Sample environment file for GNU 12.2.0 compilers

Below is a sample environment file (based on an enviroment file for the Harvard Cannon computer cluster). This file will load software libraries built with the GNU 12.2.0 compilers.

Note

This environment file shown below assumes that required software packages for GEOS-Chem Classic are available as pre-built modules. If your computer system does not have these packages pre-installed, you can build them with Spack. Please see our Build required software with Spack supplemental guide for detailed instructions.

Save the code below (with any appropriate modifications for your own computer system) to a file named ~/gcclassic.gnu12.env.

###############################################################################
#
# Environment file for GCClassic + GNU Compiler Collection 12.2.0
#
###############################################################################

# Display message (if we are in a terminal window)
if [[ $- = *i* ]] ; then
  echo "Loading modules for GEOS-Chem Classic, please wait ..."
fi

#==============================================================================
# Unload all previously-unloaded software
#==============================================================================

# Unload packages loaded with "module load"
module purge

#==============================================================================
# Load software packages for GNU 12.2.0
#==============================================================================
if [[ $- = *i* ]] ; then
  echo "... Loading FASRC-built software, please wait ..."
fi

# Pre-built modules needed for GEOS-Chem
# (NOTE: These may be named differently on your system)
module load gcc/12.2.0-fasrc01             # gcc / g++ / gfortran
module load openmpi/4.1.4-fasrc01          # MPI
module load netcdf-c/4.9.2-fasrc01         # netcdf-c
module load netcdf-fortran/4.6.0-fasrc02   # netcdf-fortran
module load flex/2.6.4-fasrc01             # Flex lexer (needed for KPP)
module load cmake/3.25.2-fasrc01           # CMake (needed to compile)

#==============================================================================
# Environment variables and related settings
# (NOTE: Lmod will define <module>_HOME variables for each loaded module)
#==============================================================================

# Make all files world-readable by default
umask 022

# Set number of threads for OpenMP.  If running in a SLURM environment,
# use the number of requested cores.  Otherwise use 8 cores for OpenMP.
if [[ "x${SLURM_CPUS_PER_TASK}" == "x" ]]; then
    export OMP_NUM_THREADS=8
else
    export OMP_NUM_THREADS="${SLURM_CPUS_PER_TASK}"
fi

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

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

# netCDF
if [[ "x${NETCDF_HOME}" == "x" ]]; then
    export NETCDF_HOME="${NETCDF_C_HOME}"
fi
export NETCDF_C_ROOT="${NETCDF_HOME}"
export NETCDF_FORTRAN_ROOT=${NETCDF_FORTRAN_HOME}

# KPP 3.0.0+
export KPP_FLEX_LIB_DIR=${FLEX_HOME}/lib64

#==============================================================================
# Set limits
#==============================================================================

ulimit -c unlimited   # coredumpsize
ulimit -u 50000       # maxproc
ulimit -v unlimited   # vmemoryuse
ulimit -s unlimited   # stacksize

#==============================================================================
# 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]}"

To activate the settings contained in the environment file, type:

$ . ~/gcclassic.gnu12.env

You may also place the above command within your GEOS-Chem run script, which will be discussed in a subsequent chapter.