Ganymed 1.0 Quick Start: Difference between revisions

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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 back to ending in "rst". The <code>cap_restart</code> file is sometimes provided with a set of restarts, but if not you can create it: is simply one line of text with the date of the restart files in the format ''<code>YYYYMMDD HHMMSS</code>'' (with a space). 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>/archive/u/aeichman/restarts/Ganymed-1_0/</code>, where they are indexed by resolution and date. If you are unfamiliar with the way that the <code>/archive</code> filesystem works, keep in mind that a <code>cp</code> from there might appear to stall while the tape is loaded -- see the NCCS documentation for details.

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> can be set to the date you want the run to stop. 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, or kill the job (described below). 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.

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> can be set to the date you want the run to stop. 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, or kill the job (described below).

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 follow 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.

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 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 back to ending in "rst".   The <code>cap_restart</code> file is sometimes provided with a set of restarts, but if not you can create it: is simply one line of text with the date of the restart files in the format ''<code>YYYYMMDD HHMMSS</code>'' (with a space).  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>/archive/u/aeichman/restarts/Ganymed-1_0/</code>, where they are indexed by resolution and date.  If you are unfamiliar with the way that the <code>/archive</code> filesystem works, keep in mind that a <code>cp</code> from there might appear to stall while the tape is loaded -- see the NCCS documentation for details.
-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> can be set to the date you want the run to stop.   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, or kill the job (described below).  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.
+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> can be set to the date you want the run to stop.   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, or kill the job (described below).
 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 follow 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.