GEOS-5 Quick Start

The following assumes that your shell is csh. Actually, the job scripts tend to assume the same thing, so I wouldn't bother trying to import too much into bash or whatever. I like bash, so I generally open a csh shell for compiling.

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 model from CVS, 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: GEOSgcm.x

Setting up to run:

1) From the .../src/Applications/GEOSgcm_App directory, we run: gcm_setup

    Note: these scripts change very often, to correct bugs and to make

updates for new platforms, etc.

     It is often advantageous to update these files to the HEAD of the

repository to get the latest versions:

     cvs upd -A gcm_*

2) After answering a few questions, the gcm_setup script produces an experiment directory

   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)

    Note:  The post-processing script will complete (i.e., add

necessary commands to) the archiving and plotting scripts as it runs.

3) You will need some more environment variables for running -- here are the contents of my .cshrc:

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

.g5_modules is simply a copy of g5_modules that you ran earlier. Larry has something more clever in his .cshrc .

3a) Copy the *rst and cap_restart files into the experiment directory EXPDIR, by default under /discovery/nobackup/USERNAME . Keep the "originals" handy since if the model crashes early in the run it might have renamed them and put them in the EXPDIR/restarts/ directory.

4) For the moment, you will have to change RC/Chem_Registry.rc so that everything under "Active Constituents" besides doing_PC is "no".

5) The script you submit, gcm_run.j, is in HOMEDIR, by default under your home directory under geos5. 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 batch parameters at the beginning are all that you will usually want to change.

6) 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.

7) During a normal run, the gcm_run script will run the model for a user-specified segment length (current default is 8 days). After each segment, the script spawns a post-processing batch job which partitions and moves the 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. The post-processing script then spawns a new batch job which will archive the data onto the mass-storage drives.

The post-processing script can be found in: .../src/GMAO_Shared/GEOS_Util/post/gcmpost.script

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.