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

Mark Adams mfadams at lbl.gov
Fri Aug 27 07:05:45 CDT 2021 

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?

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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