Thanks, but this happens w/o Kokkos. I've stripped this down and attached good/bad logs without/with Fortran bindings. Hope this helps, Thanks again, Mark On Sun, Jul 18, 2021 at 12:00 PM Stefano Zampini <[email protected]> wrote:
This is probably kokkos pulling in the dependencies where compiling kokkos source within PETSc.
Il Dom 18 Lug 2021, 16:29 Mark Adams <[email protected]> ha scritto:
Whoops, this error was just from not telling gfortran to allow long lines.
Anway, I did find that the when fortran bindings are enabled this OMP thing gets into the library. No idea how. I'll askm ORNL.
10:26 jczhang/fix-cray-mpicxx-includes/main= /gpfs/alpine/csc314/scratch/adams/petsc2$ nm /gpfs/alpine/csc314/scratch/adams/petsc2/arch-spock-opt-cray-kokkos/lib/libpetsc.so |g offload U .omp_offloading.img_cache.cray_amdgcn-amd-amdhsa U .omp_offloading.img_size.cray_amdgcn-amd-amdhsa U .omp_offloading.img_start.cray_amdgcn-amd-amdhsa 0000000001d457b0 T vecgetoffloadmask_
On Sun, Jul 18, 2021 at 8:43 AM Mark Adams <[email protected]> wrote:
Ah, your test was not on Spock ... I have something working but this is strange.
I switched to the GNU ProgEnv. and it passed the Fortran test in 'check', but this failed:
*08:26 2 jczhang/fix-cray-mpicxx-includes/main= /gpfs/alpine/csc314/scratch/adams/petsc/src/snes/tutorials$ make PETSC_DIR=/gpfs/alpine/phy122/proj-shared/spock/petsc/current/arch-dbg-gnu PETSC_ARCH="" ex40f90ftn -L/sw/spock/spack-envs/views/rocm-4.1.0/lib -lamdhip64 -lhsa-runtime64 -fPIC -g -O0 -fPIC -g -O0 -I/gpfs/alpine/phy122/proj-shared/spock/petsc/current/arch-dbg-gnu/include -I/sw/spock/spack-envs/views/rocm-4.1.0/include ex40f90.F90 -Wl,-rpath,/gpfs/alpine/phy122/proj-shared/spock/petsc/current/arch-dbg-gnu/lib -L/gpfs/alpine/phy122/proj-shared/spock/petsc/current/arch-dbg-gnu/lib -Wl,-rpath,/sw/spock/spack-envs/views/rocm-4.1.0/lib -L/sw/spock/spack-envs/views/rocm-4.1.0/lib -Wl,-rpath,/opt/cray/pe/mpich/8.1.4/ofi/gnu/9.1/lib -L/opt/cray/pe/mpich/8.1.4/ofi/gnu/9.1/lib -Wl,-rpath,/opt/cray/pe/mpich/8.1.4/gtl/lib -L/opt/cray/pe/mpich/8.1.4/gtl/lib -Wl,-rpath,/opt/cray/pe/libsci/21.04.1.1/GNU/9.1/x86_64/lib <http://21.04.1.1/GNU/9.1/x86_64/lib> -L/opt/cray/pe/libsci/21.04.1.1/GNU/9.1/x86_64/lib <http://21.04.1.1/GNU/9.1/x86_64/lib> -Wl,-rpath,/opt/cray/pe/pmi/6.0.10/lib -L/opt/cray/pe/pmi/6.0.10/lib -Wl,-rpath,/opt/cray/pe/dsmml/0.1.4/dsmml/lib -L/opt/cray/pe/dsmml/0.1.4/dsmml/lib -Wl,-rpath,/opt/cray/xpmem/2.2.40-2.1_2.7__g3cf3325.shasta/lib64 -L/opt/cray/xpmem/2.2.40-2.1_2.7__g3cf3325.shasta/lib64 -Wl,-rpath,/opt/gcc/10.2.0/snos/lib/gcc/x86_64-suse-linux/10.2.0 -L/opt/gcc/10.2.0/snos/lib/gcc/x86_64-suse-linux/10.2.0 -Wl,-rpath,/opt/gcc/10.2.0/snos/lib64 -L/opt/gcc/10.2.0/snos/lib64 -Wl,-rpath,/sw/spock/spack-envs/views/rocm-4.1.0/llvm/lib -L/sw/spock/spack-envs/views/rocm-4.1.0/llvm/lib -Wl,-rpath,/opt/gcc/10.2.0/snos/lib -L/opt/gcc/10.2.0/snos/lib -lpetsc -lhipsparse -lhipblas -lrocsparse -lrocsolver -lrocblas -lamdhip64 -lhsa-runtime64 -lstdc++ -ldl -lpmi -lmpi_gtl_hsa -lxpmem -lgfortran -lm -lsci_gnu_82_mpi -lsci_gnu_82 -lmpifort_gnu_91 -lmpi_gnu_91 -ldsmml -lgfortran -lquadmath -lpthread -lm -lgcc_s -lquadmath -lstdc++ -ldl -o ex40f90ex40f90.F90:35:132: 35 | call DMDACreate2d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_BOX,ten,ten,PETSC_DECIDE,PETSC_DECIDE,two,one, & | 1Error: Line truncated at (1) [-Werror=line-truncation]ex40f90.F90:35:132:* * ....*
But ex5f (the Fortran check test) does work manually also (sanity check).
Oddly I seem to have the cray compilers:
08:34 jczhang/fix-cray-mpicxx-includes/main= /gpfs/alpine/csc314/scratch/adams/petsc/src/snes/tutorials$ which ftn /opt/cray/pe/craype/2.7.6/bin/ftn
yet it is GNU:
08:34 jczhang/fix-cray-mpicxx-includes/main= /gpfs/alpine/csc314/scratch/adams/petsc/src/snes/tutorials$ ftn --version GNU Fortran (GCC) 10.2.0 20200723 (Cray Inc.) Copyright (C) 2020 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
The documentation says ftn should be here:
08:34 jczhang/fix-cray-mpicxx-includes/main= /gpfs/alpine/csc314/scratch/adams/petsc/src/snes/tutorials$ $GCC_PATH/bin/gfortran --version GNU Fortran (GCC) 10.2.0 20200723 (Cray Inc.) Copyright (C) 2020 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Same, but the path is not the same:
08:39 jczhang/fix-cray-mpicxx-includes/main= /gpfs/alpine/csc314/scratch/adams/petsc/src/snes/tutorials$ echo $GCC_PATH /opt/gcc/10.2.0
Anyway, thanks for your help, Mark
On Sat, Jul 17, 2021 at 11:26 PM Junchao Zhang <[email protected]> wrote:
Mark, I can reproduce this error with PrgEnv-cray, i.e., using the Cray compiler (clang-11). Previously I used PrgEnv-gnu, which did not have this error. Probably it is a problem of Spock. But I am not sure.
--Junchao Zhang
On Sat, Jul 17, 2021 at 10:17 AM Mark Adams <[email protected]> wrote:
And I can run a fortran test, with warnings, but C tests fail:
11:15 jczhang/fix-cray-mpicxx-includes/main= /gpfs/alpine/csc314/scratch/adams/petsc$ make PETSC_DIR=/gpfs/alpine/csc314/scratch/adams/petsc PETSC_ARCH=arch-spock-opt-cray-kokkos -f gmakefile test search='ts_utils_dmplexlandau_tutorials-ex1f90_0' Using MAKEFLAGS: -- search=ts_utils_dmplexlandau_tutorials-ex1f90_0 PETSC_ARCH=arch-spock-opt-cray-kokkos PETSC_DIR=/gpfs/alpine/csc314/scratch/adams/petsc FC arch-spock-opt-cray-kokkos/tests/ts/utils/dmplexlandau/tutorials/ex1f90.o FLINKER arch-spock-opt-cray-kokkos/tests/ts/utils/dmplexlandau/tutorials/ex1f90 /opt/cray/pe/cce/11.0.4/binutils/x86_64/x86_64-pc-linux-gnu/bin/ld: warning: alignment 128 of symbol `$host_init$$runtime_init_for_iso_c_binding$iso_c_binding_' in /opt/cray/pe/cce/11.0.4/cce/x86_64/lib/libmodules.so is smaller than 256 in arch-spock-opt-cray-kokkos/tests/ts/utils/dmplexlandau/tutorials/ex1f90.o /opt/cray/pe/cce/11.0.4/binutils/x86_64/x86_64-pc-linux-gnu/bin/ld: warning: alignment 64 of symbol `$data_init$iso_c_binding_' in /opt/cray/pe/cce/11.0.4/cce/x86_64/lib/libmodules.so is smaller than 256 in arch-spock-opt-cray-kokkos/tests/ts/utils/dmplexlandau/tutorials/ex1f90.o TEST arch-spock-opt-cray-kokkos/tests/counts/ts_utils_dmplexlandau_tutorials-ex1f90_0.counts ok ts_utils_dmplexlandau_tutorials-ex1f90_0 ok diff-ts_utils_dmplexlandau_tutorials-ex1f90_0
On Sat, Jul 17, 2021 at 10:53 AM Mark Adams <[email protected]> wrote:
HUmm, I can not reproduce this.
10:49 jczhang/fix-cray-mpicxx-includes/main= /gpfs/alpine/csc314/scratch/adams/petsc$ make PETSC_DIR=/gpfs/alpine/csc314/scratch/adams/petsc PETSC_ARCH=arch-spock-dbg-kokkos check Running check examples to verify correct installation Using PETSC_DIR=/gpfs/alpine/csc314/scratch/adams/petsc and PETSC_ARCH=arch-spock-dbg-kokkos gmake[3]: [/gpfs/alpine/csc314/scratch/adams/petsc/lib/petsc/conf/rules:301: ex19.PETSc] Error 2 (ignored) *******************Error detected during compile or link!******************* See http://www.mcs.anl.gov/petsc/documentation/faq.html /gpfs/alpine/csc314/scratch/adams/petsc/src/snes/tutorials ex19
********************************************************************************* cc -L/sw/spock/spack-envs/views/rocm-4.1.0/lib -lamdhip64 -lhsa-runtime64 -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -Qunused-arguments -fvisibility=hidden -g -O0 -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -Qunused-arguments -fvisibility=hidden -g -O0 -I/sw/spock/spack-envs/views/rocm-4.1.0/include -I/gpfs/alpine/csc314/scratch/adams/petsc/include -I/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/include -I/sw/spock/spack-envs/views/rocm-4.1.0/include -I/sw/spock/spack-envs/views/rocm-4.1.0/include ex19.c -Wl,-rpath,/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/lib -L/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/lib -Wl,-rpath,/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/lib -L/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/lib -Wl,-rpath,/sw/spock/spack-envs/views/rocm-4.1.0/lib -L/sw/spock/spack-envs/views/rocm-4.1.0/lib -Wl,-rpath,/opt/gcc/8.1.0/snos/lib64 -L/opt/gcc/8.1.0/snos/lib64 -Wl,-rpath,/opt/cray/pe/libsci/21.04.1.1/CRAY/9.0/x86_64/lib -L/opt/cray/pe/libsci/21.04.1.1/CRAY/9.0/x86_64/lib -Wl,-rpath,/opt/cray/pe/mpich/8.1.4/ofi/cray/9.1/lib -L/opt/cray/pe/mpich/8.1.4/ofi/cray/9.1/lib -Wl,-rpath,/opt/cray/pe/mpich/8.1.4/gtl/lib -L/opt/cray/pe/mpich/8.1.4/gtl/lib -Wl,-rpath,/opt/cray/pe/pmi/6.0.10/lib -L/opt/cray/pe/pmi/6.0.10/lib -Wl,-rpath,/opt/cray/pe/dsmml/0.1.4/dsmml/lib -L/opt/cray/pe/dsmml/0.1.4/dsmml/lib -Wl,-rpath,/opt/cray/pe/cce/11.0.4/cce/x86_64/lib -L/opt/cray/pe/cce/11.0.4/cce/x86_64/lib -Wl,-rpath,/opt/cray/xpmem/2.2.40-2.1_2.7__g3cf3325.shasta/lib64 -L/opt/cray/xpmem/2.2.40-2.1_2.7__g3cf3325.shasta/lib64 -Wl,-rpath,/opt/cray/pe/cce/11.0.4/cce-clang/x86_64/lib/clang/11.0.0/lib/linux -L/opt/cray/pe/cce/11.0.4/cce-clang/x86_64/lib/clang/11.0.0/lib/linux -Wl,-rpath,/opt/gcc/8.1.0/snos/lib/gcc/x86_64-suse-linux/8.1.0 -L/opt/gcc/8.1.0/snos/lib/gcc/x86_64-suse-linux/8.1.0 -Wl,-rpath,/opt/cray/pe/cce/11.0.4/binutils/x86_64/x86_64-pc-linux-gnu/..//x86_64-unknown-linux-gnu/lib -L/opt/cray/pe/cce/11.0.4/binutils/x86_64/x86_64-pc-linux-gnu/..//x86_64-unknown-linux-gnu/lib -lpetsc -lkokkoskernels -lkokkoscontainers -lkokkoscore -lhipsparse -lhipblas -lrocsparse -lrocsolver -lrocblas -lamdhip64 -lhsa-runtime64 -lstdc++ -ldl -lpmi -lsci_cray_mpi -lsci_cray -lmpifort_cray -lmpi_cray -lmpi_gtl_hsa -lxpmem -ldsmml -lpgas-shmem -lquadmath -lcrayacc_amdgpu -lopenacc -lmodules -lfi -lcraymath -lf -lu -lcsup -lgfortran -lpthread -lgcc_eh -lm -lclang_rt.craypgo-x86_64 -lclang_rt.builtins-x86_64 -lquadmath -lstdc++ -ldl -o ex19 ld.lld: error: /gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/lib/libpetsc.so: undefined reference to .omp_offloading.img_start.cray_amdgcn-amd-amdhsa [--no-allow-shlib-undefined] ld.lld: error: /gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/lib/libpetsc.so: undefined reference to .omp_offloading.img_size.cray_amdgcn-amd-amdhsa [--no-allow-shlib-undefined] ld.lld: error: /gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/lib/libpetsc.so: undefined reference to .omp_offloading.img_cache.cray_amdgcn-amd-amdhsa [--no-allow-shlib-undefined] clang-11: error: linker command failed with exit code 1 (use -v to see invocation) gmake[4]: *** [<builtin>: ex19] Error 1 gmake[3]: [/gpfs/alpine/csc314/scratch/adams/petsc/lib/petsc/conf/rules:301: ex3k.PETSc] Error 2 (ignored) *******************Error detected during compile or link!******************* See http://www.mcs.anl.gov/petsc/documentation/faq.html /gpfs/alpine/csc314/scratch/adams/petsc/src/snes/tutorials ex3k
********************************************************************************* hipcc -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fvisibility=hidden -g -O0 -std=c++14 -I/gpfs/alpine/csc314/scratch/adams/petsc/include -I/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/include -I/sw/spock/spack-envs/views/rocm-4.1.0/include -I/sw/spock/spack-envs/views/rocm-4.1.0/include -I/opt/cray/pe/libsci/ 21.04.1.1/CRAY/9.0/x86_64/include -I/opt/cray/pe/mpich/8.1.4/ofi/cray/9.1/include -I/opt/cray/pe/pmi/6.0.10/include -I/opt/cray/pe/dsmml/0.1.4/dsmml//include -I/opt/cray/xpmem/2.2.40-2.1_2.7__g3cf3325.shasta/include -L/opt/cray/pe/libsci/21.04.1.1/CRAY/9.0/x86_64/lib -L/opt/cray/pe/mpich/8.1.4/ofi/cray/9.1/lib -L/opt/cray/pe/mpich/8.1.4/gtl/lib -L/opt/cray/pe/pmi/6.0.10/lib -L/opt/cray/pe/dsmml/0.1.4/dsmml//lib -L/opt/cray/pe/cce/11.0.4/cce/x86_64/lib/pkgconfig/../ -L/opt/cray/xpmem/2.2.40-2.1_2.7__g3cf3325.shasta/lib64 -Wl,--as-needed,-lsci_cray_mpi,--no-as-needed -Wl,--as-needed,-lsci_cray,--no-as-needed -Wl,--as-needed,-lmpi_cray,--no-as-needed -Wl,--as-needed,-ldsmml,--no-as-needed -Wl,--as-needed,-lpgas-shmem,--no-as-needed -lpmi -ldl -lmpi_gtl_hsa -lxpmem -lquadmath -lmodules -lfi -lcraymath -lf -lu -lcsup ex3k.kokkos.cxx -Wl,-rpath,/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/lib -L/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/lib -Wl,-rpath,/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/lib -L/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/lib -Wl,-rpath,/sw/spock/spack-envs/views/rocm-4.1.0/lib -L/sw/spock/spack-envs/views/rocm-4.1.0/lib -Wl,-rpath,/opt/gcc/8.1.0/snos/lib64 -L/opt/gcc/8.1.0/snos/lib64 -Wl,-rpath,/opt/cray/pe/libsci/21.04.1.1/CRAY/9.0/x86_64/lib -L/opt/cray/pe/libsci/21.04.1.1/CRAY/9.0/x86_64/lib -Wl,-rpath,/opt/cray/pe/mpich/8.1.4/ofi/cray/9.1/lib -L/opt/cray/pe/mpich/8.1.4/ofi/cray/9.1/lib -Wl,-rpath,/opt/cray/pe/mpich/8.1.4/gtl/lib -L/opt/cray/pe/mpich/8.1.4/gtl/lib -Wl,-rpath,/opt/cray/pe/pmi/6.0.10/lib -L/opt/cray/pe/pmi/6.0.10/lib -Wl,-rpath,/opt/cray/pe/dsmml/0.1.4/dsmml/lib -L/opt/cray/pe/dsmml/0.1.4/dsmml/lib -Wl,-rpath,/opt/cray/pe/cce/11.0.4/cce/x86_64/lib -L/opt/cray/pe/cce/11.0.4/cce/x86_64/lib -Wl,-rpath,/opt/cray/xpmem/2.2.40-2.1_2.7__g3cf3325.shasta/lib64 -L/opt/cray/xpmem/2.2.40-2.1_2.7__g3cf3325.shasta/lib64 -Wl,-rpath,/opt/cray/pe/cce/11.0.4/cce-clang/x86_64/lib/clang/11.0.0/lib/linux -L/opt/cray/pe/cce/11.0.4/cce-clang/x86_64/lib/clang/11.0.0/lib/linux -Wl,-rpath,/opt/gcc/8.1.0/snos/lib/gcc/x86_64-suse-linux/8.1.0 -L/opt/gcc/8.1.0/snos/lib/gcc/x86_64-suse-linux/8.1.0 -Wl,-rpath,/opt/cray/pe/cce/11.0.4/binutils/x86_64/x86_64-pc-linux-gnu/..//x86_64-unknown-linux-gnu/lib -L/opt/cray/pe/cce/11.0.4/binutils/x86_64/x86_64-pc-linux-gnu/..//x86_64-unknown-linux-gnu/lib -lpetsc -lkokkoskernels -lkokkoscontainers -lkokkoscore -lhipsparse -lhipblas -lrocsparse -lrocsolver -lrocblas -lamdhip64 -lhsa-runtime64 -lstdc++ -ldl -lpmi -lsci_cray_mpi -lsci_cray -lmpifort_cray -lmpi_cray -lmpi_gtl_hsa -lxpmem -ldsmml -lpgas-shmem -lquadmath -lcrayacc_amdgpu -lopenacc -lmodules -lfi -lcraymath -lf -lu -lcsup -lgfortran -lpthread -lgcc_eh -lm -lclang_rt.craypgo-x86_64 -lclang_rt.builtins-x86_64 -lquadmath -lstdc++ -ldl -o ex3k /usr/lib64/gcc/x86_64-suse-linux/7/../../../../x86_64-suse-linux/bin/ld: /gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/lib/libpetsc.so: undefined reference to `.omp_offloading.img_size.cray_amdgcn-amd-amdhsa' /usr/lib64/gcc/x86_64-suse-linux/7/../../../../x86_64-suse-linux/bin/ld: /gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/lib/libpetsc.so: undefined reference to `.omp_offloading.img_start.cray_amdgcn-amd-amdhsa' /usr/lib64/gcc/x86_64-suse-linux/7/../../../../x86_64-suse-linux/bin/ld: /gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/lib/libpetsc.so: undefined reference to `.omp_offloading.img_cache.cray_amdgcn-amd-amdhsa' clang-12: error: linker command failed with exit code 1 (use -v to see invocation) gmake[4]: *** [/gpfs/alpine/csc314/scratch/adams/petsc/lib/petsc/conf/test:26: ex3k] Error 1 gmake[3]: [makefile:102: runex3k_kokkos] Error 2 (ignored) 1,25c1,4 < 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 ---
slurmstepd: error: execve(): /gpfs/alpine/csc314/scratch/adams/petsc/src/snes/tutorials/./ex3k: No such file or directory slurmstepd: error: execve(): /gpfs/alpine/csc314/scratch/adams/petsc/src/snes/tutorials/./ex3k: No such file or directory srun: error: spock01: tasks 0-1: Exited with exit code 2 srun: launch/slurm: _step_signal: Terminating StepId=272979.0 /gpfs/alpine/csc314/scratch/adams/petsc/src/snes/tutorials Possible problem with ex3k running with kokkos-kernels, diffs above ========================================= *******************Error detected during compile or link!******************* See http://www.mcs.anl.gov/petsc/documentation/faq.html /gpfs/alpine/csc314/scratch/adams/petsc/src/snes/tutorials ex5f
ftn -L/sw/spock/spack-envs/views/rocm-4.1.0/lib -lamdhip64 -lhsa-runtime64 -fPIC -g -O0 -fPIC -g -O0 -I/gpfs/alpine/csc314/scratch/adams/petsc/include -I/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/include -I/sw/spock/spack-envs/views/rocm-4.1.0/include ex5f.F90 -Wl,-rpath,/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/lib -L/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/lib -Wl,-rpath,/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/lib -L/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-dbg-kokkos/lib -Wl,-rpath,/sw/spock/spack-envs/views/rocm-4.1.0/lib -L/sw/spock/spack-envs/views/rocm-4.1.0/lib -Wl,-rpath,/opt/gcc/8.1.0/snos/lib64 -L/opt/gcc/8.1.0/snos/lib64 -Wl,-rpath,/opt/cray/pe/libsci/21.04.1.1/CRAY/9.0/x86_64/lib -L/opt/cray/pe/libsci/21.04.1.1/CRAY/9.0/x86_64/lib -Wl,-rpath,/opt/cray/pe/mpich/8.1.4/ofi/cray/9.1/lib -L/opt/cray/pe/mpich/8.1.4/ofi/cray/9.1/lib -Wl,-rpath,/opt/cray/pe/mpich/8.1.4/gtl/lib -L/opt/cray/pe/mpich/8.1.4/gtl/lib -Wl,-rpath,/opt/cray/pe/pmi/6.0.10/lib -L/opt/cray/pe/pmi/6.0.10/lib -Wl,-rpath,/opt/cray/pe/dsmml/0.1.4/dsmml/lib -L/opt/cray/pe/dsmml/0.1.4/dsmml/lib -Wl,-rpath,/opt/cray/pe/cce/11.0.4/cce/x86_64/lib -L/opt/cray/pe/cce/11.0.4/cce/x86_64/lib -Wl,-rpath,/opt/cray/xpmem/2.2.40-2.1_2.7__g3cf3325.shasta/lib64 -L/opt/cray/xpmem/2.2.40-2.1_2.7__g3cf3325.shasta/lib64 -Wl,-rpath,/opt/cray/pe/cce/11.0.4/cce-clang/x86_64/lib/clang/11.0.0/lib/linux -L/opt/cray/pe/cce/11.0.4/cce-clang/x86_64/lib/clang/11.0.0/lib/linux -Wl,-rpath,/opt/gcc/8.1.0/snos/lib/gcc/x86_64-suse-linux/8.1.0 -L/opt/gcc/8.1.0/snos/lib/gcc/x86_64-suse-linux/8.1.0 -Wl,-rpath,/opt/cray/pe/cce/11.0.4/binutils/x86_64/x86_64-pc-linux-gnu/..//x86_64-unknown-linux-gnu/lib -L/opt/cray/pe/cce/11.0.4/binutils/x86_64/x86_64-pc-linux-gnu/..//x86_64-unknown-linux-gnu/lib -lpetsc -lkokkoskernels -lkokkoscontainers -lkokkoscore -lhipsparse -lhipblas -lrocsparse -lrocsolver -lrocblas -lamdhip64 -lhsa-runtime64 -lstdc++ -ldl -lpmi -lsci_cray_mpi -lsci_cray -lmpifort_cray -lmpi_cray -lmpi_gtl_hsa -lxpmem -ldsmml -lpgas-shmem -lquadmath -lcrayacc_amdgpu -lopenacc -lmodules -lfi -lcraymath -lf -lu -lcsup -lgfortran -lpthread -lgcc_eh -lm -lclang_rt.craypgo-x86_64 -lclang_rt.builtins-x86_64 -lquadmath -lstdc++ -ldl -o ex5f /opt/cray/pe/cce/11.0.4/binutils/x86_64/x86_64-pc-linux-gnu/bin/ld: warning: alignment 128 of symbol `$host_init$$runtime_init_for_iso_c_binding$iso_c_binding_' in /opt/cray/pe/cce/11.0.4/cce/x86_64/lib/libmodules.so is smaller than 256 in /tmp/pe_30429/ex5f_1.o /opt/cray/pe/cce/11.0.4/binutils/x86_64/x86_64-pc-linux-gnu/bin/ld: warning: alignment 64 of symbol `$data_init$iso_c_binding_' in /opt/cray/pe/cce/11.0.4/cce/x86_64/lib/libmodules.so is smaller than 256 in /tmp/pe_30429/ex5f_1.o Fortran example src/snes/tutorials/ex5f run successfully with 1 MPI process Completed test examples 10:49 jczhang/fix-cray-mpicxx-includes/main= /gpfs/alpine/csc314/scratch/adams/petsc$ ll
On Fri, Jul 16, 2021 at 11:28 PM Junchao Zhang < [email protected]> wrote:
Mark, I configured with Fortran binding enabled with main + MR !4175 <https://gitlab.com/petsc/petsc/-/merge_requests/4175>
'--with-mpiexec=srun', '--with-shared-libraries=1', '--with-cc=cc', '--with-cxx=CC', '--with-fc=ftn', '--with-fortran-bindings', '--with-hip', '--with-hipc=hipcc', '--with-debugging', '--CPPFLAGS=-I${ROCM_PATH}/include', '--CXXPPFLAGS=-I${ROCM_PATH}/include', '--CC_LINKER_FLAGS=-L${ROCM_PATH}/lib -lamdhip64 -lhsa-runtime64', '--CXX_LINKER_FLAGS=-L${ROCM_PATH}/lib -lamdhip64 -lhsa-runtime64', '--FC_LINKER_FLAGS=-L${ROCM_PATH}/lib -lamdhip64 -lhsa-runtime64', '--COPTFLAGS=-g -O0', '--CXXOPTFLAGS=-g -O0', '--FOPTFLAGS=-g -O0', '--download-kokkos', '--download-kokkos-kernels', '--download-kokkos-commit=3.4.01', '--download-kokkos-kernels-commit=3.4.01', '--with-kokkos-hip-arch=VEGA908',
and 'make check' ran smoothly on a compute node
$ make check Running check examples to verify correct installation Using PETSC_DIR=/ccs/home/jczhang/petsc and PETSC_ARCH=arch-spock-cray-kokkos-dbg 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/ex3k run successfully with kokkos-kernels Fortran example src/snes/tutorials/ex5f run successfully with 1 MPI process
Completed test examples
--Junchao Zhang
On Fri, Jul 16, 2021 at 6:04 PM Mark Adams <[email protected]> wrote:
And I find that this error, on non-Kokkos C tests, is fixed by turning the fortran bindings off:
ld.lld: error: /gpfs/alpine/phy122/proj-shared/spock/petsc/current/arch-opt-cray-kokkos/lib/libpetsc.so: undefined reference to .omp_offloading.img_start.cray_amdgcn-amd-amdhsa [--no-allow-shlib-undefined] ld.lld: error: /gpfs/alpine/phy122/proj-shared/spock/petsc/current/arch-opt-cray-kokkos/lib/libpetsc.so: undefined reference to .omp_offloading.img_size.cray_amdgcn-amd-amdhsa [--no-allow-shlib-undefined] ld.lld: error: /gpfs/alpine/phy122/proj-shared/spock/petsc/current/arch-opt-cray-kokkos/lib/libpetsc.so: undefined reference to .omp_offloading.img_cache.cray_amdgcn-amd-amdhsa [--no-allow-shlib-undefined]
On Fri, Jul 16, 2021 at 3:53 PM Mark Adams <[email protected]> wrote:
Not complex. THis has some overlap with my problem w/o Kokkos.
On Fri, Jul 16, 2021 at 12:54 PM Junchao Zhang < [email protected]> wrote:
Do you use complex? post your configure.log.
--Junchao Zhang
On Fri, Jul 16, 2021 at 9:47 AM Mark Adams <[email protected]> wrote:
The simple Kokkos example is failing for me on Spock. Any ideas? Thanks,
10:44 main *= /gpfs/alpine/csc314/scratch/adams/petsc/src/snes/tutorials$ make PETSC_DIR=/gpfs/alpine/csc314/scratch/adams/petsc PETSC_ARCH=arch-spock-opt-cray-kokkos ex3k MPICH_CXX="hipcc" OMPI_CXX="hipcc" CC -L/sw/spock/spack-envs/views/rocm-4.1.0/lib -lhsa-runtime64 -L/sw/spock/spack-envs/views/rocm-4.1.0/lib -lamdhip64 -lhsa-runtime64 -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O2 -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fvisibility=hidden -g -O3 -std=c++14 -I/gpfs/alpine/csc314/scratch/adams/petsc/include -I/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-opt-cray-kokkos/include -I/gpfs/alpine/geo127/proj-shared/spock/petsc/current/arch-opt-cray-kokkos/include -I/sw/spock/spack-envs/views/rocm-4.1.0/include -I/sw/spock/spack-envs/views/rocm-4.1.0/include ex3k.kokkos.cxx -Wl,-rpath,/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-opt-cray-kokkos/lib -L/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-opt-cray-kokkos/lib -Wl,-rpath,/gpfs/alpine/geo127/proj-shared/spock/petsc/current/arch-opt-cray-kokkos/lib -L/gpfs/alpine/geo127/proj-shared/spock/petsc/current/arch-opt-cray-kokkos/lib -Wl,-rpath,/sw/spock/spack-envs/views/rocm-4.1.0/lib -L/sw/spock/spack-envs/views/rocm-4.1.0/lib -Wl,-rpath,/opt/gcc/8.1.0/snos/lib64 -L/opt/gcc/8.1.0/snos/lib64 -Wl,-rpath,/opt/cray/pe/libsci/21.04.1.1/CRAY/9.0/x86_64/lib -L/opt/cray/pe/libsci/21.04.1.1/CRAY/9.0/x86_64/lib -Wl,-rpath,/opt/cray/pe/mpich/8.1.4/ofi/cray/9.1/lib -L/opt/cray/pe/mpich/8.1.4/ofi/cray/9.1/lib -Wl,-rpath,/opt/cray/pe/mpich/8.1.4/gtl/lib -L/opt/cray/pe/mpich/8.1.4/gtl/lib -Wl,-rpath,/opt/cray/pe/pmi/6.0.10/lib -L/opt/cray/pe/pmi/6.0.10/lib -Wl,-rpath,/opt/cray/pe/dsmml/0.1.4/dsmml/lib -L/opt/cray/pe/dsmml/0.1.4/dsmml/lib -Wl,-rpath,/opt/cray/pe/cce/11.0.4/cce/x86_64/lib -L/opt/cray/pe/cce/11.0.4/cce/x86_64/lib -Wl,-rpath,/opt/cray/xpmem/2.2.40-2.1_2.7__g3cf3325.shasta/lib64 -L/opt/cray/xpmem/2.2.40-2.1_2.7__g3cf3325.shasta/lib64 -Wl,-rpath,/opt/cray/pe/cce/11.0.4/cce-clang/x86_64/lib/clang/11.0.0/lib/linux -L/opt/cray/pe/cce/11.0.4/cce-clang/x86_64/lib/clang/11.0.0/lib/linux -Wl,-rpath,/opt/gcc/8.1.0/snos/lib/gcc/x86_64-suse-linux/8.1.0 -L/opt/gcc/8.1.0/snos/lib/gcc/x86_64-suse-linux/8.1.0 -Wl,-rpath,/opt/cray/pe/cce/11.0.4/binutils/x86_64/x86_64-pc-linux-gnu/..//x86_64-unknown-linux-gnu/lib -L/opt/cray/pe/cce/11.0.4/binutils/x86_64/x86_64-pc-linux-gnu/..//x86_64-unknown-linux-gnu/lib -lpetsc -lkokkoskernels -lkokkoscontainers -lkokkoscore -lhipsparse -lhipblas -lrocsparse -lrocsolver -lrocblas -lamdhip64 -lhsa-runtime64 -lstdc++ -ldl -lpmi -lsci_cray_mpi -lsci_cray -lmpifort_cray -lmpi_cray -lmpi_gtl_hsa -lxpmem -ldsmml -lpgas-shmem -lquadmath -lcrayacc_amdgpu -lopenacc -lmodules -lfi -lcraymath -lf -lu -lcsup -lgfortran -lpthread -lgcc_eh -lm -lclang_rt.craypgo-x86_64 -lclang_rt.builtins-x86_64 -lquadmath -lstdc++ -ldl -o ex3k In file included from ex3k.kokkos.cxx:3: In file included from /gpfs/alpine/csc314/scratch/adams/petsc/include/petscdmda_kokkos.hpp:4: In file included from /gpfs/alpine/csc314/scratch/adams/petsc/include/petscvec_kokkos.hpp:14: In file included from /gpfs/alpine/csc314/scratch/adams/petsc/include/petscvec.h:9: In file included from /gpfs/alpine/csc314/scratch/adams/petsc/include/petscsys.h:42: In file included from /gpfs/alpine/csc314/scratch/adams/petsc/include/petscsystypes.h:255: In file included from /gpfs/alpine/geo127/proj-shared/spock/petsc/current/arch-opt-cray-kokkos/include/Kokkos_Complex.hpp:47: In file included from /gpfs/alpine/geo127/proj-shared/spock/petsc/current/arch-opt-cray-kokkos/include/Kokkos_Atomic.hpp:212: /gpfs/alpine/geo127/proj-shared/spock/petsc/current/arch-opt-cray-kokkos/include/impl/Kokkos_Atomic_Exchange.hpp:259:11: error: no member named 'lock_address_host_space' in namespace 'Kokkos::Impl::Kokkos::Impl'; did you mean simply 'lock_address_host_space'? while (!Impl::lock_address_host_space((void*)dest)) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ lock_address_host_space /gpfs/alpine/geo127/proj-shared/spock/petsc/current/arch-opt-cray-kokkos/include/Kokkos_HostSpace.hpp:83:6: note: 'lock_address_host_space' declared here bool lock_address_host_space(void* ptr); ^ In file included from ex3k.kokkos.cxx:3: In file included from /gpfs/alpine/csc314/scratch/adams/petsc/include/petscdmda_kokkos.hpp:4: In file included from /gpfs/alpine/csc314/scratch/adams/petsc/include/petscvec_kokkos.hpp:14: In file included from /gpfs/alpine/csc314/scratch/adams/petsc/include/petscvec.h:9: In file included from /gpfs/alpine/csc314/scratch/adams/petsc/include/petscsys.h:42: In file included from /gpfs/alpine/csc314/scratch/adams/petsc/include/petscsystypes.h:255: In file included from /gpfs/alpine/geo127/proj-shared/spock/petsc/current/arch-opt-cray-kokkos/include/Kokkos_Complex.hpp:47: In file included from /gpfs/alpine/geo127/proj-shared/spock/petsc/current/arch-opt-cray-kokkos/include/Kokkos_Atomic.hpp:212: /gpfs/alpine/geo127/proj-shared/spock/petsc/current/arch-opt-cray-kokkos/include/impl/Kokkos_Atomic_Exchange.hpp:261:3: error: no member named 'memory_fence' in namespace 'Kokkos::Impl::Kokkos'; did you mean simply 'memory_fence'? Kokkos::memory_fence(); ^~~~~~~~~~~~~~~~~~~~ memory_fence /gpfs/alpine/geo127/proj-shared/spock/petsc/current/arch-opt-cray-kokkos/include/impl/Kokkos_Memory_Fence.hpp:53:6: note: 'memory_fence' declared here void memory_fence() { ^ In file included from ex3k.kokkos.cxx:3: In file included from /gpfs/alpine/csc314/scratch/adams/petsc/include/petscdmda_kokkos.hpp:4: In file included from /gpfs/alpine/csc314/scratch/adams/petsc/include/petscvec_kokkos.hpp:14: In file included from /gpfs/alpine/csc314/scratch/adams/petsc/include/petscvec.h:9: In file included from /gpfs/alpine/csc314/scratch/adams/petsc/include/petscsys.h:42: In file included from /gpfs/alpine/csc314/scratch/adams/petsc/include/petscsystypes.h:255: In file included from /gpfs/alpine/geo127/proj-shared/spock/petsc/current/arch-opt-cray-kokkos/include/Kokkos_Complex.hpp:47: In file included from /gpfs/alpine/geo127/proj-shared/spock/petsc/current/arch-opt-cray-kokkos/include/Kokkos_Atomic.hpp:212: /gpfs/alpine/geo127/proj-shared/spock/petsc/current/arch-opt-cray-kokkos/include/impl/Kokkos_Atomic_Exchange.hpp:277:3: error: no member named 'memory_fence' in namespace 'Kokkos::Impl::Kokkos'; did you mean simply 'memory_fence'? Kokkos::memory_fence(); ^~~~~~~~~~~~~~~~~~~~ memory_fence /gpfs/alpine/geo127/proj-shared/spock/petsc/current/arch-opt-cray-kokkos/include/impl/Kokkos_Memory_Fence.hpp:53:6: note: 'memory_fence' declared here void memory_fence() { ^