[petsc-dev] kokkos test fail in branch

Sat Jun 5 13:18:08 CDT 2021

Ah, there was an old one there. I removed it and I can not compile ex3k. I
thought check always rebuilt executables. Now I get a link error:

14:12 barry/2020-11-11/cleanup-matsetvaluesdevice *=
/gpfs/alpine/csc314/scratch/adams/petsc/src/snes/tutorials$ make
PETSC_DIR=/gpfs/alpine/csc314/scratch/adams/petsc
PETSC_ARCH=arch-summit-opt-gnu-kokkos-notpl-cuda10 ex3k
PATH=/sw/sources/lsf-tools/2.0/summit/bin:/sw/summit/xalt/1.2.1/bin:/sw/summit/forge/20.0.1/bin:/autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/gcc-6.4.0/spectrum-mpi-10.3.1.2-20200121-awz2q5brde7wgdqqw4ugalrkukeub4eb/bin:/sw/summit/gcc/6.4.0/bin:/sw/summit/cuda/10.1.243/bin:/autofs/nccs-svm1_sw/summit/.swci/0-core/opt/spack/20180914/linux-rhel7-ppc64le/gcc-4.8.5/cmake-3.20.2-24ualfzy6em6ws5sbiu7rlgcuionodrm/bin:/autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/gcc-4.8.5/darshan-runtime-3.1.7-cnvxicgf5j4ap64qi6v5gxp67hmrjz43/bin:/sw/sources/hpss/bin:/opt/ibm/spectrumcomputing/lsf/
10.1.0.9/linux3.10-glibc2.17-ppc64le-csm/etc:/opt/ibm/spectrumcomputing/lsf/10.1.0.9/linux3.10-glibc2.17-ppc64le-csm/bin:/opt/ibm/csm/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/ibm/flightlog/bin:/opt/ibutils/bin:/opt/ibm/spectrum_mpi/jsm_pmix/bin:/opt/puppetlabs/bin:/usr/lpp/mmfs/bin:`dirname
nvcc` NVCC_WRAPPER_DEFAULT_COMPILER=gcc
/gpfs/alpine/csc314/scratch/adams/petsc/arch-summit-opt-gnu-kokkos-notpl-cuda10/bin/nvcc_wrapper
--expt-extended-lambda -Xcompiler -rdynamic -lineinfo -DLANDAU_DIM=2
-DLANDAU_MAX_SPECIES=10 -DPETSC_HAVE_CUDA_ATOMIC -DLANDAU_MAX_Q=4
-Xcompiler -fPIC -O3  -gencode arch=compute_70,code=sm_70
 -I/autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/gcc-6.4.0/spectrum-mpi-10.3.1.2-20200121-awz2q5brde7wgdqqw4ugalrkukeub4eb/include
-Wno-deprecated-gpu-targets
 -I/gpfs/alpine/csc314/scratch/adams/petsc/include
-I/gpfs/alpine/csc314/scratch/adams/petsc/arch-summit-opt-gnu-kokkos-notpl-cuda10/include
-I/sw/summit/cuda/10.1.243/include
 -I/autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/gcc-6.4.0/spectrum-mpi-10.3.1.2-20200121-awz2q5brde7wgdqqw4ugalrkukeub4eb/include
  -fPIC -g -DLANDAU_DIM=2 -DLANDAU_MAX_SPECIES=10 -DPETSC_HAVE_CUDA_ATOMIC
-DLANDAU_MAX_Q=4 -Werror=maybe-uninitialized -O0   ex3k.kokkos.cxx
 -Wl,-rpath,/gpfs/alpine/csc314/scratch/adams/petsc/arch-summit-opt-gnu-kokkos-notpl-cuda10/lib
-L/gpfs/alpine/csc314/scratch/adams/petsc/arch-summit-opt-gnu-kokkos-notpl-cuda10/lib
-Wl,-rpath,/gpfs/alpine/csc314/scratch/adams/petsc/arch-summit-opt-gnu-kokkos-notpl-cuda10/lib
-L/gpfs/alpine/csc314/scratch/adams/petsc/arch-summit-opt-gnu-kokkos-notpl-cuda10/lib
-L/autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/gcc-6.4.0/netlib-lapack-3.8.0-wcabdyqhdi5rooxbkqa6x5d7hxyxwdkm/lib64
-Wl,-rpath,/sw/summit/cuda/10.1.243/lib64 -L/sw/summit/cuda/10.1.243/lib64
-lpetsc -lkokkoskernels -lkokkoscontainers -lkokkoscore -lp4est -lsc -lblas
-llapack -ltriangle -lm -lz -lcudart -lcufft -lcublas -lcusparse -lcusolver
-lcurand -lstdc++ -ldl -o ex3k
nvcc_wrapper - *warning* you have set multiple optimization flags (-O*),
only the last is used because nvcc can only accept a single optimization
setting.

*/usr/bin/ld: /tmp/tmpxft_0000e0c2_00000000-10_ex3k.kokkos.o: undefined
reference to symbol
'ompi_mpi_comm_self'*/autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/gcc-6.4.0/spectrum-mpi-10.3.1.2-20200121-awz2q5brde7wgdqqw4ugalrkukeub4eb/lib/libmpi_ibm.so.3:
error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
make: *** [ex3k] Error 1

On Sat, Jun 5, 2021 at 12:16 PM Junchao Zhang <junchao.zhang at gmail.com>
wrote:

> $rm ex3k
> $make ex3k
> and run again?
>
> --Junchao Zhang
>
>
> On Sat, Jun 5, 2021 at 10:25 AM Mark Adams <mfadams at lbl.gov> wrote:
>
>> This is posted in Barry's MR, but I get this error with Kokkos-cuda on
>> Summit. Failing to open a shared lib.
>> Thoughts?
>> Mark
>>
>> 11:15 barry/2020-11-11/cleanup-matsetvaluesdevice=
>> /gpfs/alpine/csc314/scratch/adams/petsc$ make
>> PETSC_DIR=/gpfs/alpine/csc314/scratch/adams/petsc
>> PETSC_ARCH=arch-summit-opt-gnu-kokkos-notpl-cuda10 check
>> Running check examples to verify correct installation
>> Using PETSC_DIR=/gpfs/alpine/csc314/scratch/adams/petsc and
>> PETSC_ARCH=arch-summit-opt-gnu-kokkos-notpl-cuda10
>> C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process
>> C/C++ example src/snes/tutorials/ex19 run successfully with 2 MPI
>> processes
>> C/C++ example src/snes/tutorials/ex19 run successfully with cuda
>> gmake[3]: [runex3k_kokkos] Error 127 (ignored)
>> 1,25c1,2
>> < atol=1e-50, rtol=1e-08, stol=1e-08, maxit=50, maxf=10000
>> < Vec Object: Exact Solution 2 MPI processes
>> <   type: mpikokkos
>> < Process [0]
>> < 0.
>> < 0.015625
>> < 0.125
>> < Process [1]
>> < 0.421875
>> < 1.
>> < Vec Object: Forcing function 2 MPI processes
>> <   type: mpikokkos
>> < Process [0]
>> < 1e-72
>> < 1.50024
>> < 3.01563
>> < Process [1]
>> < 4.67798
>> < 7.
>> <   0 SNES Function norm 5.414682427127e+00
>> <   1 SNES Function norm 2.952582418265e-01
>> <   2 SNES Function norm 4.502293658739e-04
>> <   3 SNES Function norm 1.389665806646e-09
>> < Number of SNES iterations = 3
>> < Norm of error 1.49752e-10 Iterations 3
>> ---
>>
>>
>> *> ./ex3k: error while loading shared libraries: libpetsc.so.3.015:
>> cannot open shared object file: No such file or directory> ./ex3k: error
>> while loading shared libraries: libpetsc.so.3.015: cannot open shared
>> object file: No such file or directory*
>> /gpfs/alpine/csc314/scratch/adams/petsc/src/snes/tutorials
>>
>
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