skipping incompatible /usr/lib libraries
cponder opened this issue · 4 comments
cponder commented
I"m building on a Cray system running SLES 15 SP4.
The build gives ma a lot of these messages
/usr/bin/ld: skipping incompatible /usr/lib/librt.so when searching for -lrt
/usr/bin/ld: skipping incompatible /usr/lib/libutil.so when searching for -lutil
/usr/bin/ld: skipping incompatible /usr/lib/libdl.so when searching for -ldl
/usr/bin/ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread
/usr/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc
/usr/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm
I know these are just warnings, but my builds under Ubuntu never did this.
cponder commented
I believe the problem is that it's searching under /usr/lib before searching /usr/lib64.
However, I don't see this in the build information:
CFLAGS = -fPIC -m64 -tp=px
CXXFLAGS = -fPIC -m64 -tp=px
FFLAGS = -I/global/common/software/nvendor/perlmutter/SHARE/Utils/CUDA/12.0.1.0_525.85.12/include -I/global/common/software/nvendor/perlmutter/SHARE/Utils/CUDA/12.0.1.0_525.85.12/include/CL -I/global/common/software/nvendor/perlmutter/SHARE/Utils/CUDA/12.0.1.0_525.85.12/extras/CUPTI/include -I/global/common/software/nvendor/perlmutter/SHARE/Utils/CUDA/12.0.1.0_525.85.12/extras/Debugger/include -I/global/common/software/nvendor/perlmutter/SHARE/Utils/CUDA/12.0.1.0_525.85.12/nvvm/include -I/global/common/software/nvendor/perlmutter/SHARE/Utils/HWLoc/2.8.0/PGI-23.1_CUDA-12.0.1.0_525.85.12/include -I/global/common/software/nvendor/perlmutter/SHARE/Utils/OpenMPI/4.1.5/PGI-23.1_CUDA-12.0.1.0_525.85.12_UCX-1.13.1_HWLoc-2.8.0_ZLib-1.2.13/include -I/global/common/software/nvendor/perlmutter/SHARE/Utils/OpenMPI/4.1.5/PGI-23.1_CUDA-12.0.1.0_525.85.12_UCX-1.13.1_HWLoc-2.8.0_ZLib-1.2.13/lib
FCFLAGS = -fPIC -m64 -tp=px
LDFLAGS = -L/global/common/software/nvendor/perlmutter/SHARE/Utils/CUDA/12.0.1.0_525.85.12/lib64 -L/global/common/software/nvendor/perlmutter/SHARE/Utils/CUDA/12.0.1.0_525.85.12/driver -L/global/common/software/nvendor/perlmutter/SHARE/Utils/CUDA/12.0.1.0_525.85.12/extras/CUPTI/lib64 -L/global/common/software/nvendor/perlmutter/SHARE/Utils/CUDA/12.0.1.0_525.85.12/extras/Debugger/lib64 -L/global/common/software/nvendor/perlmutter/SHARE/Utils/CUDA/12.0.1.0_525.85.12/nvvm/lib64 -L/global/common/software/nvendor/perlmutter/SHARE/Utils/HWLoc/2.8.0/PGI-23.1_CUDA-12.0.1.0_525.85.12/lib -L/global/common/software/nvendor/perlmutter/SHARE/Utils/OpenMPI/4.1.5/PGI-23.1_CUDA-12.0.1.0_525.85.12_UCX-1.13.1_HWLoc-2.8.0_ZLib-1.2.13/lib -L/global/common/software/nvendor/perlmutter/SHARE/Utils/PGI/23.1/Linux_x86_64/23.1/cuda/lib64 -lnvidia-ml
cponder commented
Likewise with the MPI compiles:
--> mpicc --show | xargs explode ' '
pgcc
-I/global/common/software/nvendor/perlmutter/SHARE/Utils/OpenMPI/4.1.5/PGI-23.1_CUDA-12.0.1.0_525.85.12_LIBFABRIC-1.15.2.0_HWLoc-2.8.0_ZLib-1.2.13/include
-L/global/common/software/nvendor/perlmutter/SHARE/Utils/OpenMPI/4.1.5/PGI-23.1_CUDA-12.0.1.0_525.85.12_LIBFABRIC-1.15.2.0_HWLoc-2.8.0_ZLib-1.2.13/lib
-L/global/common/software/nvendor/perlmutter/SHARE/Utils/HWLoc/2.8.0/PGI-23.1_CUDA-12.0.1.0_525.85.12/lib
-Wl,-rpath
-Wl,/global/common/software/nvendor/perlmutter/SHARE/Utils/OpenMPI/4.1.5/PGI-23.1_CUDA-12.0.1.0_525.85.12_LIBFABRIC-1.15.2.0_HWLoc-2.8.0_ZLib-1.2.13/lib
-Wl,-rpath
-Wl,/global/common/software/nvendor/perlmutter/SHARE/Utils/HWLoc/2.8.0/PGI-23.1_CUDA-12.0.1.0_525.85.12/lib
-Wl,--enable-new-dtags
-lmpi
--> mpifort --show | xargs explode ' '
pgfortran
-I/global/common/software/nvendor/perlmutter/SHARE/Utils/OpenMPI/4.1.5/PGI-23.1_CUDA-12.0.1.0_525.85.12_LIBFABRIC-1.15.2.0_HWLoc-2.8.0_ZLib-1.2.13/include
-I/global/common/software/nvendor/perlmutter/SHARE/Utils/OpenMPI/4.1.5/PGI-23.1_CUDA-12.0.1.0_525.85.12_LIBFABRIC-1.15.2.0_HWLoc-2.8.0_ZLib-1.2.13/lib
-L/global/common/software/nvendor/perlmutter/SHARE/Utils/OpenMPI/4.1.5/PGI-23.1_CUDA-12.0.1.0_525.85.12_LIBFABRIC-1.15.2.0_HWLoc-2.8.0_ZLib-1.2.13/lib
-L/global/common/software/nvendor/perlmutter/SHARE/Utils/HWLoc/2.8.0/PGI-23.1_CUDA-12.0.1.0_525.85.12/lib
-Wl,-rpath
-Wl,/global/common/software/nvendor/perlmutter/SHARE/Utils/OpenMPI/4.1.5/PGI-23.1_CUDA-12.0.1.0_525.85.12_LIBFABRIC-1.15.2.0_HWLoc-2.8.0_ZLib-1.2.13/lib
-Wl,-rpath
-Wl,/global/common/software/nvendor/perlmutter/SHARE/Utils/HWLoc/2.8.0/PGI-23.1_CUDA-12.0.1.0_525.85.12/lib
-Wl,--enable-new-dtags
-lmpi_usempif08
-lmpi_usempi_ignore_tkr
-lmpi_mpifh
-lmpi
cponder commented
And the paths:
--> explode : $LD_LIBRARY_PATH
/global/common/software/nvendor/perlmutter/SHARE/Utils/OpenMPI/4.1.5/PGI-23.1_CUDA-12.0.1.0_525.85.12_LIBFABRIC-1.15.2.0_HWLoc-2.8.0_ZLib-1.2.13/lib
/opt/cray/libfabric/1.15.2.0/lib64
/global/common/software/nvendor/perlmutter/SHARE/Utils/HWLoc/2.8.0/PGI-23.1_CUDA-12.0.1.0_525.85.12/lib
/global/common/software/nvendor/perlmutter/SHARE/Utils/PGI/23.1/Linux_x86_64/23.1/compilers/lib
/global/common/software/nvendor/perlmutter/SHARE/Utils/CUDA/12.0.1.0_525.85.12/nvvm/lib64
/global/common/software/nvendor/perlmutter/SHARE/Utils/CUDA/12.0.1.0_525.85.12/extras/Debugger/lib64
/global/common/software/nvendor/perlmutter/SHARE/Utils/CUDA/12.0.1.0_525.85.12/extras/CUPTI/lib64
/global/common/software/nvendor/perlmutter/SHARE/Utils/CUDA/12.0.1.0_525.85.12/lib64
/lib64
/usr/lib64
/lib
/usr/lib
/usr/local/lib
/usr/libexec
/usr/local/libexec
/global/homes/c/cponder/PerlMutter/lib
/global/common/software/nvendor/perlmutter/SHARE/Utils/CUDA/12.0.1.0_525.85.12/driver
wkliao commented
It appears to me you are running on Perlmutter at NERSC.
Could you please provide the information about loaded modules,
i.e. output of command "module list", and the configure command used.