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

Mark Adams mfadams at lbl.gov
Fri Aug 27 15:28:13 CDT 2021 

On Fri, Aug 27, 2021 at 3:56 PM Junchao Zhang <junchao.zhang at gmail.com>
wrote:

>
>
> On Fri, Aug 27, 2021, 1:52 PM Mark Adams <mfadams at lbl.gov> wrote:
>
>> 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.
>>
> --with-nvcc=nvcc_wrapper
>

What do I specify for cc and CC?


> 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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