GEOS-5 Quick Start

This section describes the minimum steps required to build and run GEOS-5 on discover. You should successfully complete the steps in these instructions before doing anything more complicated.

Checking Out and Compiling GEOS-5

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.

Set the following three environment variables:

setenv CVS_RSH ssh
setenv CVSROOT :ext:USERID@c-sourcemotel.gsfc.nasa.gov:/cvsroot/esma
setenv BASEDIR /discover/nobackup/projects/gmao/share/dao_ops/Baselibs/v3.1.5_build1

where USERID is, of course, your NCCS user-ID. Then, issue the command:

cvs co -r  Fortuna-1_4  Fortuna

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

source g5_modules

If you then type

module list

you should see:

Currently Loaded Modulefiles:
  1) comp/intel-9.1.052   2) lib/mkl-9.1.023      3) mpi/impi-3.2.011

If this all worked, then type:

gmake install

This will build the model. It will take about 40 minutes. If this works, it should create a directory under GEOSagcm called Linux/bin. In here you should find the executable: GEOSgcm.x .

Running GEOS-5

Setting up to run:

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

gcm_setup

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 144 91.

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:

post (containing the post-processing job script)
archive (containing an incomplete archiving job script)
plot (containing an incomplete plotting job script)

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:

umask 022
unlimit
limit stacksize unlimited
source ~/.g5_modules
set arch = `uname`
setenv LD_LIBRARY_PATH ${LIBRARY_PATH}:${BASEDIR}/${arch}/lib

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.

Output and Plots

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).

If a monthly average file was made, the post-processing script will also check to see if it should spawn a plot job. Currently, our criteria for plotting is: 1) if the month created was February or August, AND 2) there are at least 3 monthly average files, then a plotting job for the seasons DJF or JJA will be issued. The plots are created as gifs in EXPDIR/plots.

The post-processing script can be found in: 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.