x11efc7e3 in _ZN6thrust6detail11vector_baseIiNS_16device_allocatorIiEEEC2Em
at /usr/local/cuda-11.7/include/thrust/detail/vector_base.inl:65
#18 0x11eda3c7 in _ZN6thrust13device_vectorIiNS_16device_allocatorIiEEEC4Em
at /usr/local/cuda-11.7/include/thrust/device_vector.h:88
#19 0x11eda3c7 in MatSeqAIJCUSPARSECopyToGPU
at /home/mnv/Software/petsc/src/mat/impls/aij/seq/seqcusparse/aijcusparse.cu:2488
#20 0x11edc6b7 in MatSetPreallocationCOO_SeqAIJCUSPARSE
at /home/mnv/Software/petsc/src/mat/impls/aij/seq/seqcusparse/aijcusparse.cu:4300
#18 0x11eda3c7 in _ZN6thrust13device_vectorIiNS_16device_allocatorIiEEEC4Em
at /usr/local/cuda-11.7/include/thrust/device_vector.h:88
#19 0x11eda3c7 in MatSeqAIJCUSPARSECopyToGPU
at /home/mnv/Software/petsc/src/mat/impls/aij/seq/seqcusparse/aijcusparse.cu:2488
#20 0x11edc6b7 in MatSetPreallocationCOO_SeqAIJCUSPARSE
at /home/mnv/Software/petsc/src/mat/impls/aij/seq/seqcusparse/aijcusparse.cu:4300
#21 0x11e91bc7 in MatSetPreallocationCOO
at /home/mnv/Software/petsc/src/mat/utils/gcreate.c:650
#21 0x11e91bc7 in MatSetPreallocationCOO
at /home/mnv/Software/petsc/src/mat/utils/gcreate.c:650
#22 0x1316d5ab in MatConvert_AIJ_HYPRE
at /home/mnv/Software/petsc/src/mat/impls/hypre/mhypre.c:648
#22 0x1316d5ab in MatConvert_AIJ_HYPRE
at /home/mnv/Software/petsc/src/mat/impls/hypre/mhypre.c:648
#23 0x11e3b463 in MatConvert
at /home/mnv/Software/petsc/src/mat/interface/matrix.c:4428
#23 0x11e3b463 in MatConvert
at /home/mnv/Software/petsc/src/mat/interface/matrix.c:4428
#24 0x14072213 in PCSetUp_HYPRE
at /home/mnv/Software/petsc/src/ksp/pc/impls/hypre/hypre.c:254
#24 0x14072213 in PCSetUp_HYPRE
at /home/mnv/Software/petsc/src/ksp/pc/impls/hypre/hypre.c:254
#25 0x1276a9db in PCSetUp
at /home/mnv/Software/petsc/src/ksp/pc/interface/precon.c:1069
#25 0x1276a9db in PCSetUp
at /home/mnv/Software/petsc/src/ksp/pc/interface/precon.c:1069
#26 0x127d923b in KSPSetUp
at /home/mnv/Software/petsc/src/ksp/ksp/interface/itfunc.c:415
#27 0x127e033f in KSPSolve_Private
#26 0x127d923b in KSPSetUp
at /home/mnv/Software/petsc/src/ksp/ksp/interface/itfunc.c:415
#27 0x127e033f in KSPSolve_Private
at /home/mnv/Software/petsc/src/ksp/ksp/interface/itfunc.c:836
at /home/mnv/Software/petsc/src/ksp/ksp/interface/itfunc.c:836
#28 0x127e6f07 in KSPSolve
at /home/mnv/Software/petsc/src/ksp/ksp/interface/itfunc.c:1082
#28 0x127e6f07 in KSPSolve
at /home/mnv/Software/petsc/src/ksp/ksp/interface/itfunc.c:1082
#29 0x1280d70b in kspsolve_
at /home/mnv/Software/petsc/arch-linux-c-dbg/src/ksp/ksp/interface/ftn-auto/itfuncf.c:335
#29 0x1280d70b in kspsolve_
at /home/mnv/Software/petsc/arch-linux-c-dbg/src/ksp/ksp/interface/ftn-auto/itfuncf.c:335
#30 0x1140858f in __globmat_solver_MOD_glmat_solver
at ../../Source/pres.f90:3130
#30 0x1140858f in __globmat_solver_MOD_glmat_solver
at ../../Source/pres.f90:3130
#31 0x119faddf in pressure_iteration_scheme
at ../../Source/main.f90:1449
#32 0x1196c15f in fds
at ../../Source/main.f90:688
#31 0x119faddf in pressure_iteration_scheme
at ../../Source/main.f90:1449
#32 0x1196c15f in fds
at ../../Source/main.f90:688
#33 0x11a126f3 in main
at ../../Source/main.f90:6
#33 0x11a126f3 in main
at ../../Source/main.f90:6
--------------------------------------------------------------------------
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 1 with PID 3028180 on node enki11 exited on signal 6 (Aborted).
--------------------------------------------------------------------------
Seems the issue stems from the call to KSPSOLVE, line 3130 in fds/Source/pres.f90.
Well, thank you for taking the time to look at this and also let me know if these threads should be moved to the issue tracker, or other venue.
Best,
Marcos
________________________________
From: Junchao Zhang <junchao.zhang at gmail.com>
Sent: Monday, August 14, 2023 4:37 PM
To: Vanella, Marcos (Fed) <marcos.vanella at nist.gov>; PETSc users list <petsc-users at mcs.anl.gov>
Subject: Re: [petsc-users] CUDA error trying to run a job with two mpi processes and 1 GPU
I don't see a problem in the matrix assembly.
If you point me to your repo and show me how to build it, I can try to reproduce.
--Junchao Zhang
On Mon, Aug 14, 2023 at 2:53 PM Vanella, Marcos (Fed) <marcos.vanella at nist.gov<mailto:marcos.vanella at nist.gov>> wrote:
Hi Junchao, I've tried for my case using the -ksp_type gmres and -pc_type asm with -mat_type aijcusparse -sub_pc_factor_mat_solver_type cusparse as (I understand) is done in the ex60. The error is always the same, so it seems it is not related to ksp,pc. Indeed it seems to happen when trying to offload the Matrix to the GPU:
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 ???
...
#8 0x20003935fc6b in ???
#9 0x11ec769b in _ZN6thrust8cuda_cub14throw_on_errorE9cudaErrorPKc
at /usr/local/cuda-11.7/include/thrust/system/cuda/detail/util.h:225
#10 0x11ec769b 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 0x11efd6a3 in _ZN6thrust20uninitialized_fill_nINS_8cuda_cub3tagENS_10device_ptrIiEEmiEET0_RKNS_6detail21execution_policy_baseIT_EES5_T1_RKT2_
#9 0x11ec769b in _ZN6thrust8cuda_cub14throw_on_errorE9cudaErrorPKc
at /usr/local/cuda-11.7/include/thrust/system/cuda/detail/util.h:225
#10 0x11ec769b 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 0x11efd6a3 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 0x11efd6a3 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
at /usr/local/cuda-11.7/include/thrust/detail/uninitialized_fill.inl:55
#12 0x11efd6a3 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 0x11efd6a3 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 0x11efd6a3 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 0x11efd6a3 in _ZN6thrust6detail11vector_baseIiNS_16device_allocatorIiEEE12default_initEm
#13 0x11efd6a3 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 0x11efd6a3 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 0x11efd6a3 in _ZN6thrust6detail11vector_baseIiNS_16device_allocatorIiEEE12default_initEm
at /usr/local/cuda-11.7/include/thrust/detail/vector_base.inl:220
at /usr/local/cuda-11.7/include/thrust/detail/vector_base.inl:220
#16 0x11efd6a3 in _ZN6thrust6detail11vector_baseIiNS_16device_allocatorIiEEE12default_initEm
at /usr/local/cuda-11.7/include/thrust/detail/vector_base.inl:213
#17 0x11efd6a3 in _ZN6thrust6detail11vector_baseIiNS_16device_allocatorIiEEEC2Em
at /usr/local/cuda-11.7/include/thrust/detail/vector_base.inl:65
#18 0x11edb287 in _ZN6thrust13device_vectorIiNS_16device_allocatorIiEEEC4Em
at /usr/local/cuda-11.7/include/thrust/device_vector.h:88
#19 0x11edb287 in MatSeqAIJCUSPARSECopyToGPU
at /home/mnv/Software/petsc/src/mat/impls/aij/seq/seqcusparse/aijcusparse.cu:2488<http://aijcusparse.cu:2488/>
#20 0x11edfd1b in MatSeqAIJCUSPARSEGetIJ
...
...
This is the piece of fortran code I have doing this within my Poisson solver:
! Create Parallel PETSc Sparse matrix for this ZSL: Set diag/off diag blocks nonzeros per row to 5.
CALL MATCREATEAIJ(MPI_COMM_WORLD,ZSL%NUNKH_LOCAL,ZSL%NUNKH_LOCAL,ZSL%NUNKH_TOTAL,ZSL%NUNKH_TOTAL,&
7,PETSC_NULL_INTEGER,7,PETSC_NULL_INTEGER,ZSL%PETSC_ZS%A_H,PETSC_IERR)
CALL MATSETFROMOPTIONS(ZSL%PETSC_ZS%A_H,PETSC_IERR)
DO IROW=1,ZSL%NUNKH_LOCAL
DO JCOL=1,ZSL%NNZ_D_MAT_H(IROW)
! PETSC expects zero based indexes.1,Global I position (zero base),1,Global J position (zero base)
CALL MATSETVALUES(ZSL%PETSC_ZS%A_H,1,ZSL%UNKH_IND(NM_START)+IROW-1,1,ZSL%JD_MAT_H(JCOL,IROW)-1,&
ZSL%D_MAT_H(JCOL,IROW),INSERT_VALUES,PETSC_IERR)
ENDDO
ENDDO
CALL MATASSEMBLYBEGIN(ZSL%PETSC_ZS%A_H, MAT_FINAL_ASSEMBLY, PETSC_IERR)
CALL MATASSEMBLYEND(ZSL%PETSC_ZS%A_H, MAT_FINAL_ASSEMBLY, PETSC_IERR)
Note that I allocate d_nz=7 and o_nz=7 per row (more than enough size), and add nonzero values one by one. I wonder if there is something related to this that the copying to GPU does not like.
Thanks,
Marcos
________________________________
From: Junchao Zhang <junchao.zhang at gmail.com<mailto:junchao.zhang at gmail.com>>
Sent: Monday, August 14, 2023 3:24 PM
To: Vanella, Marcos (Fed) <marcos.vanella at nist.gov<mailto:marcos.vanella at nist.gov>>
Cc: PETSc users list <petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>>; Satish Balay <balay at mcs.anl.gov<mailto:balay at mcs.anl.gov>>
Subject: Re: [petsc-users] CUDA error trying to run a job with two mpi processes and 1 GPU
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<mailto: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<mailto:junchao.zhang at gmail.com>>
Sent: Friday, August 11, 2023 5:52 PM
To: Vanella, Marcos (Fed) <marcos.vanella at nist.gov<mailto:marcos.vanella at nist.gov>>
Cc: PETSc users list <petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>>; Satish Balay <balay at mcs.anl.gov<mailto: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<mailto: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<http://aijcusparse.cu:2488/>
#20 0x11eef623 in MatSeqAIJCUSPARSEMergeMats
at /home/mnv/Software/petsc/src/mat/impls/aij/seq/seqcusparse/aijcusparse.cu:4696<http://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<http://aijcusparse.cu:2488/>
#20 0x11eef623 in MatSeqAIJCUSPARSEMergeMats
at /home/mnv/Software/petsc/src/mat/impls/aij/seq/seqcusparse/aijcusparse.cu:4696<http://aijcusparse.cu:4696/>
#21 0x11f0682b in MatMPIAIJGetLocalMatMerge_MPIAIJCUSPARSE
at /home/mnv/Software/petsc/src/mat/impls/aij/mpi/mpicusparse/mpiaijcusparse.cu:251<http://mpiaijcusparse.cu:251/>
#21 0x11f0682b in MatMPIAIJGetLocalMatMerge_MPIAIJCUSPARSE
at /home/mnv/Software/petsc/src/mat/impls/aij/mpi/mpicusparse/mpiaijcusparse.cu:251<http://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<mailto:junchao.zhang at gmail.com>>
Sent: Friday, August 11, 2023 3:35 PM
To: Vanella, Marcos (Fed) <marcos.vanella at nist.gov<mailto:marcos.vanella at nist.gov>>; PETSc users list <petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>>; Satish Balay <balay at mcs.anl.gov<mailto: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<mailto: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<mailto: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<mailto:junchao.zhang at gmail.com>>
Sent: Friday, August 11, 2023 3:04 PM
To: Vanella, Marcos (Fed) <marcos.vanella at nist.gov<mailto:marcos.vanella at nist.gov>>
Cc: petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov> <petsc-users at mcs.anl.gov<mailto: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<mailto: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<http://aijcusparse.cu:4452/>
#17 0x55bb46c5b27c in MatSetPreallocationCOO_MPIAIJCUSPARSE_Basic
at /home/mnv/Software/petsc/src/mat/impls/aij/mpi/mpicusparse/mpiaijcusparse.cu:173<http://mpiaijcusparse.cu:173/>
#18 0x55bb46c5b27c in MatSetPreallocationCOO_MPIAIJCUSPARSE
at /home/mnv/Software/petsc/src/mat/impls/aij/mpi/mpicusparse/mpiaijcusparse.cu:222<http://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<mailto:junchao.zhang at gmail.com>>
Sent: Friday, August 11, 2023 10:52 AM
To: Vanella, Marcos (Fed) <marcos.vanella at nist.gov<mailto:marcos.vanella at nist.gov>>
Cc: petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov> <petsc-users at mcs.anl.gov<mailto: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<mailto: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
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