<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class=""><br class=""></div> 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 <div class=""><br class=""></div><div class=""> Barry</div><div class=""> <br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jun 5, 2021, at 1:18 PM, Mark Adams <<a href="mailto:mfadams@lbl.gov" class="">mfadams@lbl.gov</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">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:<div class=""><br class=""></div><div class="">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<br class="">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/<a href="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" class="">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</a> 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<br class="">nvcc_wrapper - *warning* you have set multiple optimization flags (-O*), only the last is used because nvcc can only accept a single optimization setting.<br class=""><b class="">/usr/bin/ld: /tmp/tmpxft_0000e0c2_00000000-10_ex3k.kokkos.o: undefined reference to symbol 'ompi_mpi_comm_self'<br class=""></b>/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<br class="">collect2: error: ld returned 1 exit status<br class="">make: *** [ex3k] Error 1<br class=""></div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sat, Jun 5, 2021 at 12:16 PM Junchao Zhang <<a href="mailto:junchao.zhang@gmail.com" class="">junchao.zhang@gmail.com</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr" class="">$rm ex3k<div class="">$make ex3k</div><div class="">and run again?<br class=""></div><div class=""><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><br class=""></div><div dir="ltr" class="">--Junchao Zhang</div></div></div><br class=""></div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sat, Jun 5, 2021 at 10:25 AM Mark Adams <<a href="mailto:mfadams@lbl.gov" target="_blank" class="">mfadams@lbl.gov</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr" class="">This is posted in Barry's MR, but I get this error with Kokkos-cuda on Summit. Failing to open a shared lib.<div class="">Thoughts?</div><div class="">Mark<br class=""><div class=""><br class=""></div><div class="">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<br class="">Running check examples to verify correct installation<br class="">Using PETSC_DIR=/gpfs/alpine/csc314/scratch/adams/petsc and PETSC_ARCH=arch-summit-opt-gnu-kokkos-notpl-cuda10<br class="">C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process<br class="">C/C++ example src/snes/tutorials/ex19 run successfully with 2 MPI processes<br class="">C/C++ example src/snes/tutorials/ex19 run successfully with cuda<br class="">gmake[3]: [runex3k_kokkos] Error 127 (ignored)<br class="">1,25c1,2<br class="">< atol=1e-50, rtol=1e-08, stol=1e-08, maxit=50, maxf=10000<br class="">< Vec Object: Exact Solution 2 MPI processes<br class="">< type: mpikokkos<br class="">< Process [0]<br class="">< 0.<br class="">< 0.015625<br class="">< 0.125<br class="">< Process [1]<br class="">< 0.421875<br class="">< 1.<br class="">< Vec Object: Forcing function 2 MPI processes<br class="">< type: mpikokkos<br class="">< Process [0]<br class="">< 1e-72<br class="">< 1.50024<br class="">< 3.01563<br class="">< Process [1]<br class="">< 4.67798<br class="">< 7.<br class="">< 0 SNES Function norm 5.414682427127e+00<br class="">< 1 SNES Function norm 2.952582418265e-01<br class="">< 2 SNES Function norm 4.502293658739e-04<br class="">< 3 SNES Function norm 1.389665806646e-09<br class="">< Number of SNES iterations = 3<br class="">< Norm of error 1.49752e-10 Iterations 3<br class="">---<br class=""><b class="">> ./ex3k: error while loading shared libraries: libpetsc.so.3.015: cannot open shared object file: No such file or directory<br class="">> ./ex3k: error while loading shared libraries: libpetsc.so.3.015: cannot open shared object file: No such file or directory<br class=""></b>/gpfs/alpine/csc314/scratch/adams/petsc/src/snes/tutorials<br class=""></div></div></div>
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