[petsc-users] runtime error on Summit with nvhpc21.7

[Mark Adams]

I think the problem is that I build with MPICC and they use nvcc_wrapper. I
could just try building PETSc with CC=nvcc_wrapper, but it was not clear if
this was the way to go.
I will try it.
Thanks,
Mark

On Fri, Aug 27, 2021 at 10:50 AM Junchao Zhang <junchao.zhang at gmail.com>
wrote:

>
>
>
> On Fri, Aug 27, 2021 at 7:06 AM Mark Adams <mfadams at lbl.gov> wrote:
>
>> I have a user (cc'ed) that has a C++ code and is using a PETSc that I
>> built. He is getting this runtime error.
>>
>> 'make check' runs clean and I built snes/tutorial/ex1 manually, to get a
>> link line, and it ran fine.
>> I appended the users link line and my test.
>>
>> I see that they are using Kokkos' "nvcc_wrapper". Should I rebuild PETSc
>> using that, maybe we just need to make sure we are both using the same
>> underlying compiler or should they use mpiCC?
>>
> It looks like they used nvcc_wrapper to replace nvcc.  You can ask them to
> use nvcc directly to see what happens. But the error happened in petsc
> initialization, petscsys_petscinitializenohelp, so I doubt it helps.  The
> easy way is to just attach a debugger.
>
>>
>> Thanks,
>> Mark
>>
>>
>> [e13n16:591873] *** Process received signal ***
>>
>> [e13n16:591873] Signal: Segmentation fault (11)
>>
>> [e13n16:591873] Signal code: Invalid permissions (2)
>>
>> [e13n16:591873] Failing at address: 0x102c87e0
>>
>> [e13n16:591873] [ 0]
>> linux-vdso64.so.1(__kernel_sigtramp_rt64+0x0)[0x2000000504d8]
>>
>> [e13n16:591873] [ 1] [e13n16:591872] *** Process received signal ***
>>
>> [e13n16:591872] Signal: Segmentation fault (11)
>>
>> [e13n16:591872] Signal code: Invalid permissions (2)
>>
>> [e13n16:591872] Failing at address: 0x102c87e0
>>
>> [e13n16:591872] [ 0]
>> linux-vdso64.so.1(__kernel_sigtramp_rt64+0x0)[0x2000000504d8]
>>
>> [e13n16:591872] [ 1] [e13n16:591871] *** Process received signal ***
>>
>> [e13n16:591871] Signal: Segmentation fault (11)
>>
>> [e13n16:591871] Signal code: Invalid permissions (2)
>>
>> [e13n16:591871] Failing at address: 0x102c87e0
>>
>> [e13n16:591871] [ 0]
>> linux-vdso64.so.1(__kernel_sigtramp_rt64+0x0)[0x2000000504d8]
>>
>> [e13n16:591871] [ 1]
>> /autofs/nccs-svm1_sw/summit/nvhpc_sdk/rhel8/Linux_ppc64le/21.7/compilers/lib/libnvf.so(pgf90_str_copy_klen+0x1fc)[0x200004a79ee4]
>>
>> [e13n16:591871] [ 2] [e13n16:591874] *** Process received signal ***
>>
>> [e13n16:591874] Signal: Segmentation fault (11)
>>
>> [e13n16:591874] Signal code: Invalid permissions (2)
>>
>> [e13n16:591874] Failing at address: 0x102c87e0
>>
>> [e13n16:591874] [ 0]
>> linux-vdso64.so.1(__kernel_sigtramp_rt64+0x0)[0x2000000504d8]
>>
>> [e13n16:591874] [ 1]
>> /autofs/nccs-svm1_sw/summit/nvhpc_sdk/rhel8/Linux_ppc64le/21.7/compilers/lib/libnvf.so(pgf90_str_copy_klen+0x1fc)[0x200004a79ee4]
>>
>> [e13n16:591874] [ 2]
>> /gpfs/alpine/world-shared/phy122/lib/install/summit/petsc/current/opt-nvhpc21.7b/lib/libpetsc.so.3.015(petscsys_petscinitializenohelp_+0xf4)[0x20000097b3ec]
>>
>> [e13n16:591874] [ 3]
>> /ccs/home/scheinberg/new_install/build/bin/xgc-es-cpp[0x10131dd8]
>>
>> [e13n16:591874] [ 4]
>> /ccs/home/scheinberg/new_install/build/bin/xgc-es-cpp[0x10015c60]
>>
>> [e13n16:591874] [ 5]
>> /ccs/home/scheinberg/new_install/build/bin/xgc-es-cpp[0x1005a8b0]
>>
>> [e13n16:591874] [ 6]
>> /ccs/home/scheinberg/new_install/build/bin/xgc-es-cpp[0x10015b14]
>>
>> [e13n16:591874] [ 7]
>> /ccs/home/scheinberg/new_install/build/bin/xgc-es-cpp[0x10014cd0]
>>
>> [e13n16:591874] [ 8]
>> /gpfs/alpine/world-shared/phy122/lib/install/summit/petsc/current/opt-nvhpc21.7b/lib/libpetsc.so.3.015(petscsys_petscinitializenohelp_+0xf4)[0x20000097b3ec]
>>
>> [e13n16:591871] [ 3]
>> /ccs/home/scheinberg/new_install/build/bin/xgc-es-cpp[0x10131dd8]
>>
>> [e13n16:591871] [ 4]
>> /ccs/home/scheinberg/new_install/build/bin/xgc-es-cpp[0x10015c60]
>>
>> [e13n16:591871] [ 5]
>> /ccs/home/scheinberg/new_install/build/bin/xgc-es-cpp[0x1005a8b0]
>>
>> [e13n16:591871] [ 6]
>> /ccs/home/scheinberg/new_install/build/bin/xgc-es-cpp[0x10015b14]
>>
>> [e13n16:591871] [ 7]
>> /ccs/home/scheinberg/new_install/build/bin/xgc-es-cpp[0x10014cd0]
>>
>> [e13n16:591871] [ 8]
>> /usr/lib/gcc/ppc64le-redhat-linux/8/../../../../lib64/power9/libc.so.6(+0x24078)[0x200005934078]
>>
>> [e13n16:591871] [ 9]
>> /usr/lib/gcc/ppc64le-redhat-linux/8/../../../../lib64/power9/libc.so.6(__libc_start_main+0xb4)[0x200005934264]
>>
>> [e13n16:591871] *** End of error message ***
>>
>>
>> /usr/lib/gcc/ppc64le-redhat-linux/8/../../../../lib64/power9/libc.so.6(+0x24078)[0x200005934078]
>>
>> [e13n16:591874] [ 9]
>> /usr/lib/gcc/ppc64le-redhat-linux/8/../../../../lib64/power9/libc.so.6(__libc_start_main+0xb4)[0x200005934264]
>>
>> [e13n16:591874] *** End of error message ***
>>
>>
>> /autofs/nccs-svm1_sw/summit/nvhpc_sdk/rhel8/Linux_ppc64le/21.7/compilers/lib/libnvf.so(pgf90_str_copy_klen+0x1fc)[0x200004a79ee4]
>>
>> [e13n16:591872] [ 2]
>> /gpfs/alpine/world-shared/phy122/lib/install/summit/petsc/current/opt-nvhpc21.7b/lib/libpetsc.so.3.015(petscsys_petscinitializenohelp_+0xf4)[0x20000097b3ec]
>>
>> [e13n16:591872] [ 3]
>> /ccs/home/scheinberg/new_install/build/bin/xgc-es-cpp[0x10131dd8]
>>
>> [e13n16:591872] [ 4]
>> /ccs/home/scheinberg/new_install/build/bin/xgc-es-cpp[0x10015c60]
>>
>> [e13n16:591872] [ 5]
>> /ccs/home/scheinberg/new_install/build/bin/xgc-es-cpp[0x1005a8b0]
>>
>> [e13n16:591872] [ 6]
>> /ccs/home/scheinberg/new_install/build/bin/xgc-es-cpp[0x10015b14]
>>
>> [e13n16:591872] [ 7]
>> /ccs/home/scheinberg/new_install/build/bin/xgc-es-cpp[0x10014cd0]
>>
>> [e13n16:591872] [ 8]
>> /usr/lib/gcc/ppc64le-redhat-linux/8/../../../../lib64/power9/libc.so.6(+0x24078)[0x200005934078]
>>
>> [e13n16:591872] [ 9]
>> /usr/lib/gcc/ppc64le-redhat-linux/8/../../../../lib64/power9/libc.so.6(__libc_start_main+0xb4)[0x200005934264]
>>
>> [e13n16:591872] *** End of error message ***
>>
>>
>> /autofs/nccs-svm1_sw/summit/nvhpc_sdk/rhel8/Linux_ppc64le/21.7/compilers/lib/libnvf.so(pgf90_str_copy_klen+0x1fc)[0x200004a79ee4]
>>
>> [e13n16:591873] [ 2]
>> /gpfs/alpine/world-shared/phy122/lib/install/summit/petsc/current/opt-nvhpc21.7b/lib/libpetsc.so.3.015(petscsys_petscinitializenohelp_+0xf4)[0x20000097b3ec]
>>
>> [e13n16:591873] [ 3]
>> /ccs/home/scheinberg/new_install/build/bin/xgc-es-cpp[0x10131dd8]
>>
>> [e13n16:591873] [ 4]
>> /ccs/home/scheinberg/new_install/build/bin/xgc-es-cpp[0x10015c60]
>>
>> [e13n16:591873] [ 5]
>> /ccs/home/scheinberg/new_install/build/bin/xgc-es-cpp[0x1005a8b0]
>>
>> [e13n16:591873] [ 6]
>> /ccs/home/scheinberg/new_install/build/bin/xgc-es-cpp[0x10015b14]
>>
>> [e13n16:591873] [ 7]
>> /ccs/home/scheinberg/new_install/build/bin/xgc-es-cpp[0x10014cd0]
>>
>> [e13n16:591873] [ 8]
>> /usr/lib/gcc/ppc64le-redhat-linux/8/../../../../lib64/power9/libc.so.6(+0x24078)[0x200005934078]
>>
>> [e13n16:591873] [ 9]
>> /usr/lib/gcc/ppc64le-redhat-linux/8/../../../../lib64/power9/libc.so.6(__libc_start_main+0xb4)[0x200005934264]
>>
>> [e13n16:591873] *** End of error message ***
>>
>> ERROR:  One or more process (first noticed rank 1) terminated with signal
>> 11 (core dumped)
>>
>>
>>
>>
>> /gpfs/alpine/world-shared/phy122/lib/install/summit/kokkos/nvhpc21.7/bin/nvcc_wrapper
>> -arch=sm_70 CMakeFiles/xgc-es-cpp.dir/xgc-es-cpp_build_info.F90.o -o
>> bin/xgc-es-cpp  -Wl,-rpath,/gpfs/alpine/world-shared/phy122/lib/install/summit/petsc/current/opt-nvhpc21.7b/lib:/gpfs/alpine/world-shared/phy122/lib/install/summit/adios2/devel/nvhpc/lib64
>> liblibxgc-es-cpp.a
>> /sw/summit/spack-envs/base/opt/linux-rhel8-ppc64le/nvhpc-21.7/netlib-lapack-3.9.1-b5iqtudpwjumes5gsdol3bzsh7qlv7mf/lib64/liblapack.so
>> /sw/summit/spack-envs/base/opt/linux-rhel8-ppc64le/nvhpc-21.7/netlib-lapack-3.9.1-b5iqtudpwjumes5gsdol3bzsh7qlv7mf/lib64/libblas.so
>> /gpfs/alpine/world-shared/phy122/lib/install/summit/petsc/current/opt-nvhpc21.7b/lib/libpetsc.so
>> /gpfs/alpine/world-shared/phy122/lib/install/summit/petsc/current/opt-nvhpc21.7b/lib/libparmetis.so
>> /gpfs/alpine/world-shared/phy122/lib/install/summit/petsc/current/opt-nvhpc21.7b/lib/libmetis.so
>> /sw/summit/spack-envs/base/opt/linux-rhel8-ppc64le/nvhpc-21.7/fftw-3.3.9-bzi7deue27ijd7xm4zn7pt22u4sj47g4/lib/libfftw3.so
>> libs/pspline/libpspline.a libs/camtimers/libtimers.a
>> /autofs/nccs-svm1_sw/summit/nvhpc_sdk/rhel8/Linux_ppc64le/21.7/compilers/lib/libacchost.so
>> /gpfs/alpine/world-shared/phy122/lib/install/summit/adios2/devel/nvhpc/lib64/libadios2_fortran_mpi.so.2.7.1
>> /gpfs/alpine/world-shared/phy122/lib/install/summit/adios2/devel/nvhpc/lib64/libadios2_fortran.so.2.7.1
>> /gpfs/alpine/world-shared/phy122/lib/install/summit/kokkos/DEFAULT/install/lib64/libkokkoscontainers.a
>> /gpfs/alpine/world-shared/phy122/lib/install/summit/kokkos/DEFAULT/install/lib64/libkokkoscore.a
>> /usr/lib64/libcuda.so
>> /autofs/nccs-svm1_sw/summit/nvhpc_sdk/rhel8/Linux_ppc64le/21.7/cuda/11.0/lib64/libcudart.so
>> /usr/lib64/libdl.so -lmpi_ibm_usempif08 -lmpi_ibm_usempi_ignore_tkr
>> -lmpi_ibm_mpifh -lnvf
>> -Wl,-rpath-link,/gpfs/alpine/world-shared/phy122/lib/install/summit/adios2/devel/nvhpc/lib64
>>
>>
>>
>> 19:39 main= /gpfs/alpine/csc314/scratch/adams/petsc/src/snes/tutorials$
>> make
>> PETSC_DIR=/gpfs/alpine/world-shared/phy122/lib/install/summit/petsc/current/opt-nvhpc21.7
>> PETSC_ARCH="" ex1
>> *mpicc* -fPIC -g -fast  -fPIC -g -fast
>>  -I/gpfs/alpine/world-shared/phy122/lib/install/summit/petsc/current/opt-nvhpc21.7/include
>>     ex1.c
>>  -Wl,-rpath,/gpfs/alpine/world-shared/phy122/lib/install/summit/petsc/current/opt-nvhpc21.7/lib
>> -L/gpfs/alpine/world-shared/phy122/lib/install/summit/petsc/current/opt-nvhpc21.7/lib
>> -Wl,-rpath,/gpfs/alpine/world-shared/phy122/lib/install/summit/petsc/current/opt-nvhpc21.7/lib
>> -L/gpfs/alpine/world-shared/phy122/lib/install/summit/petsc/current/opt-nvhpc21.7/lib
>> -Wl,-rpath,/sw/summit/spack-envs/base/opt/linux-rhel8-ppc64le/nvhpc-21.7/spectrum-mpi-10.4.0.3-20210112-nv7jd363ym3n4zpgornfbq6bh4tqjyak/lib
>> -L/sw/summit/spack-envs/base/opt/linux-rhel8-ppc64le/nvhpc-21.7/spectrum-mpi-10.4.0.3-20210112-nv7jd363ym3n4zpgornfbq6bh4tqjyak/lib
>> -Wl,-rpath,/sw/summit/spack-envs/base/opt/linux-rhel8-ppc64le/nvhpc-21.7/hdf5-1.10.7-nfhjvzsshg5qihqv44y5ji6ihsqpd73v/lib
>> -L/sw/summit/spack-envs/base/opt/linux-rhel8-ppc64le/nvhpc-21.7/hdf5-1.10.7-nfhjvzsshg5qihqv44y5ji6ihsqpd73v/lib
>> -Wl,-rpath,/sw/summit/spack-envs/base/opt/linux-rhel8-ppc64le/nvhpc-21.7/netlib-lapack-3.9.1-b5iqtudpwjumes5gsdol3bzsh7qlv7mf/lib64
>> -L/sw/summit/spack-envs/base/opt/linux-rhel8-ppc64le/nvhpc-21.7/netlib-lapack-3.9.1-b5iqtudpwjumes5gsdol3bzsh7qlv7mf/lib64
>> -Wl,-rpath,/autofs/nccs-svm1_sw/summit/nvhpc_sdk/rhel8/Linux_ppc64le/21.7/compilers/lib
>> -L/autofs/nccs-svm1_sw/summit/nvhpc_sdk/rhel8/Linux_ppc64le/21.7/compilers/lib
>> -Wl,-rpath,/usr/lib/gcc/ppc64le-redhat-linux/8
>> -L/usr/lib/gcc/ppc64le-redhat-linux/8 -lpetsc -llapack -lblas -lparmetis
>> -lmetis -lstdc++ -ldl -lpthread -lmpiprofilesupport -lmpi_ibm_usempif08
>> -lmpi_ibm_usempi_ignore_tkr -lmpi_ibm_mpifh -lmpi_ibm -lnvf -lnvomp
>> -latomic -lnvhpcatm -lnvcpumath -lnvc -lrt -lm -lgcc_s -lstdc++ -ldl -o ex1
>> 19:40 main= /gpfs/alpine/csc314/scratch/adams/petsc/src/snes/tutorials$ *mpicc
>> --version*
>>
>> *nvc 21.7-0 linuxpower target on Linuxpower*
>> NVIDIA Compilers and Tools
>> Copyright (c) 2021, NVIDIA CORPORATION & AFFILIATES.  All rights reserved.
>> 19:40 main= /gpfs/alpine/csc314/scratch/adams/petsc/src/snes/tutorials$
>> jsrun -n 1 ./ex1 -ksp_monitor
>>     0 KSP Residual norm 6.041522986797e+00
>>     1 KSP Residual norm 1.042493382631e+00
>>     2 KSP Residual norm 7.950907844730e-16
>>     0 KSP Residual norm 4.786756692342e+00
>>     1 KSP Residual norm 1.426392207750e-01
>>     2 KSP Residual norm 1.801079604472e-15
>>     0 KSP Residual norm 2.986456323228e+00
>>     1 KSP Residual norm 7.669888809223e-02
>>     2 KSP Residual norm 3.744083117256e-16
>>     0 KSP Residual norm 2.306244667700e-01
>>     1 KSP Residual norm 1.355550749587e-02
>>     2 KSP Residual norm 5.845524837731e-17
>>     0 KSP Residual norm 1.936314002654e-03
>>     1 KSP Residual norm 2.125593590819e-04
>>     2 KSP Residual norm 6.987141455073e-20
>>     0 KSP Residual norm 1.435593531990e-07
>>     1 KSP Residual norm 2.588271385567e-08
>>     2 KSP Residual norm 3.942196167935e-23
>>
>>
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