[petsc-dev] Kokkos make error on Spock
Mark Adams
mfadams at lbl.gov
Sun Jul 18 07:43:15 CDT 2021
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 $GCC_PATH
/opt/gcc/10.2.0
Anyway, thanks for your help,
Mark
On Sat, Jul 17, 2021 at 11:26 PM Junchao Zhang <junchao.zhang at gmail.com>
wrote:
> Mark, I can reproduce this error with PrgEnv-cray, i.e., using the Cray
> compiler (clang-11). Previously I used PrgEnv-gnu, which did not have this
> error.
> Probably it is a problem of Spock. But I am not sure.
>
> --Junchao Zhang
>
>
> On Sat, Jul 17, 2021 at 10:17 AM Mark Adams <mfadams at lbl.gov> wrote:
>
>> And I can run a fortran test, with warnings, but C tests fail:
>>
>> 11:15 jczhang/fix-cray-mpicxx-includes/main=
>> /gpfs/alpine/csc314/scratch/adams/petsc$ 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 <mfadams at 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.zhang at 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 <mfadams at 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 <mfadams at 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.zhang at gmail.com> wrote:
>>>>>>
>>>>>>> Do you use complex? post your configure.log.
>>>>>>>
>>>>>>> --Junchao Zhang
>>>>>>>
>>>>>>>
>>>>>>> On Fri, Jul 16, 2021 at 9:47 AM Mark Adams <mfadams at 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() {
>>>>>>>> ^
>>>>>>>>
>>>>>>>
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