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

Fri Aug 27 09:49:59 CDT 2021

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
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20210827/80400ecc/attachment-0001.html>