GEOS-5 Quick Start

This page describes the minimum steps required to build and run GEOS-5 Fortuna 2.0 on discover. You should successfully complete the steps in these instructions before doing anything more complicated. FORTUNA 2.0 IS NOW DEPRECATED AND MINIMALLY SUPPORTED, AS IS THIS DOCUMENTATION. PLEASE SEE THE DOCUMENTATION FOR THE LATEST VERSION.

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 the source code repository with the proper ssh configuration -- see the progress repository quick start: https://progress.nccs.nasa.gov/trac/admin/wiki/CVSACL.

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.

Furthermore, model builds should be created in your space under /discover/nobackup, as creating them under your home directory will quickly wipe out your disk quota.

Set the following three environment variables:

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

where USERID is, of course, your repository username, which should be the same as your NASA and NCCS username. Then, issue the command:

cvs co -r  Fortuna-2_0  Fortuna

This should check out the latest stable version of the model from the repository 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

First of all, to run jobs on the cluster you will need to set up passwordless ssh (which operates within the cluster). To do so, run the following from your discover home directory:

cd .ssh
ssh-keygen -t dsa
cat id_dsa.pub >>  authorized_keys

Similarly, transferring the daily output files (in monthly tarballs) requires passwordless authentication from discover to palm. While in ~/.ssh on discover, run

 ssh-keygen -t dsa

Then, log into palm and cut and paste the contents of the id_rsa.pub and id_dsa.pub files on discover into the ~/.ssh/authorized_keys file on palm.

To set the model up to run, in 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 one of the available lat-lon domain sizes, the dimensions separated by a space. For your first time out you will probably want to enter 144 91 (corresponding to ~2 degree resolution). Towards the end it will ask you for a group ID -- the default is g0602 (GMAO modeling group). Enter whatever is appropriate, as necessary. 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. The umask 022 is not strictly necessary, but it will make the various files readable to others, which will facilitate data sharing and user support. Your home directory ~USERID is also inaccessible to others by default; running chmod 755 ~ is helpful.

Copy the restart (initial condition) files and associated cap_restart into EXPDIR. Keep the "originals" handy since if the job stumbles early in the run it might stop after having renamed them. The model expects restart filenames to end in "rst" but produces them with the date and time appended, so you may have to rename them. The cap_restart file is simply one line of text with the date of the restart files in the format YYYYMMDD<space>HHMMSS. The boundary conditions/forcings are provided by symbolic links created by the run script. If you need an arbitrary set of restarts, you can copy them from /discover/nobackup/aeichman/restarts/Fortuna-2_0/144x91/20080327_benchmark.

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 per segment, the internal between saving restarts) and NUM_SGMT (the number of segments attempted in a job) to maximize your run time. Leave END_DATE alone in Fortuna 2.0 -- there is a bug that erroneously resubmits the script after this date. You can stop the run by commenting out the qsub $HOMDIR/gcm_run.j at the end of the script, which will prevent the script from being resubmitted. 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 USERID, or stdout with tail -f /discover/pbs_spool/JOBID.OU, JOBID being returned by qsub and displayed with qstat. Jobs can be killed with qdel JOBID. The standard out and standard error will be delivered as files to the working directory at the time you submitted the 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 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 are: 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.

The contents of the output files (including which variables get saved) may be configured in the HOMEDIR/HISTORY/tmpl -- a good description of this file may be found at http://modelingguru.nasa.gov/clearspace/docs/DOC-1190 .