GEOS-5 Quick Start: Difference between revisions

Line 11:

setenv BASEDIR /discover/nobackup/projects/gmao/share/dao_ops/Baselibs/v3.1.5_build1

where USERID is, of course, your NCCS user-ID. Then, issue the command:

where ''USERID'' is, of course, your NCCS user-ID. Then, issue the command:

cvs co -r Fortuna-1_4 Fortuna

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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 the lat-lon domain size, the dimensions separated by a space. For you first time out you will probably want to enter <code>144 91</code>.

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:

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:

*''post'' (containing the post-processing job script)

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*''plot'' (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 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.

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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 the <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>).

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

@@ Line 11: / Line 11: @@
   setenv BASEDIR /discover/nobackup/projects/gmao/share/dao_ops/Baselibs/v3.1.5_build1
-where USERID is, of course, your NCCS user-ID.  Then, issue the command:
+where ''USERID'' is, of course, your NCCS user-ID.  Then, issue the command:
   cvs co -r  Fortuna-1_4  Fortuna
@@ Line 44: / Line 44: @@
 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 the lat-lon domain size, the dimensions separated by a space.  For you first time out you will probably want to enter <code>144 91</code>.
-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:
+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:
 *''post''  (containing the post-processing job script)
@@ Line 50: / Line 50: @@
 *''plot''  (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 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.
@@ Line 73: / Line 73: @@
 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 the <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>).
+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