Hi Alexandre, I don't see mpifort linking against `-lpnetcdf`. Maybe check the logs and see if it is actually picking up on PnetCDF being available?
Alan On Fri, 31 Mar 2023 at 16:01, Strube, Alexandre <[email protected]> wrote: > I am trying to install ESMF-8.3.0-foss-2022a.eb here. I always end up with > this error at the install step: > > make chkdir_apps > > make[5]: Entering directory > '/dev/shm/strube1/jurecadc/ESMF/8.3.0/foss-2022a/esmf-8.3.0/src/apps/ESMF_PrintInfo' > > make[5]: Leaving directory > '/dev/shm/strube1/jurecadc/ESMF/8.3.0/foss-2022a/esmf-8.3.0/src/apps/ESMF_PrintInfo' > > mpifort -m64 -mcmodel=small -pthread -Wl,--no-as-needed -fopenmp > -L/p/project/ccstao/cstao05/easybuild/jurecadc/software/ESMF/8.3.0-foss-2022a/lib > -L/p/software/jurecadc/stages/2023/software/netCDF/4.9.0-gompi-2022a/lib64 > -L/p/software/jurecadc/stages/2023/software/netCDF-Fortran/4.6.0-gompi-2022a/lib > -L/p/software/jurecadc/stages/2023/software/bzip2/1.0.8-GCCcore-11.3.0/lib64 > -L/p/software/jurecadc/stages/2023/software/bzip2/1.0.8-GCCcore-11.3.0/lib > -L/p/software/jurecadc/stages/2023/software/netCDF/4.9.0-gompi-2022a/lib64 > -L/p/software/jurecadc/stages/2023/software/netCDF/4.9.0-gompi-2022a/lib > -L/p/software/jurecadc/stages/2023/software/GCCcore/11.3.0/lib64 > -L/p/software/jurecadc/stages/2023/software/GCCcore/11.3.0/lib > -L/p/software/jurecadc/stages/2023/software/GCCcore/11.3.0/lib/gcc/x86_64-pc-linux-gnu/11.3.0/../../../../lib64/ > -Wl,-rpath,/p/project/ccstao/cstao05/easybuild/jurecadc/software/ESMF/8.3.0-foss-2022a/lib > -Wl,-rpath,/p/software/jurecadc/stages/2023/software/PnetCDF/1.12.3-gompi-2022a/lib64 > -Wl,-rpath,/p/software/jurecadc/stages/2023/software/PnetCDF/1.12.3-gompi-2022a/lib > -Wl,-rpath,/p/software/jurecadc/stages/2023/software/libarchive/3.6.1-GCCcore-11.3.0/lib64 > -Wl,-rpath,/p/software/jurecadc/stages/2023/software/libarchive/3.6.1-GCCcore-11.3.0/lib > -Wl,-rpath,/p/software/jurecadc/stages/2023/software/netCDF-C++4/4.3.1-gompi-2022a/lib64 > -Wl,-rpath,/p/software/jurecadc/stages/2023/software/netCDF-C++4/4.3.1-gompi-2022a/lib > -Wl,-rpath,/p/software/jurecadc/stages/2023/software/netCDF-Fortran/4.6.0-gompi-2022a/lib64 > -Wl,-rpath,/p/software/jurecadc/stages/2023/software/netCDF-Fortran/4.6.0-gompi-2022a/lib > -Wl,-rpath,/p/software/jurecadc/stages/2023/software/netCDF/4.9.0-gompi-2022a/lib64 > -Wl,-rpath,/p/software/jurecadc/stages/2023/software/netCDF/4.9.0-gompi-2022a/lib > -Wl,-rpath,/p/software/jurecadc/stages/2023/software/FFTW.MPI/3.3.10-gompi-2022a/lib64 > -Wl,-rpath,/p/software/jurecadc/stages/2023/software/FFTW.MPI/3.3.10-gompi-2022a/lib > -Wl,-rpath,/p/software/jurecadc/stages/2023/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib64 > -Wl,-rpath,/p/software/jurecadc/stages/2023/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib > -Wl,-rpath,/p/software/jurecadc/stages/2023/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib64 > -Wl,-rpath,/p/software/jurecadc/stages/2023/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib > -Wl,-rpath,/p/software/jurecadc/stages/2023/software/GCCcore/11.3.0/lib64 > -Wl,-rpath,/p/software/jurecadc/stages/2023/software/GCCcore/11.3.0/lib > -Wl,-rpath,/p/software/jurecadc/stages/2023/software/netCDF/4.9.0-gompi-2022a/lib64 > -Wl,-rpath,/p/software/jurecadc/stages/2023/software/netCDF-Fortran/4.6.0-gompi-2022a/lib > -Wl,-rpath,/p/software/jurecadc/stages/2023/software/bzip2/1.0.8-GCCcore-11.3.0/lib64 > -Wl,-rpath,/p/software/jurecadc/stages/2023/software/bzip2/1.0.8-GCCcore-11.3.0/lib > -Wl,-rpath,/p/software/jurecadc/stages/2023/software/netCDF/4.9.0-gompi-2022a/lib64 > -Wl,-rpath,/p/software/jurecadc/stages/2023/software/netCDF/4.9.0-gompi-2022a/lib > -Wl,-rpath,/p/software/jurecadc/stages/2023/software/GCCcore/11.3.0/lib64 > -Wl,-rpath,/p/software/jurecadc/stages/2023/software/GCCcore/11.3.0/lib > -Wl,-rpath,/p/software/jurecadc/stages/2023/software/GCCcore/11.3.0/lib/gcc/x86_64-pc-linux-gnu/11.3.0/../../../../lib64/ > -o > /p/project/ccstao/cstao05/easybuild/jurecadc/software/ESMF/8.3.0-foss-2022a/bin/ESMF_PrintInfo > /dev/shm/strube1/jurecadc/ESMF/8.3.0/foss-2022a/esmf-8.3.0//obj/objO/Linux.gfortran.64.openmpi.default/src/apps/ESMF_PrintInfo/ESMF_PrintInfo.o > -lesmf -lrt -lstdc++ -ldl > -L/p/software/jurecadc/stages/2023/software/PnetCDF/1.12.3-gompi-2022a/lib64 > -L/p/software/jurecadc/stages/2023/software/PnetCDF/1.12.3-gompi-2022a/lib > -L/p/software/jurecadc/stages/2023/software/libarchive/3.6.1-GCCcore-11.3.0/lib64 > -L/p/software/jurecadc/stages/2023/software/libarchive/3.6.1-GCCcore-11.3.0/lib > -L/p/software/jurecadc/stages/2023/software/netCDF-C++4/4.3.1-gompi-2022a/lib64 > -L/p/software/jurecadc/stages/2023/software/netCDF-C++4/4.3.1-gompi-2022a/lib > -L/p/software/jurecadc/stages/2023/software/netCDF-Fortran/4.6.0-gompi-2022a/lib64 > -L/p/software/jurecadc/stages/2023/software/netCDF-Fortran/4.6.0-gompi-2022a/lib > -L/p/software/jurecadc/stages/2023/software/netCDF/4.9.0-gompi-2022a/lib64 > -L/p/software/jurecadc/stages/2023/software/netCDF/4.9.0-gompi-2022a/lib > -L/p/software/jurecadc/stages/2023/software/FFTW.MPI/3.3.10-gompi-2022a/lib64 > -L/p/software/jurecadc/stages/2023/software/FFTW.MPI/3.3.10-gompi-2022a/lib > -L/p/software/jurecadc/stages/2023/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib64 > -L/p/software/jurecadc/stages/2023/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib > -L/p/software/jurecadc/stages/2023/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib64 > -L/p/software/jurecadc/stages/2023/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib > -L/p/software/jurecadc/stages/2023/software/GCCcore/11.3.0/lib64 > -L/p/software/jurecadc/stages/2023/software/GCCcore/11.3.0/lib -lflexiblas > -lgfortran -lnetcdf -lnetcdff -lnetcdf -lnetcdf -lpioc > > /p/software/jurecadc/stages/2023/software/binutils/2.38-GCCcore-11.3.0/bin/ld: > /p/software/jurecadc/stages/2023/software/netCDF/4.9.0-gompi-2022a/lib64/libnetcdf.so: > undefined reference to symbol 'ncmpi_inq_dim' > > /p/software/jurecadc/stages/2023/software/binutils/2.38-GCCcore-11.3.0/bin/ld: > /p/software/jurecadc/stages/2023/software/PnetCDF/1.12.3-gompi-2022a/lib64/libpnetcdf.so.4: > error adding symbols: DSO missing from command line > > collect2: error: ld returned 1 exit status > > > Our FOSS should be the same as upstream, except we default to MKL. > > The `ncmpi_inq_dim` is from PnetCDF, which I added to the dependencies. If > I don’t, I get the same undefined reference error anyway. > > Any hints? > > > Dr. Alexandre Strube > [email protected] > Helmholtz AI > Jülich Supercomputing Centre > Forschungszentrum Juelich GmbH > 52425 Jülich, Germany > Phone: +49 2461 61-3866 > > JSC is the coordinator of the > John von Neumann Institute for Computing (NIC) > and member of the > Gauss Centre for Supercomputing (GCS) > >
