GEOS-5 Quick Start: Difference between revisions

The following assumes that you know your way around Unix, have successfully logged into your NCCS account (presumably on the '''discover''' cluster) and have an account on '''sourcemotel'''.  The commands below assume that your shell is ''csh''.  Since the scripts to build and run GEOS-5  tend to be written in the same, you shouldn't bother trying to import too much into an alternative shell.  If you prefer a different shell, it is easiest just to open a ''csh'' process to build the model and your experiment.

This should check out the latest stable version of the model from '''sourcemotel''' and create a directory called <code>GEOSagcm</code>.  ''cd'' into ''GEOSagcm/src'' and ''source'' the file called ''g5_modules'':

From the  ''GEOSagcm/src/Applications/GEOSgcm_App'' directory, we run:

The ''gcm_setup'' script asks you a few questions such as an experiment name (with no spaces, called EXPID) and description (spaces ok).  It will also ask you for the model resolution, expecting the lat-lon domain size, the dimensions separated by a space.  For you first time out you will probably want to enter <code>144 91</code>.

The rest of the questions provide defaults which will be suitable for now, so just press enter for these.  The script produces an experiment directory (EXPDIR) in your space as ''/discover/nobackup/USERID/EXPID'', which contains, among other things, the sub-directories:

The post-processing script will complete (i.e., add necessary commands to) the archiving and plotting scripts as it runs.  The setup script that you ran also creates an experiment home directory (HOMEDIR) as ''~USERID/geos5/EXPID'' containing the run scripts and GEOS resource (''.rc'') files.

The run scripts need some more environment variables -- here are the minimum contents of a ''.cshrc'':

where ''.g5_modules'' is simply a copy of the ''g5_modules'' that you ran earlier before compiling.   

Copy the restart (initial condition) and ''cap_restart'' (t=t0) files into EXPDIR.  Keep the "originals" handy since if the model crashes early in the run it might have renamed them.  The model expects restarts to end in "rst" but produces them with the date at time appended to the filename, so you may have to rename them.  The ''cap_restart'' file is simply one line of text with the format "YYYYMMDD HHMMSS".  The boundary conditions/forcings are provided by symbolic links created by the run script.

The script you submit, ''gcm_run.j'', is in HOMEDIR.  It should be ready to go as is, though you may eventually want to tune JOB_SGMT (the number of days between saving restarts, called segments) and NUM_SGMT (the number of segments attempted in a job) to maximize your run time.  END_DATE can be changed to your end date, or just left as is.  Commenting out the ''qsub gcm_run.j'' at the end of the script will stop it, too.  Those and the PBS (batch system) parameters at the beginning are all that you will usually want to change in the script.

Submit the job with ''qsub gcm_run.j''.  You can keep track of it with qstat or ''qstat | grep USERNAME'', or stdout with ''tail -f /discovery/pbs_spool/JOBID.OU'', JOBID being returned by qsub and displayed with qstat.  Jobs can be killed with ''qdel JOBID''.  The stdout and stderr will be delivered as files to HOMEDIR at the end of a job.

During a normal run, the ''gcm_run.j'' script will run the model for the segment length (current default is 8 days).  The model creates output files (with an ''nc4'' extension), also called collections (of output variables), in the ''EXPDIR/scratch'' directory.  After each segment, the script moves the output to the ''EXPDIR/holding'' and spawns a post-processing batch job which partitions and moves the output files  within the ''holding'' directory to their own distinct collection directory, which is again partitioned into the appropriate year and month.  The  post processing script then checks to

see if  a full month of data is present.  If not, the post-processing job ends.  If there is a full month, the script will then run the time-averaging executable to produce a monthly mean file in ''EXPDIR/geos_gcm_*''.  The post-processing script then spawns a new batch job which will archive the data onto the mass-storage drives (''/archive/u/USERID/GEOS5.0/EXPID'').

the seasons DJF or JJA will be issued.  The plots are created as gifs in ''EXPDIR/plots''.

''GEOSagcm/src/GMAO_Shared/GEOS_Util/post/gcmpost.script''.  The ''nc4'' output files can be opened and plotted with ''gradsnc4'' -- see http://www.iges.org/grads/gadoc/tutorial.html for a tutorial, but use ''sdfopen'' instead of ''open''.