(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Is it because your branch is out of date?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 <mfad...@lbl.gov> 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)
>
> ~
> ~
> ~
> ~
> ~
> ~
> ~
>
