[petsc-users] Spock link error
Mark Adams
mfadams at lbl.gov
Sun Sep 19 08:29:18 CDT 2021
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
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