[petsc-dev] Kokkos make error on Spock

Fri Jul 16 16:19:35 CDT 2021

I don't understand this when linking ex19
   ld.lld: error:
/gpfs/alpine/csc314/scratch/adams/petsc/arch-spock-opt-cray-kokkos/lib/libpetsc.so:
undefined reference to .omp_offloading.img_start.cray_amdgcn-amd-amdhsa
[--no-allow-shlib-undefined]
Do you have a stale libpetsc.so?

For ex3k, it is a makefile problem (I am fixing). If you do not directly
build an executable from *.kokkos.cxx, then you can avoid this problem.
 For example,  snes/tests/ex13 works with kokkos options on Spock.

--Junchao Zhang

On Fri, Jul 16, 2021 at 2:53 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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