Ganymed 4.0 Quick Start: Difference between revisions

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setenv CVS_RSH ssh

setenv CVSROOT :ext:''USERID''@~~cvsacl~~:/cvsroot/esma

setenv CVSROOT :ext:''USERID''@cvsacldirect:/cvsroot/esma

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-~~4_0_BETA3 Ganymed~~

cvs co -r Ganymed-4_0 GEOSagcm

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=== Compiling the Model ===

<code>cd</code> into <code>GEOSagcm/src</code> and <code>source</code> the file called <code>g5_modules</code>:

First, you need to set <code>ESMADIR</code>. For example, if your <code>src/</code> directory is:

/home/mathomp4/Models/Ganymed-4_0/GEOSagcm/src

then you should set:

setenv ESMADIR /home/mathomp4/Models/Ganymed-4_0/GEOSagcm

Next, <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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c1440 - 1/16 deg ( 7-km)

For your first time out you will probably want to enter <code>c48</code> (corresponding to ~2 degree resolution with the cubed sphere). On the next ~~seven~~ questions, ~~hit~~ enter to accept the default:

For your first time out you will probably want to enter <code>c48</code> (corresponding to ~2 degree resolution with the cubed sphere). On the next eight questions, hitting enter to accept the default will let you run a PChem run:

Enter the Atmospheric Model Vertical Resolution: LM (Default: 72)

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 Reynolds) Default

o2 (1/4-deg, 1440x720 MERRA-2)

o3 (1/8-deg, 2880x1440 OSTIA)

Do you wish to run GOCART? (Default: NO or FALSE)

Enter the tag or directory (/filename) of the HISTORY.AGCM.rc.tmpl to use

(To use HISTORY.AGCM.rc.tmpl from current build, Type: Current )

-------------------------------------------------------------------------

Hit ENTER to use Default Tag/Location: (Current)

'''NOTE''': Some things are easier if your HOME and EXPERIMENT directories are the same. For the next two, look carefully at the default and make sure they are both pointing to the same <code>nobackup</code> location.

Enter Desired Location for the HOME Directory (to contain scripts and RC files)

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----------------------------------

Default: /discover/nobackup/''USER''/''EXPID''

Enter Desired Location for the EXPERIMENT Directory (to contain model output and restart files)

Hit ENTER to use Default Location:

----------------------------------

Default: ~''USER''/geos5/''EXPID''

/discover/nobackup/''USER''/''EXPID''

Enter Location for Build directory containing: src/ Linux/ etc...

Hit ENTER to use Default Location:

----------------------------------

Default: /discover/nobackup/''USER''/GEOSgcm

After these it will ask you for a group ID -- the default is ~~g0602~~ (GMAO modeling group). Enter whatever is appropriate, as necessary.

After these it will ask you for a group ID -- the default for this writer is g0620 (GMAO modeling group). Enter whatever is appropriate, as necessary.

Current GROUPS: g0620 gmaoint

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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 (''HOMDIR'') as either in <code>~''USERID''/geos5/''EXPID''</code> (if you accepted the default) or in <code>/discover/nobackup/''USERID''/''EXPID''</code> (if you followed the above advice) containing the run scripts and GEOS resource (<code>.rc</code>) files.

== Running GEOS-5 ==

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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.

Copy the restart (initial condition) files and associated <code>cap_restart</code> into ''EXPDIR''. You can get an arbitrary set of restarts by copying the contents of the directory <code>/archive/u/aeichman/restarts/Ganymed-4_0/~~C48~~/19800103/</code>, containing 2-degree cubed sphere restarts from Jan. 3, 1980, and their corresponding <code>cap_restart</code>. 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''. You can get an arbitrary set of restarts by copying the contents of the directory <code>/archive/u/aeichman/restarts/Ganymed-4_0/c48/19800103/</code>, containing 2-degree cubed sphere restarts from Jan. 3, 1980, and their corresponding <code>cap_restart</code>. 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).

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 ''EXPDIR''/slurm-''JOBID''.out</code>, ''JOBID'' being returned by <code>qsub</code> and displayed with <code>qstat</code>. Jobs can be killed with <code>qdel ''JOBID''</code>.

== Output and Plots ==

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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 .

----

'''Back to [[GEOS-5 Documentation for Ganymed 4.0]]'''

Contact Matthew Thompson at GMAO with questions and comments

@@ Line 18: / Line 18: @@
   setenv CVS_RSH ssh
-  setenv CVSROOT :ext:''USERID''@cvsacl:/cvsroot/esma
+  setenv CVSROOT :ext:''USERID''@cvsacldirect:/cvsroot/esma
 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-4_0_BETA3 Ganymed
+  cvs co -r Ganymed-4_0 GEOSagcm
@@ Line 29: / Line 29: @@
 === Compiling the Model ===
-<code>cd</code> into <code>GEOSagcm/src</code> and <code>source</code> the file called <code>g5_modules</code>:
+First, you need to set <code>ESMADIR</code>. For example, if your <code>src/</code> directory is:
+ /home/mathomp4/Models/Ganymed-4_0/GEOSagcm/src
+then you should set:
+ setenv ESMADIR /home/mathomp4/Models/Ganymed-4_0/GEOSagcm
+Next, <code>cd</code> into <code>GEOSagcm/src</code> and <code>source</code> the file called <code>g5_modules</code>:
   source g5_modules
@@ Line 89: / Line 97: @@
                                  c1440 - 1/16 deg ( 7-km)
-For your first time out you will probably want to enter <code>c48</code> (corresponding to ~2 degree resolution with the cubed sphere).  On the next seven questions, hit enter to accept the default:
+For your first time out you will probably want to enter <code>c48</code> (corresponding to ~2 degree resolution with the cubed sphere).  On the next eight questions, hitting enter to accept the default will let you run a PChem run:
+ Enter the Atmospheric Model Vertical Resolution: LM (Default: 72)
   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  Reynolds) Default
                                                    o2 (1/4-deg, 1440x720  MERRA-2)
                                                    o3 (1/8-deg, 2880x1440 OSTIA)
   Do you wish to run GOCART? (Default: NO or FALSE)
   Enter the tag or directory (/filename) of the HISTORY.AGCM.rc.tmpl to use
   (To use HISTORY.AGCM.rc.tmpl from current build, Type:  Current         )
   -------------------------------------------------------------------------
   Hit ENTER to use Default Tag/Location: (Current)
+'''NOTE''': Some things are easier if your HOME and EXPERIMENT directories are the same. For the next two, look carefully at the default and make sure they are both pointing to the same <code>nobackup</code> location.
   Enter Desired Location for the HOME Directory (to contain scripts and RC files)
@@ Line 109: / Line 121: @@
   ----------------------------------
   Default:  /discover/nobackup/''USER''/''EXPID''
   Enter Desired Location for the EXPERIMENT Directory (to contain model output and restart files)
   Hit ENTER to use Default Location:
   ----------------------------------
   Default:  ~''USER''/geos5/''EXPID''
+ /discover/nobackup/''USER''/''EXPID''
   Enter Location for Build directory containing:  src/ Linux/ etc...
   Hit ENTER to use Default Location:
   ----------------------------------
   Default:  /discover/nobackup/''USER''/GEOSgcm
-After these it will ask you for a group ID -- the default is g0602 (GMAO modeling group).  Enter whatever is appropriate, as necessary.
+After these it will ask you for a group ID -- the default for this writer is g0620 (GMAO modeling group).  Enter whatever is appropriate, as necessary.
    Current GROUPS: g0620 gmaoint
@@ Line 143: / Line 156: @@
-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 (''HOMDIR'') as either in <code>~''USERID''/geos5/''EXPID''</code> (if you accepted the default) or in <code>/discover/nobackup/''USERID''/''EXPID''</code> (if you followed the above advice) containing the run scripts and GEOS resource (<code>.rc</code>) files.
 == Running GEOS-5 ==
@@ Line 157: / Line 170: @@
 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.
-Copy the restart (initial condition) files and associated <code>cap_restart</code> into ''EXPDIR''.  You can get an arbitrary set of restarts by copying the contents of the directory <code>/archive/u/aeichman/restarts/Ganymed-4_0/C48/19800103/</code>, containing 2-degree cubed sphere restarts from Jan. 3, 1980, and their corresponding <code>cap_restart</code>.  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''.  You can get an arbitrary set of restarts by copying the contents of the directory <code>/archive/u/aeichman/restarts/Ganymed-4_0/c48/19800103/</code>, containing 2-degree cubed sphere restarts from Jan. 3, 1980, and their corresponding <code>cap_restart</code>.  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).
-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 ''EXPDIR''/slurm-''JOBID''.out</code>, ''JOBID'' being returned by <code>qsub</code> and displayed with <code>qstat</code>.  Jobs can be killed with <code>qdel ''JOBID''</code>.
 == Output and Plots ==
@@ Line 178: / Line 191: @@
 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 .
+----
 '''Back to [[GEOS-5 Documentation for Ganymed 4.0]]'''
+Contact Matthew Thompson at GMAO with questions and comments