GEOS-5 Quick Start: Difference between revisions

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This page describes the minimum steps required to build and run GEOS-5 on discover. You should successfully complete the steps in these instructions before doing anything more complicated.

This page describes the minimum steps required to build and run GEOS-5 Fortuna 2.0 on discover. You should successfully complete the steps in these instructions before doing anything more complicated. '''FORTUNA 2.0 IS NOW DEPRECATED AND MINIMALLY SUPPORTED, AS IS THIS DOCUMENTATION. PLEASE SEE THE DOCUMENTATION FOR THE LATEST VERSION'''.

== Checking Out and Compiling GEOS-5 ==

The following assumes that you know your way around Unix, have successfully logged into your NCCS account (presumably on the '''discover''' cluster) and have an account on ~~'''progress'''~~ with the proper <code>ssh</code> ~~preparation~~ -- see the progress repository quick start: https://progress.nccs.nasa.gov/trac/admin/wiki/~~QuickStart~~.

The following assumes that you know your way around Unix, have successfully logged into your NCCS account (presumably on the '''discover''' cluster) and have an account on the source code repository with the proper <code>ssh</code> configuration -- see the progress repository quick start: https://progress.nccs.nasa.gov/trac/admin/wiki/CVSACL.

The commands below assume that your shell is <code>csh</code>. Since the scripts to build and run GEOS-5 tend to be written in the same, you shouldn't bother trying to import too much into an alternative shell. If you prefer a different shell, it is easiest just to open a <code>csh</code> process to build the model and your experiment.

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setenv CVS_RSH ssh

setenv CVSROOT :ext:''USERID''@~~progress~~.nccs.nasa.gov:/cvsroot/esma

setenv CVSROOT :ext:''USERID''@progressdirect.nccs.nasa.gov:/cvsroot/esma

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

where ''USERID'' is, of course, your ~~'''progress'''~~ 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-2_0 Fortuna

This should check out the latest stable version of the model from ~~'''progress'''~~ 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>:

source g5_modules

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== 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 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

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 <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>).

@@ Line 1: / Line 1: @@
-This page describes the minimum steps required to build and run GEOS-5 on discover.  You should successfully complete the steps in these instructions before doing anything more complicated.
+This page describes the minimum steps required to build and run GEOS-5 Fortuna 2.0 on discover.  You should successfully complete the steps in these instructions before doing anything more complicated.  '''FORTUNA 2.0 IS NOW DEPRECATED AND MINIMALLY SUPPORTED, AS IS THIS DOCUMENTATION.  PLEASE SEE THE DOCUMENTATION FOR THE LATEST VERSION'''.
 == Checking Out and Compiling GEOS-5 ==
-The following assumes that you know your way around Unix, have successfully logged into your NCCS account (presumably on the '''discover''' cluster) and have an account on '''progress''' with the proper <code>ssh</code> preparation -- see the progress repository quick  start: https://progress.nccs.nasa.gov/trac/admin/wiki/QuickStart.
+The following assumes that you know your way around Unix, have successfully logged into your NCCS account (presumably on the '''discover''' cluster) and have an account on the source code repository with the proper <code>ssh</code> configuration -- see the progress repository quick  start: https://progress.nccs.nasa.gov/trac/admin/wiki/CVSACL.
 The commands below assume that your shell is <code>csh</code>.  Since the scripts to build and run GEOS-5  tend to be written in the same, you shouldn't bother trying to import too much into an alternative shell.  If you prefer a different shell, it is easiest just to open a <code>csh</code> process to build the model and your experiment.
@@ Line 12: / Line 12: @@
   setenv CVS_RSH ssh
-  setenv CVSROOT :ext:''USERID''@progress.nccs.nasa.gov:/cvsroot/esma
+  setenv CVSROOT :ext:''USERID''@progressdirect.nccs.nasa.gov:/cvsroot/esma
   setenv BASEDIR /discover/nobackup/projects/gmao/share/dao_ops/Baselibs/v3.1.5_build1
-where ''USERID'' is, of course, your '''progress''' 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-2_0  Fortuna
-This should check out the latest stable version of the model from '''progress''' 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>:
   source g5_modules
@@ Line 87: / Line 87: @@
 == 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 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
+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  <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>).