GEOS-5

Ganymed 1.0 Quick Start: Difference between revisions

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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 Ganymed-1_0 -d Ganymed-1_0 Ganymed
  cvs co -r Ganymed-1_0_p7 -d Ganymed-1_0_p7 Ganymed




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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.
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, cd to <code>Ganymed-1_0/src/Applications/GEOSgcm_App</code> and run:


  gcm_setup
  ./gcm_setup


The <code>gcm_setup</code> script asks you to provide an experiment name :
The <code>gcm_setup</code> script asks you to provide an experiment name :
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  Enter the Dynamical Core to use:  FV (Lat-Lon), FV3 (Cubed-Sphere)
  Enter the Dynamical Core to use:  FV (Lat-Lon), FV3 (Cubed-Sphere)


Enter <code>FV</code> for lat-lon.  On the next six questions, hit enter to accept the default:
Enter <code>FV</code> for lat-lon.  On the next seven questions, hit enter to accept the default:
   
   
  Do you wish to run the COUPLED Ocean/Sea-Ice Model? (Default: NO or FALSE)
  Do you wish to run the COUPLED Ocean/Sea-Ice Model? (Default: NO or FALSE)
Enter the Data_Ocean Horizontal Resolution code: o1 (1  -deg,  360x180, (e.g. Reynolds) Default)
                                                o8 (1/8-deg, 2880x1440, (e.g. OSTIA))


  Do you wish to run GOCART? (Default: NO or FALSE)
  Do you wish to run GOCART? (Default: NO or FALSE)
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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:
The script produces an experiment directory (''EXPDIR'') in your space as <code>/discover/nobackup/''USERID''/''EXPID''</code>, which contains the files and sub-directories:
 
*<code>AGCM.rc</code> -- resource file with specifications of boundary conditions, initial conditions, parameters, etc.
*<code>archive/</code> -- contains job script for archiving output
*<code>CAP.rc</code> -- resource file with run job parameters
*<code>ExtData.rc</code> -- sample resource file for external data, not used
*<code>forecasts/</code> -- contains scripts used for data assimilation mode
*<code>gcm_run.j</code> -- run script
*<code>GEOSgcm.x</code> -- model executable
*<code>HISTORY.rc</code> -- resource file specifying the fields in the model that are output as data
*<code>plot/</code> -- contains plotting job script template and .rc file
*<code>post/</code> -- contains the script template and .rc file for post-processing model output
*<code>RC/</code> -- contains resource files for various components of the model
*<code>regress/</code> -- contains scripts for doing regression testing of model


*<code>post</code>  (containing the script template and .rc file for post processing model output)
*<code>archive</code>  (containing an archiving job script template)
*<code>plot</code>  (containing plotting job script template and .rc file)


The post-processing script will generate 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.  (You can also specify the experiment home directory to be the same as the experiment directory.)
The post-processing script will generate 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.  (You can also specify the experiment home directory to be the same as the experiment directory.)


== Running GEOS-5 ==


The run scripts need some environment variables set in <code>~/.cshrc</code> (regardless of which login shell you use -- the GEOS-5 scripts use <code>csh</code>).  Here are the minimum contents of a <code>.cshrc</code>:
Before running the model, there is some more setup to be completed.  The run scripts need some environment variables set in <code>~/.cshrc</code> (regardless of which login shell you use -- the GEOS-5 scripts use <code>csh</code>).  Here are the minimum contents of a <code>.cshrc</code>:


  umask 022
  umask 022
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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.
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.


== Running GEOS-5 ==
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: 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.
 
 
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 often 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 date and resolution.
 


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.  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.
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.
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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== Output and Plots ==
== 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 15 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
During a normal run, the <code>gcm_run.j</code> script will run the model for the segment length (current default is 15 days in model time).  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''/geosgcm_*</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>).
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''/geosgcm_*</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>).


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