[petsc-users] Spock link error
Stefano Zampini
stefano.zampini at gmail.com
Sun Sep 19 08:43:59 CDT 2021
Are you following the user advices here
https://docs.olcf.ornl.gov/systems/spock_quick_start_guide.html#compiling-with-the-cray-compiler-wrappers-cc-or-cc
?
Il giorno dom 19 set 2021 alle ore 16:30 Mark Adams <mfadams at lbl.gov> ha
scritto:
> I am getting to see this error. It seems to be suggesting that I turn
> --no-allow-shlib-undefined off.
> Any ideas?
> Thanks,
> Mark
>
> 09:09 main= /gpfs/alpine/csc314/scratch/adams/petsc$ make
> PETSC_DIR=/gpfs/alpine/phy122/proj-shared/spock/petsc/current/arch-opt-cray-new
> PETSC_ARCH="" check
> Running check examples to verify correct installation
> Using
> PETSC_DIR=/gpfs/alpine/phy122/proj-shared/spock/petsc/current/arch-opt-cray-new
> and PETSC_ARCH=
> gmake[3]:
> [/gpfs/alpine/phy122/proj-shared/spock/petsc/current/arch-opt-cray-new/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 -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas
> -fstack-protector -Qunused-arguments -fvisibility=hidden -g -O2 -fPIC
> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas
> -fstack-protector -Qunused-arguments -fvisibility=hidden -g -O2
> -I/gpfs/alpine/phy122/proj-shared/spock/petsc/current/arch-opt-cray-new/include
> -I/opt/rocm-4.2.0/include ex19.c
> -Wl,-rpath,/gpfs/alpine/phy122/proj-shared/spock/petsc/current/arch-opt-cray-new/lib
> -L/gpfs/alpine/phy122/proj-shared/spock/petsc/current/arch-opt-cray-new/lib
> -Wl,-rpath,/gpfs/alpine/phy122/proj-shared/spock/petsc/current/arch-opt-cray-new/lib
> -L/gpfs/alpine/phy122/proj-shared/spock/petsc/current/arch-opt-cray-new/lib
> -Wl,-rpath,/opt/rocm-4.2.0/lib -L/opt/rocm-4.2.0/lib
> -Wl,-rpath,/opt/cray/pe/gcc/8.1.0/snos/lib64
> -L/opt/cray/pe/gcc/8.1.0/snos/lib64 -Wl,-rpath,/opt/cray/pe/libsci/
> 21.06.1.1/CRAY/9.0/x86_64/lib -L/opt/cray/pe/libsci/
> 21.06.1.1/CRAY/9.0/x86_64/lib
> -Wl,-rpath,/opt/cray/pe/mpich/8.1.7/ofi/cray/10.0/lib
> -L/opt/cray/pe/mpich/8.1.7/ofi/cray/10.0/lib
> -Wl,-rpath,/opt/cray/pe/mpich/default/gtl/lib
> -L/opt/cray/pe/mpich/default/gtl/lib
> -Wl,-rpath,/opt/cray/pe/dsmml/0.1.5/dsmml/lib
> -L/opt/cray/pe/dsmml/0.1.5/dsmml/lib -Wl,-rpath,/opt/cray/pe/pmi/6.0.12/lib
> -L/opt/cray/pe/pmi/6.0.12/lib
> -Wl,-rpath,/opt/cray/pe/cce/12.0.1/cce/x86_64/lib
> -L/opt/cray/pe/cce/12.0.1/cce/x86_64/lib
> -Wl,-rpath,/opt/cray/xpmem/2.2.40-2.1_2.44__g3cf3325.shasta/lib64
> -L/opt/cray/xpmem/2.2.40-2.1_2.44__g3cf3325.shasta/lib64
> -Wl,-rpath,/opt/cray/pe/cce/12.0.1/cce-clang/x86_64/lib/clang/12.0.0/lib/linux
> -L/opt/cray/pe/cce/12.0.1/cce-clang/x86_64/lib/clang/12.0.0/lib/linux
> -Wl,-rpath,/opt/cray/pe/gcc/8.1.0/snos/lib/gcc/x86_64-suse-linux/8.1.0
> -L/opt/cray/pe/gcc/8.1.0/snos/lib/gcc/x86_64-suse-linux/8.1.0
> -Wl,-rpath,/opt/cray/pe/cce/12.0.1/binutils/x86_64/x86_64-unknown-linux-gnu/lib
> -L/opt/cray/pe/cce/12.0.1/binutils/x86_64/x86_64-unknown-linux-gnu/lib
> -Wl,-rpath,/opt/cray/pe/cce/12.0.1/binutils/x86_64/x86_64-pc-linux-gnu/..//x86_64-unknown-linux-gnu/lib
> -L/opt/cray/pe/cce/12.0.1/binutils/x86_64/x86_64-pc-linux-gnu/..//x86_64-unknown-linux-gnu/lib
> -lpetsc -lparmetis -lmetis -lhipsparse -lhipblas -lrocsparse -lrocsolver
> -lrocblas -lrocrand -lamdhip64 -lstdc++ -ldl -lmpifort_cray -lmpi_cray
> -lmpi_gtl_hsa -ldsmml -lpmi -lxpmem -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-new/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-new/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-new/lib/libpetsc.so:
> undefined reference to .omp_offloading.img_cache.cray_amdgcn-amd-amdhsa
> [--no-allow-shlib-undefined]*
> clang-12: 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 -fPIC -g -O2 -fPIC -g -O2
> -I/gpfs/alpine/phy122/proj-shared/spock/petsc/current/arch-opt-cray-new/include
> -I/opt/rocm-4.2.0/include ex5f.F90
> -Wl,-rpath,/gpfs/alpine/phy122/proj-shared/spock/petsc/current/arch-opt-cray-new/lib
> -L/gpfs/alpine/phy122/proj-shared/spock/petsc/current/arch-opt-cray-new/lib
> -Wl,-rpath,/gpfs/alpine/phy122/proj-shared/spock/petsc/current/arch-opt-cray-new/lib
> -L/gpfs/alpine/phy122/proj-shared/spock/petsc/current/arch-opt-cray-new/lib
> -Wl,-rpath,/opt/rocm-4.2.0/lib -L/opt/rocm-4.2.0/lib
> -Wl,-rpath,/opt/cray/pe/gcc/8.1.0/snos/lib64
> -L/opt/cray/pe/gcc/8.1.0/snos/lib64 -Wl,-rpath,/opt/cray/pe/libsci/
> 21.06.1.1/CRAY/9.0/x86_64/lib -L/opt/cray/pe/libsci/
> 21.06.1.1/CRAY/9.0/x86_64/lib
> -Wl,-rpath,/opt/cray/pe/mpich/8.1.7/ofi/cray/10.0/lib
> -L/opt/cray/pe/mpich/8.1.7/ofi/cray/10.0/lib
> -Wl,-rpath,/opt/cray/pe/mpich/default/gtl/lib
> -L/opt/cray/pe/mpich/default/gtl/lib
> -Wl,-rpath,/opt/cray/pe/dsmml/0.1.5/dsmml/lib
> -L/opt/cray/pe/dsmml/0.1.5/dsmml/lib -Wl,-rpath,/opt/cray/pe/pmi/6.0.12/lib
> -L/opt/cray/pe/pmi/6.0.12/lib
> -Wl,-rpath,/opt/cray/pe/cce/12.0.1/cce/x86_64/lib
> -L/opt/cray/pe/cce/12.0.1/cce/x86_64/lib
> -Wl,-rpath,/opt/cray/xpmem/2.2.40-2.1_2.44__g3cf3325.shasta/lib64
> -L/opt/cray/xpmem/2.2.40-2.1_2.44__g3cf3325.shasta/lib64
> -Wl,-rpath,/opt/cray/pe/cce/12.0.1/cce-clang/x86_64/lib/clang/12.0.0/lib/linux
> -L/opt/cray/pe/cce/12.0.1/cce-clang/x86_64/lib/clang/12.0.0/lib/linux
> -Wl,-rpath,/opt/cray/pe/gcc/8.1.0/snos/lib/gcc/x86_64-suse-linux/8.1.0
> -L/opt/cray/pe/gcc/8.1.0/snos/lib/gcc/x86_64-suse-linux/8.1.0
> -Wl,-rpath,/opt/cray/pe/cce/12.0.1/binutils/x86_64/x86_64-unknown-linux-gnu/lib
> -L/opt/cray/pe/cce/12.0.1/binutils/x86_64/x86_64-unknown-linux-gnu/lib
> -Wl,-rpath,/opt/cray/pe/cce/12.0.1/binutils/x86_64/x86_64-pc-linux-gnu/..//x86_64-unknown-linux-gnu/lib
> -L/opt/cray/pe/cce/12.0.1/binutils/x86_64/x86_64-pc-linux-gnu/..//x86_64-unknown-linux-gnu/lib
> -lpetsc -lparmetis -lmetis -lhipsparse -lhipblas -lrocsparse -lrocsolver
> -lrocblas -lrocrand -lamdhip64 -lstdc++ -ldl -lmpifort_cray -lmpi_cray
> -lmpi_gtl_hsa -ldsmml -lpmi -lxpmem -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/12.0.1/binutils/x86_64/x86_64-pc-linux-gnu/bin/ld:
> warning: alignment 128 of symbol
> `$host_init$$runtime_init_for_iso_c_binding$iso_c_binding_' in
> /opt/cray/pe/cce/12.0.1/cce/x86_64/lib/libmodules.so is smaller than 256 in
> /tmp/pe_39617/ex5f_1.o
> /opt/cray/pe/cce/12.0.1/binutils/x86_64/x86_64-pc-linux-gnu/bin/ld:
> warning: alignment 64 of symbol `$data_init$iso_c_binding_' in
> /opt/cray/pe/cce/12.0.1/cce/x86_64/lib/libmodules.so is smaller than 256 in
> /tmp/pe_39617/ex5f_1.o
> Fortran example src/snes/tutorials/ex5f run successfully with 1 MPI process
> Completed test examples
> 09:12 main= /gpfs/alpine/csc314/scratch/adams/petsc$ module list
>
> Currently Loaded Modules:
> 1) craype-x86-rome 4) perftools-base/21.05.0
> 7) cray-pmi-lib/6.0.12 10) cray-dsmml/0.1.5 13) PrgEnv-cray/8.1.0
> 16) rocm/4.2.0 19) autoconf/2.69
> 2) libfabric/1.11.0.4.75 5) xpmem/2.2.40-2.1_2.44__g3cf3325.shasta
> 8) cce/12.0.1 11) cray-mpich/8.1.7 14) DefApps/default
> 17) emacs/27.2 20) automake/1.16.3
> 3) craype-network-ofi 6) cray-pmi/6.0.12
> 9) craype/2.7.8 12) cray-libsci/21.06.1.1 15)
> craype-accel-amd-gfx908 18) zlib/1.2.11 21) libtool/2.4.6
>
>
>
--
Stefano
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