Difference between revisions of "Sample initialization script for GEOS-Chem"
From Geos-chem
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#[[GEOS-Chem_coding_and_debugging|Coding and debugging]] | #[[GEOS-Chem_coding_and_debugging|Coding and debugging]] | ||
#[[GEOS-Chem_overview#Further_reading|Further reading]] | #[[GEOS-Chem_overview#Further_reading|Further reading]] | ||
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== Sample initialization script using Lmod modules == | == Sample initialization script using Lmod modules == | ||
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# %%%%% Load modules for GNU Fortran 7.1 %%%%% | # %%%%% Load modules for GNU Fortran 7.1 %%%%% | ||
# | # | ||
| − | # NOTE: | + | # NOTE: Your module load commands may be different than these. |
| + | # Ask your IT staff for more information. | ||
#============================================================================== | #============================================================================== | ||
echo "Loading modules for compiler gfortran71 ..." | echo "Loading modules for compiler gfortran71 ..." | ||
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fi | fi | ||
| − | + | # GC_LIB | |
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | # GC_LIB | + | |
if [[ "x$NETCDF_LIB" == x ]]; then | if [[ "x$NETCDF_LIB" == x ]]; then | ||
export GC_LIB="$NETCDF_HOME/lib" | export GC_LIB="$NETCDF_HOME/lib" | ||
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fi | fi | ||
| − | # GC_INCLUDE | + | # GC_INCLUDE |
if [[ "x$NETCDF_INCLUDE" == x ]]; then | if [[ "x$NETCDF_INCLUDE" == x ]]; then | ||
export GC_INCLUDE="$NETCDF_HOME/include" | export GC_INCLUDE="$NETCDF_HOME/include" | ||
| Line 136: | Line 130: | ||
fi | fi | ||
| − | # GC_BIN | + | # GC_BIN |
export GC_BIN="$NETCDF_HOME/bin" | export GC_BIN="$NETCDF_HOME/bin" | ||
Revision as of 21:46, 19 December 2019
Previous | Next | Getting Started with GEOS-Chem
- Minimum system requirements
- Configuring your computational environment
- Specifying compilers for GEOS-Chem
- Specifying software libraries for GEOS-Chem
- Specifying parallelization settings
- A sample initialization script
- Downloading source code
- Downloading data directories
- Creating run directories
- Configuring runs
- Compiling
- Running
- Output files
- Visualizing and processing output
- Coding and debugging
- Further reading
Sample initialization script using Lmod modules
This sample initialization script is based on an actual script used on the Harvard Cannon cluster. The script uses the Lmod module system to load the GNU Fortran compiler version 7.1 (which is part of the GNU Compiler Collection, or GCC). The script is named init.gc-classic.gfortran71.centos7 and can be invoked with:
source init.gc-classic.gfortran.centos7
The module load commands may be different on your system.
#==============================================================================
# %%%%% Clear existing environment variables %%%%%
#==============================================================================
unset PERL_HOME
unset IDL_HOME
unset EMACS_HOME
unset CC
unset CXX
unset FC
unset F77
unset F90
unset NETCDF_BIN
unset NETCDF_HOME
unset NETCDF_INCLUDE
unset NETCDF_LIB
unset NETCDF_FORTRAN_BIN
unset NETCDF_FORTRAN_HOME
unset NETCDF_FORTRAN_INCLUDE
unset NETCDF_FORTRAN_LIB
unset GC_BIN
unset GC_INCLUDE
unset GC_LIB
unset GC_F_BIN
unset GC_F_INCLUDE
unset GC_F_LIB
unset OMP_NUM_THREADS
unset OMP_STACKSIZE
#==============================================================================
# %%%%% Load modules for GNU Fortran 7.1 %%%%%
#
# NOTE: Your module load commands may be different than these.
# Ask your IT staff for more information.
#==============================================================================
echo "Loading modules for compiler gfortran71 ..."
module purge
module load git/2.17.0-fasrc01
module load perl/5.26.1-fasrc01
module load IDL/8.4.1-fasrc01
module load flex/2.6.4-fasrc01
module load gcc/7.1.0-fasrc01
module load openmpi/2.1.0-fasrc02
module load netcdf/4.3.2-fasrc05
module load netcdf-fortran/4.4.0-fasrc03
module load cdo/1.9.4-fasrc02
module load nco/4.7.4-fasrc01
module load ncview/2.1.7-fasrc02
module load emacs/26.1-fasrc01
module load cmake/3.12.1-fasrc01
module list
# Define F90 and F77 environment variables (may be needed by some software)
export F90=$FC
export F77=$FC
#==============================================================================
# %%%%% Settings for OpenMP parallelization %%%%%
#==============================================================================
# Max out the stack memory for OpenMP
# Asking for a huge number will just give you the max availble
export OMP_STACKSIZE=500m
# By default, set the number of threads for OpenMP parallelization to 1
export OMP_NUM_THREADS=1
# Redefine number threads for OpenMP parallelization
# (a) If in a SLURM partition, set OMP_NUM_THREADS = SLURM_CPUS_PER_TASK
# (b) Or, set OMP_NUM_THREADS to the optional first argument that is passed
if [[ -n "${SLURM_CPUS_PER_TASK+1}" ]]; then
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
elif [[ "$#" -eq 1 ]]; then
if [[ "x$1" != "xignoreeof" ]]; then
export OMP_NUM_THREADS=$1
fi
fi
echo "Number of OpenMP threads: $OMP_NUM_THREADS"
#==============================================================================
# %%%%% Define relevant environment variables %%%%%
#==============================================================================
# Machine architecture
export ARCH=`uname -s`
# NETCDF_HOME
if [[ "x$NETCDF_HOME" == x ]]; then
export NETCDF_HOME=`nc-config --prefix`
fi
# GC_LIB
if [[ "x$NETCDF_LIB" == x ]]; then
export GC_LIB="$NETCDF_HOME/lib"
else
export GC_LIB="$NETCDF_LIB"
fi
# GC_INCLUDE
if [[ "x$NETCDF_INCLUDE" == x ]]; then
export GC_INCLUDE="$NETCDF_HOME/include"
else
export GC_INCLUDE="$NETCDF_INCLUDE"
fi
# GC_BIN
export GC_BIN="$NETCDF_HOME/bin"
# If the netCDF-Fortran library is loaded separately
# then also define the GC_F_* environment variables (deprecated)
if [[ "x$NETCDF_FORTRAN_HOME" != x ]]; then
export NETCDF_FORTRAN_BIN="$NETCDF_FORTRAN_HOME/bin"
export GC_F_BIN="$NETCDF_FORTRAN_HOME/bin"
export GC_F_INCLUDE="$NETCDF_FORTRAN_INCLUDE"
export GC_F_LIB="$NETCDF_FORTRAN_LIB"
fi
