Looks like the MPI libraries are not being passed to the NVCC internal compiler (gcc). This would normally be setup in MPI.py, please send configure.log
Barry > On Jun 5, 2021, at 1:18 PM, Mark Adams <[email protected]> wrote: > > 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 > > <http://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:%60dirname> > 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 <[email protected] > <mailto:[email protected]>> wrote: > $rm ex3k > $make ex3k > and run again? > > --Junchao Zhang > > > On Sat, Jun 5, 2021 at 10:25 AM Mark Adams <[email protected] > <mailto:[email protected]>> wrote: > This is posted in Barry's MR, but I get this error with Kokkos-cuda on > Summit. Failing to open a shared lib. > Thoughts? > Mark > > 11:15 barry/2020-11-11/cleanup-matsetvaluesdevice= > /gpfs/alpine/csc314/scratch/adams/petsc$ 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
