[petsc-users] make check error on Spock
Mark Adams
mfadams at lbl.gov
Fri Jul 16 13:43:07 CDT 2021
I get this error on Spock.
Any ideas?
14:36 main *= /gpfs/alpine/csc314/scratch/adams/petsc$ make
PETSC_DIR=/gpfs/alpine/phy122/proj-shared/spock/petsc/current/arch-opt-cray
PETSC_ARCH="" check
Running check examples to verify correct installation
Using
PETSC_DIR=/gpfs/alpine/phy122/proj-shared/spock/petsc/current/arch-opt-cray
and PETSC_ARCH=
gmake[3]:
[/gpfs/alpine/phy122/proj-shared/spock/petsc/current/arch-opt-cray/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 -lhsa-runtime64
-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 -fPIC -Wall
-Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector
-Qunused-arguments -fvisibility=hidden -g
-I/sw/spock/spack-envs/views/rocm-4.1.0/include
-I/gpfs/alpine/phy122/proj-shared/spock/petsc/current/arch-opt-cray/include
-I/sw/spock/spack-envs/base/opt/linux-sles15-x86_64/gcc-7.5.0/zlib-1.2.11-xujqx3ri73tbwmcwoolo3jnn6ti6vwsh/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/phy122/proj-shared/spock/petsc/current/arch-opt-cray/lib
-L/gpfs/alpine/phy122/proj-shared/spock/petsc/current/arch-opt-cray/lib
-Wl,-rpath,/gpfs/alpine/phy122/proj-shared/spock/petsc/current/arch-opt-cray/lib
-L/gpfs/alpine/phy122/proj-shared/spock/petsc/current/arch-opt-cray/lib
-Wl,-rpath,/sw/spock/spack-envs/base/opt/linux-sles15-x86_64/gcc-7.5.0/zlib-1.2.11-xujqx3ri73tbwmcwoolo3jnn6ti6vwsh/lib
-L/sw/spock/spack-envs/base/opt/linux-sles15-x86_64/gcc-7.5.0/zlib-1.2.11-xujqx3ri73tbwmcwoolo3jnn6ti6vwsh/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 -lp4est -lsc -lz -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/phy122/proj-shared/spock/petsc/current/arch-opt-cray/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/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/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
*******************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 -lhsa-runtime64 -fPIC -g
-fPIC -g
-I/gpfs/alpine/phy122/proj-shared/spock/petsc/current/arch-opt-cray/include
-I/sw/spock/spack-envs/base/opt/linux-sles15-x86_64/gcc-7.5.0/zlib-1.2.11-xujqx3ri73tbwmcwoolo3jnn6ti6vwsh/include
-I/sw/spock/spack-envs/views/rocm-4.1.0/include ex5f.F90
-Wl,-rpath,/gpfs/alpine/phy122/proj-shared/spock/petsc/current/arch-opt-cray/lib
-L/gpfs/alpine/phy122/proj-shared/spock/petsc/current/arch-opt-cray/lib
-Wl,-rpath,/gpfs/alpine/phy122/proj-shared/spock/petsc/current/arch-opt-cray/lib
-L/gpfs/alpine/phy122/proj-shared/spock/petsc/current/arch-opt-cray/lib
-Wl,-rpath,/sw/spock/spack-envs/base/opt/linux-sles15-x86_64/gcc-7.5.0/zlib-1.2.11-xujqx3ri73tbwmcwoolo3jnn6ti6vwsh/lib
-L/sw/spock/spack-envs/base/opt/linux-sles15-x86_64/gcc-7.5.0/zlib-1.2.11-xujqx3ri73tbwmcwoolo3jnn6ti6vwsh/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 -lp4est -lsc -lz -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$iso_c_binding_' in
/opt/cray/pe/cce/11.0.4/cce/x86_64/lib/libmodules.so is smaller than 256 in
/tmp/pe_44489/ex5f_1.o
/opt/cray/pe/cce/11.0.4/binutils/x86_64/x86_64-pc-linux-gnu/bin/ld:
warning: alignment 64 of symbol `$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_44489/ex5f_1.o
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