GNU Fortran module error

[Ajmal-1301]

Your name

Ajmal

Your affiliation

North Carolina State University

Please provide a clear and concise description of your question or discussion topic.

Hi,
I was following the GEOS-Chem tutorial and was compiling the code, and I got the following error,

File ‘/usr/local/pgi/linux86-64/2018/netcdf/netcdf-4.5.0/openmpi-2.1.2/include/netcdf.mod’ opened at (1) is not a GNU Fortran module file

the code is not going to the correct location where I loaded my netcdf module, which is at (/usr/local/apps/netcdf/4.9.2-openmpi5.0.3/)

I think the traced the issue to the HEMCOBuildproperties.txt file which is providing the location and not the location where I loaded the module
HEMCOBuildProperties.txt

Thanks

[yantosca]

Thanks for writing @Ajmal-1301. I think the issue is that yuou are using a netCDF library that is built with the PGI compiler, which is not supported by GEOS-Chem.

File ‘/usr/local/pgi/linux86-64/2018/netcdf/netcdf-4.5.0/openmpi-2.1.2/include/netcdf.mod’ opened at (1) is not a GNU Fortran module file

You need to build GEOS-Chem with the same version of the compiler that your netCDF and OpenMPI libraries have been built with. Otherwise it will result in an error similar to that above.

[Ajmal-1301]

Hi @yantosca
Thank you for replying, I am not sure I follow but this is the environment file I loaded before building

###############################################################################`
# Environment file for GCClassic + GNU compilers`
#
###############################################################################`

# Unload all modules first
module purge

# Load modules
module load cmake`
module load openmpi-gcc/openmpi5.0.5-gcc11.4.1
module load netcdf/4.9.2-openmpi5.0.3

#==============================================================================
# Environment variables and related settings
# (NOTE: We will have to define <module>_HOME variables manually, based on what GEOS-Chem needs)
#==============================================================================

# Set number of threads for OpenMP.

# In our LSF script, we may want to start with just shared memory parallelization, where we use multiple cores on a *single* node
## this would look like this in our LSF script:
### #BSUB -R span[hosts=1]
### export OMP_NUM_THREADS="${LSB_DJOB_NUMPROC}"

# Max out the stacksize memory limit
export OMP_STACKSIZE="500m"

# Compilers
export CC="gcc"
export CXX="g++"
export FC="gfortran"
export F77="${FC}"

# netCDF
export NETCDF_HOME=/usr/local/apps/netcdf/4.9.2-openmpi5.0.3/
export NETCDF_C_ROOT="${NETCDF_HOME}"
export NETCDF_FORTRAN_ROOT="${NETCDF_HOME}"

# MPI
export MPI_HOME=/usr/local/apps/openmpi/5.0.5-gcc11.4.1/

# KPP 3.0.0+
# (not worrying with this for now). export KPP_FLEX_LIB_DIR="${FLEX_HOME}/lib64"


#==============================================================================
# Print information
#==============================================================================

module list

echo ""
echo "Environment:"
echo ""
echo "CC : ${CC}"
echo "CXX : ${CXX}"
echo "FC : ${FC}"
echo "KPP_FLEX_LIB_DIR : ${KPP_FLEX_LIB_DIR}"
echo "MPI_HOME : ${MPI_HOME}"
echo "NETCDF_HOME : ${NETCDF_HOME}"
echo "NETCDF_FORTRAN_HOME : ${NETCDF_FORTRAN_HOME}"
echo "OMP_NUM_THREADS : ${OMP_NUM_THREADS}"
echo ""
echo "Done sourcing ${BASH_SOURCE[0]}"

[yantosca]

Thanks @Ajmal-1301 for the environment file. A couple of thoughts:

1. You haven't explicitly loaded a module for the GNU compilers. Therefore it is probably just defaulting to the version in /usr/bin (the default location for libraries).

2. I still believe that these modules:

module load openmpi-gcc/openmpi5.0.5-gcc11.4.1
module load netcdf/4.9.2-openmpi5.0.3

were built with the PGI compiler instead of with the GNU compiler. You can use the

$ module spider netcdf

and

$ module spider netcdf-fortran

commands to find a version of the netCDF libraries on your system that were built with the GNU compilers.

If you do not have netcdf or netcdf-fortran libraries that were built with GNU compilers, you can build them yourselves following the instructions on ReadTheDocs:

• Build required software with Spack