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 <mfad...@lbl.gov> 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 $GCC_PATH > /opt/gcc/10.2.0 > > Anyway, thanks for your help, > Mark > > On Sat, Jul 17, 2021 at 11:26 PM Junchao Zhang <junchao.zh...@gmail.com> > wrote: > >> Mark, I can reproduce this error with PrgEnv-cray, i.e., using the Cray >> compiler (clang-11). Previously I used PrgEnv-gnu, which did not have this >> error. >> Probably it is a problem of Spock. But I am not sure. >> >> --Junchao Zhang >> >> >> On Sat, Jul 17, 2021 at 10:17 AM Mark Adams <mfad...@lbl.gov> wrote: >> >>> And I can run a fortran test, with warnings, but C tests fail: >>> >>> 11:15 jczhang/fix-cray-mpicxx-includes/main= >>> /gpfs/alpine/csc314/scratch/adams/petsc$ 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 <mfad...@lbl.gov> 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 <junchao.zh...@gmail.com> >>>> 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 <mfad...@lbl.gov> 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 <mfad...@lbl.gov> wrote: >>>>>> >>>>>>> Not complex. THis has some overlap with my problem w/o Kokkos. >>>>>>> >>>>>>> On Fri, Jul 16, 2021 at 12:54 PM Junchao Zhang < >>>>>>> junchao.zh...@gmail.com> wrote: >>>>>>> >>>>>>>> Do you use complex? post your configure.log. >>>>>>>> >>>>>>>> --Junchao Zhang >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Jul 16, 2021 at 9:47 AM Mark Adams <mfad...@lbl.gov> 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() { >>>>>>>>> ^ >>>>>>>>> >>>>>>>>