Fortuna 2.2 Quick Start: Difference between revisions
New page: 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... |
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This page describes the minimum steps required to build and run GEOS-5 Fortuna 2. | This page describes the minimum steps required to build and run GEOS-5 Fortuna 2.2 on discover. You should successfully complete the steps in these instructions before doing anything more complicated. | ||
== Checking Out and Compiling GEOS-5 == | == Checking Out and Compiling GEOS-5 == | ||
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where ''USERID'' is, of course, your repository username, which should be the same as your NASA and NCCS username. Then, issue the command: | 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- | cvs co -r Fortuna-2_2_p1 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>: | 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>: | ||
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Currently Loaded Modulefiles: | Currently Loaded Modulefiles: | ||
1) comp/intel-11.0.083 | 1) comp/intel-11.0.083 2) mpi/impi-3.2.2.006 | ||
If this all worked, then type: | If this all worked, then type: | ||
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cat id_dsa.pub >> authorized_keys | cat id_dsa.pub >> authorized_keys | ||
Similarly, transferring the daily output files (in monthly tarballs) requires passwordless authentication from '''discover''' to ''' | Similarly, transferring the daily output files (in monthly tarballs) requires passwordless authentication from '''discover''' to '''dirac'''. While in <code>~/.ssh</code> on '''discover''', run | ||
ssh-keygen -t dsa | ssh-keygen -t dsa | ||
Then, log into ''' | Then, log into '''dirac''' 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 '''dirac'''. 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: | To set the model up to run, in the <code>GEOSagcm/src/Applications/GEOSgcm_App</code> directory we run: | ||
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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. | 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 2.2 where it did not in Fortuna 2.0. Also in Fortuna 2.2, 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. | 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. | ||
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<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>. | <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 | The contents of the output files (including which variables get saved) may be configured in the <code>''HOMEDIR''/HISTORY.rc</code> -- a good description of this file may be found at http://modelingguru.nasa.gov/clearspace/docs/DOC-1190 . | ||