View source for Fortuna 2.1 Quick Start

This page describes the minimum steps required to build and run GEOS-5 Fortuna 2.1 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 the source code repository with the proper <code>ssh</code> configuration -- see the progress repository quick  start: https://progress.nccs.nasa.gov/trac/admin/wiki/CVSACL.  

The commands below assume that your shell is <code>csh</code>.  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 <code>csh</code> process to build the model and your experiment.

Furthermore, model builds should be created in your space under <code>/discover/nobackup</code>, 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_1_p2 Fortuna

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

 source g5_modules

If you then type 

 module list 

you should see:

 Currently Loaded Modulefiles:
  1) comp/intel-11.0.083                       2) other/mpi/mvapich2-1.4.1/intel-11.0.083

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 <code>GEOSagcm</code> called <code>Linux/bin</code>.  In here you should find the executable: <code>GEOSgcm.x</code> .

== Running GEOS-5 ==

First of all, to run jobs on the cluster you will need to set up passwordless <code>ssh</code> (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 <code>~/.ssh</code> on '''discover''', run 

  ssh-keygen -t dsa

Then, log into  '''palm''' and cut and paste the contents of the <code>id_rsa.pub</code> and <code>id_dsa.pub</code> files on '''discover''' into the  <code>~/.ssh/authorized_keys</code> file on   '''palm'''.  Problems with <code>ssh</code> should be referred to NCCS support.

To set the model up to run, in the  <code>GEOSagcm/src/Applications/GEOSgcm_App</code> directory we run:

 gcm_setup

The <code>gcm_setup</code> 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 <code>144 91</code> (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 <code>/discover/nobackup/''USERID''/''EXPID''</code>, which contains, among other things, the sub-directories:

*<code>post</code>  (containing the post-processing job script)
*<code>archive</code>  (containing an incomplete archiving job script)
*<code>plot</code>  (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 <code>~''USERID''/geos5/''EXPID''</code>  containing the run scripts and GEOS resource (<code>.rc</code>) files.


The run scripts need some more environment variables -- here are the minimum contents of a <code>.cshrc</code>:

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

where <code>.g5_modules</code> is simply a copy of the <code>g5_modules</code> that you ran earlier before compiling.  The <code>umask 022</code> 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 <code>~''USERID''</code> is also inaccessible to others by default; running <code>chmod 755 ~</code> is helpful.

Copy the restart (initial condition) files and associated <code>cap_restart</code> 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 <code>cap_restart</code> 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 <code>/discover/nobackup/aeichman/test2_1</code>.


The script you submit, <code>gcm_run.j</code>, is in ''HOMEDIR''.  It should be ready to go as is.  The parameter END_DATE in <code>CAP.rc</code> (previously in <code>gcm_run.j</code>) can be set to the date you want the run to stop -- this works in Fortuna 2.1 where it did not in Fortuna 2.0.  Also in Fortuna 2.1, you may edit the <code>.rc</code> files directly instead of template  (<code>.tmpl</code>).   An alternative way to stop the run is by commenting out the line <code> if ( $capdate < $enddate ) qsub $HOMDIR/gcm_run.j</code> at the end of the script, which will prevent the script from being resubmitted, or rename the script file.  You may eventually want to tune parameters in the <code>CAP.rc</code> file JOB_SGMT (the number of days per segment, the interval between saving restarts) and NUM_SGMT (the number of segments attempted in a job) to maximize your run time.  

Submit the job with <code>qsub gcm_run.j</code>.  You can keep track of it with <code>qstat</code> or <code>qstat | grep ''USERID''</code>, or stdout with <code>tail -f /discover/pbs_spool/''JOBID''.OU</code>, ''JOBID'' being returned by <code>qsub</code> and displayed with <code>qstat</code>.  Jobs can be killed with <code>qdel ''JOBID''</code>.  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 <code>gcm_run.j</code> script will run the model for the segment length (current default is 8 days).  The model creates output files (with an <code>nc4</code> extension), also called collections (of output variables), in  <code>''EXPDIR''/scratch</code> directory.  After each segment, the script moves the output to the <code>''EXPDIR''/holding</code> and spawns a post-processing batch job which partitions and moves the output files  within the <code>holding</code> 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 <code>''EXPDIR''/geos_gcm_*</code>.  The post-processing script then spawns a new batch job which will archive the data onto the mass-storage drives (<code>/archive/u/''USERID''/GEOS5.0/''EXPID''</code>).

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 <code>''EXPDIR''/plots</code>.

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

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