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Compilation fails because libnetcdf.so has undefined references to HDF5 related symbols.

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I

irowe1

New member
Hello,

I am working on installing WRF 4.2 on a Linux HPC. I am having trouble compiling because during the portion where diffwrf io_netcdf is being built, something is not linked correctly and I get the following error:
Code: 
/project/ssmith_uksr/WRF_ARW/netcdf/lib/libnetcdf.so: undefined reference to `H5Pset_dxpl_mpio'
/project/ssmith_uksr/WRF_ARW/netcdf/lib/libnetcdf.so: undefined reference to `H5Pset_fapl_mpio'
/project/ssmith_uksr/WRF_ARW/netcdf/lib/libnetcdf.so: undefined reference to `H5Pset_all_coll_metadata_ops'
/project/ssmith_uksr/WRF_ARW/netcdf/lib/libnetcdf.so: undefined reference to `H5Pset_coll_metadata_write'
make[2]: [diffwrf] Error 1 (ignored)

I have NetCDF 4.6.3 and NetCDF-Fortran 4.4.5 together in one folder pointed to by $NETCDF, and I also have HDF5 1.10.5 and pnetcdf 1.11.1 installed and loaded. I have attached my configure.wrf and my script I wrote to set my environment variables before running.

To narrow things down, I went back to the compilation tutorial here (https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php) and one of the commands triggers the same errors. If I run
Code: 
mpiifort 02_fortran+c+netcdf+mpi_f.o 02_fortran+c+netcdf+mpi_c.o      -L${NETCDF}/lib -lnetcdff -lnetcdf
, I get the same errors as the code box up top. If I load PHDF5 instead of HDF5, this runs just fine.

I have HDF5 installed and pointed to by $HDF5. I tried to change this to point to my PHDF5 install, but when I did that my configure script failed:
Code: 
************************** W A R N I N G ************************************
NETCDF4 IO features are requested, but this installation of NetCDF           
  /project/ssmith_uksr/WRF_ARW/netcdf
DOES NOT support these IO features.                                          

Please make sure NETCDF version is 4.1.3 or later and was built with         
--enable-netcdf4

I would appreciate any assistance in figuring out why this is happening and how to fix it.
 

Attachments

  • configure.wrf
    23.3 KB · Views: 50
  • setenv.txt
    281 bytes · Views: 66
Seems like posting on this forum is a good rubber duck learning process for me. On my system, there were two versions of HDF5 with very similar names. One was compiled with the Intel toolchain (opt/ohpc/pub/libs/intel/hdf5/1.10.5) , and one was built with the intel compiler toolchain and the impi MPI stack (/opt/ohpc/pub/libs/intel/impi/hdf5/1.10.5). I was able to fix this problem by setting my $HDF5 environment variable to to the second one. The path to the PHDF5 directory (/opt/ohpc/pub/moduledeps/intel-impi/phdf5/1.10.5) was a total red herring.
 
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