I was doing 'make ex5k.kokkos' It would be nice if that failed, but it building now. Thanks, On Thu, Jun 3, 2021 at 10:57 AM Junchao Zhang <[email protected]> wrote:
(Moved to petsc-dev)
Mark, Is it because your branch is out of date? petsc should use nvcc_wapper to compile ex5k.kokkos.cxx. See mine $cd ~/petsc/src/mat/tutorials $ make ex5k PATH=/home/jczhang/spack/opt/spack/linux-ubuntu18.04-skylake_avx512/gcc-8.3.0/gdb-9.1-bzjzolog57gom5anscfcb3oe6uqr6s6m/bin:/home/jczhang/spack/opt/spack/linux-ubuntu18.04-skylake_avx512/gcc-8.3.0/bear-2.2.0-xhfk3moyh7jled6o62f3om557iia6oun/bin:/home/jczhang/spack/opt/spack/linux-ubuntu18.04-skylake_avx512/gcc-8.3.0/perl-5.30.3-2boymujkmxezayez4emfw5sw5wuqgar6/bin:/home/jczhang/spack/opt/spack/linux-ubuntu18.04-skylake_avx512/gcc-8.3.0/openmpi-4.0.2-7vmyqiyk4iyvdeoqpux7fyoce6mjt7iw/bin:/home/jczhang/spack/opt/spack/linux-ubuntu18.04-skylake_avx512/gcc-8.3.0/cuda-10.2.89-uy4hlcnd7svrcahaguwx4bzl7ujoqx2v/bin:/nfs/gce/software/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.3.0/cmake-3.20.0-vov726r/bin:/nfs/gce/software/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.3.0/gcc-8.3.0-fjpc5ys/bin:/home/jczhang/soft/bin:/home/jczhang/spack/bin:/home/jczhang/arm/forge/20.2/bin:/home/jczhang/.vscode-server/data/User/globalStorage/llvm-vs-code-extensions.vscode-clangd/install/10.0.0/clangd_10.0.0/bin:/home/jczhang/.vscode-server/bin/054a9295330880ed74ceaedda236253b4f39a335/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:`dirname nvcc` NVCC_WRAPPER_DEFAULT_COMPILER=gcc /home/jczhang/petsc/linux-kokkos-dbg/bin/nvcc_wrapper --expt-extended-lambda -Xcompiler -fPIC -g -gencode arch=compute_70,code=sm_70 -I/home/jczhang/spack/opt/spack/linux-ubuntu18.04-skylake_avx512/gcc-8.3.0/openmpi-4.0.2-7vmyqiyk4iyvdeoqpux7fyoce6mjt7iw/include -Wno-deprecated-gpu-targets -I/home/jczhang/petsc/include -I/home/jczhang/petsc/linux-kokkos-dbg/include -I/home/jczhang/spack/opt/spack/linux-ubuntu18.04-skylake_avx512/gcc-8.3.0/openmpi-4.0.2-7vmyqiyk4iyvdeoqpux7fyoce6mjt7iw/include -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O0 ex5k.kokkos.cxx -Wl,-rpath,/home/jczhang/petsc/linux-kokkos-dbg/lib -L/home/jczhang/petsc/linux-kokkos-dbg/lib -Wl,-rpath,/home/jczhang/petsc/linux-kokkos-dbg/lib -L/home/jczhang/petsc/linux-kokkos-dbg/lib -lpetsc -lkokkoskernels -lkokkoscontainers -lkokkoscore -llapack -lblas -lm -lcudart -lcufft -lcublas -lcusparse -lcusolver -lcurand -lX11 -lquadmath -lstdc++ -ldl -o ex5k
--Junchao Zhang
On Thu, Jun 3, 2021 at 8:32 AM Mark Adams <[email protected]> wrote:
I am getting this error:
09:22 adams/landau-mass-opt= /gpfs/alpine/csc314/scratch/adams/petsc/src/mat/tutorials$ make PETSC_DIR=/gpfs/alpine/csc314/scratch/adams/petsc PETSC_ARCH=arch-summit-opt-gnu-kokkos-notpl-cuda10 ex5k.kokkos mpicxx -fPIC -g -DLANDAU_DIM=2 -DLANDAU_MAX_SPECIES=10 -DPETSC_HAVE_CUDA_ATOMIC -DLANDAU_MAX_Q=4 -O0 -fPIC -g -DLANDAU_DIM=2 -DLANDAU_MAX_SPECIES=10 -DPETSC_HAVE_CUDA_ATOMIC -DLANDAU_MAX_Q=4 -O0 -fPIC -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 ex5k.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 ex5k.kokkos In file included from /gpfs/alpine/csc314/scratch/adams/petsc/arch-summit-opt-gnu-kokkos-notpl-cuda10/include/KokkosCore_Config_SetupBackend.hpp:47:0, from /gpfs/alpine/csc314/scratch/adams/petsc/arch-summit-opt-gnu-kokkos-notpl-cuda10/include/Kokkos_Macros.hpp:109, from /gpfs/alpine/csc314/scratch/adams/petsc/arch-summit-opt-gnu-kokkos-notpl-cuda10/include/Kokkos_Core_fwd.hpp:52, from /gpfs/alpine/csc314/scratch/adams/petsc/arch-summit-opt-gnu-kokkos-notpl-cuda10/include/Kokkos_Core.hpp:51, from ex5k.kokkos.cxx:10: /gpfs/alpine/csc314/scratch/adams/petsc/arch-summit-opt-gnu-kokkos-notpl-cuda10/include/setup/Kokkos_Setup_Cuda.hpp:54:2: error: #error "KOKKOS_ENABLE_CUDA defined but the compiler is not defining the __CUDACC__ macro as expected" #error \ ^~~~~ In file included from /sw/summit/cuda/10.1.243/include/crt/common_functions.h:267:0, from /sw/summit/cuda/10.1.243/include/cuda_runtime.h:115, from /gpfs/alpine/csc314/scratch/adams/petsc/arch-summit-opt-gnu-kokkos-notpl-cuda10/include/setup/Kokkos_Setup_Cuda.hpp:68, from /gpfs/alpine/csc314/scratch/adams/petsc/arch-summit-opt-gnu-kokkos-notpl-cuda10/include/KokkosCore_Config_SetupBackend.hpp:47, from /gpfs/alpine/csc314/scratch/adams/petsc/arch-summit-opt-gnu-kokkos-notpl-cuda10/include/Kokkos_Macros.hpp:109, from /gpfs/alpine/csc314/scratch/adams/petsc/arch-summit-opt-gnu-kokkos-notpl-cuda10/include/Kokkos_Core_fwd.hpp:52, from /gpfs/alpine/csc314/scratch/adams/petsc/arch-summit-opt-gnu-kokkos-notpl-cuda10/include/Kokkos_Core.hpp:51, from ex5k.kokkos.cxx:10: /sw/summit/cuda/10.1.243/include/crt/math_functions.h:8944:72: error: 'int std::isnan(double)' conflicts with a previous declaration __DEVICE_FUNCTIONS_DECL__ __cudart_builtin__ int isnan(double x) throw(); ^ Here is my config file:
#!/usr/bin/env python # -lnvToolsExt
if __name__ == '__main__': import sys import os sys.path.insert(0, os.path.abspath('config')) import configure configure_options = [ '--with-fc=0', '--CFLAGS=-fPIC -g -DLANDAU_DIM=2 -DLANDAU_MAX_SPECIES=10 -DPETSC_HAVE_CUDA_ATOMIC -DLANDAU_MAX_Q=4', '--CXXFLAGS=-fPIC -g -DLANDAU_DIM=2 -DLANDAU_MAX_SPECIES=10 -DPETSC_HAVE_CUDA_ATOMIC -DLANDAU_MAX_Q=4', '--COPTFLAGS=-O0', '--CXXOPTFLAGS=-O0', '--CUDAOPTFLAGS=-O0', # 'LIBS= -L'+os.environ['CUDAPATH']+'/lib64 -lnvToolsExt', '--CUDAFLAGS=-Xcompiler -rdynamic -lineinfo -DLANDAU_DIM=2 -DLANDAU_MAX_SPECIES=10 -DPETSC_HAVE_CUDA_ATOMIC -DLANDAU_MAX_Q=4', '--with-ssl=0', '--with-batch=0', '--with-cxx=mpicxx', '--with-mpiexec=jsrun -g1 ', '--with-openmp=0', # '--with-threadsafety=1', # '--with-log=0', '--with-cuda=1', '--with-cuda-gencodearch=70', '--with-cudac=nvcc', '--download-p4est=1', '--download-zlib', # '--download-hdf5=1', # '--download-metis', # '--download-superlu_dist', # '--download-superlu_dist-commit=HEAD', # '--download-hypre-configure-arguments=HYPRE_CUDA_SM=70', #'--with-hwloc=0', # '--download-parmetis', #'--download-hypre', '--download-triangle', #'--download-amgx', #'--download-fblaslapack', '--with-blaslapack-lib=-L' + os.environ['OLCF_NETLIB_LAPACK_ROOT'] + '/lib64 -lblas -llapack', #'--download-openblas', '--with-cc=mpicc', #'--with-fc=mpif90', '--with-shared-libraries=1', # '--known-mpi-shared-libraries=1', '--with-x=0', '--with-64-bit-indices=0', '--with-debugging=1', '--download-kokkos', '--with-ctable=0', '--with-make-np=8', '--download-kokkos-kernels', # '--with-kokkos-cuda-arch=VOLTA70', '--with-kokkos-kernels-tpl=0',
'--download-kokkos-cmake-arguments=-DKokkos_ENABLE_AGGRESSIVE_VECTORIZATION=ON -DKokkos_ARCH_POWER9=ON', # '--download-kokkos-commit=origin/develop', # '--download-kokkos-kernels-commit=origin/develop', 'PETSC_ARCH=arch-summit-opt-gnu-kokkos-notpl-cuda10', ] configure.petsc_configure(configure_options)
~ ~ ~ ~ ~ ~ ~