Or run the script from the command line

If your computer system does not use a scheduler, or if you are logged into an Amazon Web Services (AWS) cloud instance, then you can run GEOS-Chem Classic directly from the terminal command line.

Here is a sample run script for interactive use. It is similar to the run script shown previously, with a few edits:

#!/bin/bash

###############################################################################
### Sample GEOS-Chem run script for interactive use
###############################################################################

# Set the proper # of threads for OpenMP
export OMP_NUM_THREADS=8

# Max out stack memory available to GEOS-Chem
ulimit -s unlimited
export OMP_STACKSIZE=500m

# Run GEOS-Chem.  The "time" command will return CPU and wall times.
# Stdout and stderr will be directed to the "GC.log" log file
# (you can change the log file name below if you wish)
time -p ./gcclassic > GC.log 2>&1

# Exit normally
exit 0

The modifications entail:

  1. Removing the SLURM-specific commands (i.e. #SBATCH, $SLURM_CPUS__PER_TASK, and srun).

  2. Manually specifying the number of cores that you wish GEOS-Chem to use (export $OMP_NUM_THREADS=8).

    Note

    If you are logged into an AWS cloud instance, you can add

    export OMP_NUM_THREADS=`ncpus`

    to the run script. This will automatically set OMP_NUM_THREADS to the available number of cores.

To run GEOS-Chem interactively, type:

$ ./geoschem.run > GC.log 2>&1 &

This will run the job in the background. To monitor the progress of the job you can type:

$ tail -f GC.log

which will show the contents of the log file as they are being written.

Another way to view output from GEOS-Chem in real time is to use the tee command . This will print output to the screen and also send the same output to a log file. Type:

$ ./geoschem.run | tee GC.log