Run a simulation¶
Note
Another useful resource for instructions on running HEMCO is our YouTube tutorial.
Run interactively¶
First, navigate to your run directory (if you aren’t already there):
$ cd /path/to/hemco/run/dir
You can run HEMCO standalone interactively at the command line by typing:
$ ./hemco_standalone -c HEMCO_sa_Config.rc
where -c
specifies the path to the
HEMCO_sa_Config.rc
configuraiton file.
Run as batch job¶
Batch job run scripts will vary based on what job scheduler you have
available. The example run script included in HEMCO standalone run
directories (runHEMCO.sh
) is for use with SLURM. You may
modify this file for your system and preferences as needed.
At the top of all batch job scripts are configurable run settings. Most critically are requested # cores, # nodes, time, and memory. Figuring out the optimal values for your run can take some trial and error.
To submit a batch job using SLURM:
$ sbatch runHEMCO.sh
Standard output will be sent to a log file HEMCO_SA.log
once
the job is started. Standard error will be sent to a file specific to
your scheduler, e.g. slurm-jobid.out
if using SLURM, unless
you configure your run script to do otherwise.
If your computational cluster uses a different job scheduler, e.g. Grid Engine, LSF, or PBS, check with your IT staff or search the internet for how to configure and submit batch jobs. For each job scheduler, batch job configurable settings and acceptable formats are available on the internet and are often accessible from the command line. For example, type man sbatch to scroll through options for SLURM, including various ways of specifying number of cores, time and memory requested.
Verify a successful run¶
There are several ways to verify that your run was successful.
NetCDF files are present in the
OutputDir/
subdirectory;The HEMCO log file
HEMCO.log
ends withHEMCO X.Y.Z FINISHED.
;Standard output file
HEMCO_SA.log
ends withHEMCO_STANDALONE FINISHED!
;The job scheduler log does not contain any error messages
If it looks like something went wrong, scan through the log files to determine where there may have been an error. Here are a few debugging tips:
Review all of your configuration files to ensure you have proper setup
Check to make sure you have downloaded all input files needed for your HEMCO standalone simulation.
If you cannot figure out where the problem is please do not hesitate to create a GitHub issue.