See https://earthsystemmodeling.org/docs/release/ESMF_5_2_0p1/ESMF_usrdoc/node9.html#sec:pnetcdf
On Fri, 31 Mar 2023 at 17:18, Alan O'Cais <[email protected]> wrote: > Looking at the easyconfig, you probably need to add some extra args: > https://github.com/easybuilders/easybuild-easyconfigs/blob/develop/easybuild/easyconfigs/e/ESMF/ESMF-8.3.0-foss-2022a.eb#L31-L32 > > On Fri, 31 Mar 2023 at 17:17, Alan O'Cais <[email protected]> wrote: > >> 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) >>> >>>
