GEOS-5 Quick Start: Difference between revisions

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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>.

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).

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:

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The script you submit, <code>gcm_run.j</code>, 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. END_DATE can be changed to your end date, or just left as is. Commenting out the <code>qsub gcm_run.j</code> 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 <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 /discovery/pbs_spool/''JOBID''.OU</code>, ''JOBID'' being returned by qsub and displayed with qstat. Jobs can be killed with <code>qdel ''JOBID''</code>. The standard out and standard error will be delivered as files to ''HOMEDIR'' at the end of a job.

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 /discovery/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 ''HOMEDIR'' at the end of a job.

== Output and Plots ==

@@ Line 42: / Line 42: @@
   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>.
+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).
 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:
@@ Line 68: / Line 68: @@
 The script you submit, <code>gcm_run.j</code>, 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.  END_DATE can be changed to your end date, or just left as is.  Commenting out the <code>qsub gcm_run.j</code> 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 <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 /discovery/pbs_spool/''JOBID''.OU</code>, ''JOBID'' being returned by qsub and displayed with qstat.  Jobs can be killed with <code>qdel ''JOBID''</code>.  The standard out and standard error will be delivered as files to ''HOMEDIR'' at the end of a job.
+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 /discovery/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 ''HOMEDIR'' at the end of a job.
 == Output and Plots ==