Ganymed 4.0 User's Guide: Difference between revisions

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This page describes in detail how to set up and optimize a global model run of GEOS-5 Ganymed 3.0 on NCCS discover and NAS pleiades and generally make the model do what you want. It assumes that you have already run the model as described in [[Ganymed 3.0 Quick Start]].

This page describes in detail how to set up and optimize a global model run of GEOS-5 Ganymed 4.0 on NCCS discover and NAS pleiades and generally make the model do what you want. It assumes that you have already run the model as described in [[Ganymed 4.0 Quick Start]].

'''Back to [[GEOS-5 Documentation for Ganymed 3.0]]'''

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

== Compiling the Model ==

Most of the time for longer runs you will be using a release version of the model, perhaps compiled with a different version of one or more of the model's gridded components, defined by subdirectories in the source code. This process starts with checking out the stock model from the repository using the command

Most of the time for longer runs you will be using a release version of the model, perhaps compiled with a different version of one or more of the model's gridded components, as defined by subdirectories in the source code. This process starts with checking out the stock model from the repository using the command

cvs co -r ''TAGNAME'' -d ''DIRECTORY'' ~~Fortuna~~

cvs co -r ''TAGNAME'' -d ''DIRECTORY'' Ganymed

where ''TAGNAME'' is the model "tag" (version). A tag in <code>cvs</code> marks the various versions of the source files in the repository that together make up a particular version of the model. A sample release tag is <code>Ganymed-~~3_0_p1~~</code>, indicating the latest patch of version Ganymed 3.0 for general use ~~(there is a <code>Ganymed-3_0_p2</code> patch for operations -- don't use it unless you know otherwise)~~. ''DIRECTORY'' is the directory that the source code tree will be created. If you are using a stock model tag it is reasonable to name the directory the same as the tag. This directory determines which model in presumably your space a particular experiment is using. Some scripts use the environment variable <code>ESMADIR</code>, which should be set to the absolute (full) pathname of this directory.

where ''TAGNAME'' is the model "tag" (version). A tag in <code>cvs</code> marks the various versions of the source files in the repository that together make up a particular version of the model. A sample release tag is <code>Ganymed-4_0_BETA8</code>, indicating the latest patch of version Ganymed 4.0 for general use. ''DIRECTORY'' is the directory that the source code tree will be created. If you are using a stock model tag it is reasonable to name the directory the same as the tag. This directory determines which model in presumably your space a particular experiment is using. Some scripts use the environment variable <code>ESMADIR</code>, which should be set to the absolute (full) pathname of this directory.

When a modified version of some component of the model is saved to the repository, the tag it uses -- different from the standard model tag -- is supposed to be applied at most only to the directories with modified files. This means that if you need to use some variant tag of a gridded component, you will have to <code>cd</code> to that directory and update to the variant tag. So, for example, if you needed to apply updates to the SatSim gridded component, you would have to <code>cd</code> several levels down to the directory <code>GEOSsatsim_GridComp</code> and run

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== Setting up a Global Model Run ==

The following describes how to set up a global model run. The procedure to set up a single column model run is described in [[Ganymed 3.0 Single Column Model]].

The following describes how to set up a global model run. The procedure to set up a single column model run is described in [[Ganymed 4.0 Single Column Model]].

=== Using <code>gcm_setup</code> ===

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<pre>

Enter the Data_Ocean Horizontal Resolution code: o1 (1 -deg, 360x180~~, (e.g.~~ Reynolds) Default)

Enter the Data_Ocean Horizontal Resolution code: o1 (1 -deg, 360x180 Reynolds) Default

o8 (1/8-deg, 2880x1440~~, (e.g.~~ OSTIA))

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

o8 (1/8-deg, 2880x1440 OSTIA)

</pre>

This selects the source of SST boundary conditions, 1 degree Reynolds or 1/8 degree OSTIA.

This selects the source of SST boundary conditions, 1 degree Reynolds, 1/4 degree MERRA-2 or 1/8 degree OSTIA.

Unless you are using a higher-resolution experiment, the default will suffice.

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Hit ENTER to use Default Location:

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

Default: /discover/nobackup/aeichman/Ganymed-~~3_0_p1~~

Default: /discover/nobackup/aeichman/Ganymed-4_0_BETA8

</pre>

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<pre>

Current GROUPS: g0620

Current GROUPS: g0620 gmaoint q_warp q_warp-test

Enter your GROUP ID for Current EXP: (Default: g0620)

</pre>

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Done!

-----

Build Directory: /discover/nobackup/aeichman/Ganymed-~~3_0_p1~~

Build Directory: /discover/nobackup/aeichman/ Ganymed-4_0_BETA8

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

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The following executable has been placed in your Experiment Directory:

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

/discover/nobackup/aeichman/Ganymed-~~3_0_p1~~/Linux/bin/GEOSgcm.x

/discover/nobackup/aeichman/Ganymed-4_0_BETA8/Linux/bin/GEOSgcm.x

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A cleanly completed model run will leave a set of restarts and the corresponding <code>cap_restart</code> in its experiment directory. Another source is <code>/archive/u/aeichman/restarts</code>. Restarts are also left during runs in date-labeled tarballs in the <code>restarts</code> directory under the experiment directory before being transferred to the user's <code>/archive</code> space. You may have to create the <code>cap_restart</code>, which is simply one line of text with the date of the restart files in the format ''YYYYMMDD HHMMSS'' (with a space).

Failing the above sources, you can convert restarts from different resolutions and model versions, including MERRA, as described in [[Regridding Restarts for Ganymed 1.0]].

Failing the above sources, you can convert restarts from different resolutions and model versions, including MERRA, as described in [[Regridding Restarts for Ganymed 4.0]].

== What Happens During a Run ==

@@ Line 1: / Line 1: @@
-This page describes in detail how to set up and optimize a global model run of GEOS-5 Ganymed 3.0 on NCCS discover and NAS pleiades and generally make the model do what you want.  It assumes that you have already run the model as described in [[Ganymed 3.0 Quick Start]].
+This page describes in detail how to set up and optimize a global model run of GEOS-5 Ganymed 4.0 on NCCS discover and NAS pleiades and generally make the model do what you want.  It assumes that you have already run the model as described in [[Ganymed 4.0 Quick Start]].
-'''Back to [[GEOS-5 Documentation for Ganymed 3.0]]'''
+'''Back to [[GEOS-5 Documentation for Ganymed 4.0]]'''
 == Compiling the Model ==
-Most of the time for longer runs you will be using a release version of the model, perhaps compiled with a different version of one or more of the model's gridded components, defined by subdirectories in the source code.  This process starts with checking out the stock model from the repository using the command
+Most of the time for longer runs you will be using a release version of the model, perhaps compiled with a different version of one or more of the model's gridded components, as defined by subdirectories in the source code.  This process starts with checking out the stock model from the repository using the command
-   cvs co -r  ''TAGNAME'' -d ''DIRECTORY'' Fortuna
+   cvs co -r  ''TAGNAME'' -d ''DIRECTORY'' Ganymed
-where ''TAGNAME'' is the model "tag" (version).  A tag in <code>cvs</code> marks the various versions of the source files in the repository that together make up a particular version of the model.  A sample release tag is <code>Ganymed-3_0_p1</code>, indicating the latest patch of version Ganymed 3.0 for general use (there is a <code>Ganymed-3_0_p2</code> patch for operations -- don't use it unless you know otherwise). ''DIRECTORY'' is the directory that the source code tree will be created.  If you are using a stock model tag it is reasonable to name the directory the same as the tag.  This directory determines which model in presumably your space a particular experiment is using.  Some scripts use the environment variable <code>ESMADIR</code>, which should be set to the absolute (full) pathname of this directory.
+where ''TAGNAME'' is the model "tag" (version).  A tag in <code>cvs</code> marks the various versions of the source files in the repository that together make up a particular version of the model.  A sample release tag is <code>Ganymed-4_0_BETA8</code>, indicating the latest patch of version Ganymed 4.0 for general use. ''DIRECTORY'' is the directory that the source code tree will be created.  If you are using a stock model tag it is reasonable to name the directory the same as the tag.  This directory determines which model in presumably your space a particular experiment is using.  Some scripts use the environment variable <code>ESMADIR</code>, which should be set to the absolute (full) pathname of this directory.
 When a modified version of some component of the model is saved to the repository, the tag it uses -- different from the standard model tag -- is supposed to be applied at most only to the directories with modified files.  This means that if you need to use some variant tag of a gridded component, you will have to <code>cd</code> to that directory and update to the variant tag.  So, for example, if you needed to apply updates to the SatSim gridded component, you would have to <code>cd</code> several levels down to the directory <code>GEOSsatsim_GridComp</code> and run
@@ Line 20: / Line 20: @@
 == Setting up a Global Model Run ==
-The following describes how to set up a global model run.  The procedure to set up a single column model run is described in [[Ganymed 3.0 Single Column Model]].
+The following describes how to set up a global model run.  The procedure to set up a single column model run is described in [[Ganymed 4.0 Single Column Model]].
 === Using <code>gcm_setup</code> ===
@@ Line 71: / Line 71: @@
 <pre>
-Enter the Data_Ocean Horizontal Resolution code: o1 (1  -deg,   360x180, (e.g. Reynolds) Default)
+Enter the Data_Ocean Horizontal Resolution code: o1 (1  -deg,  360x180  Reynolds) Default
-                                                  o8 (1/8-deg, 2880x1440, (e.g. OSTIA))
+                                                 o2 (1/4-deg, 1440x720  MERRA-2)
+                                                  o8 (1/8-deg, 2880x1440 OSTIA)
 </pre>
-This selects the source of SST boundary conditions, 1 degree Reynolds or 1/8 degree OSTIA.
+This selects the source of SST boundary conditions, 1 degree Reynolds, 1/4 degree MERRA-2 or 1/8 degree OSTIA.
 Unless you are using a higher-resolution experiment, the default will suffice.
@@ Line 129: / Line 130: @@
 Hit ENTER to use Default Location:
 ----------------------------------
-Default:  /discover/nobackup/aeichman/Ganymed-3_0_p1
+Default:  /discover/nobackup/aeichman/Ganymed-4_0_BETA8
 </pre>
@@ Line 135: / Line 136: @@
 <pre>
-Current GROUPS: g0620
+Current GROUPS: g0620 gmaoint q_warp q_warp-test
 Enter your GROUP ID for Current EXP: (Default: g0620)
 </pre>
@@ Line 165: / Line 166: @@
 Done!
 -----
-Build Directory: /discover/nobackup/aeichman/Ganymed-3_0_p1
+Build Directory: /discover/nobackup/aeichman/ Ganymed-4_0_BETA8
 ----------------
@@ Line 172: / Line 173: @@
 The following executable has been placed in your Experiment Directory:
 ----------------------------------------------------------------------
-/discover/nobackup/aeichman/Ganymed-3_0_p1/Linux/bin/GEOSgcm.x
+/discover/nobackup/aeichman/Ganymed-4_0_BETA8/Linux/bin/GEOSgcm.x
@@ Line 195: / Line 196: @@
 A cleanly completed model run will leave a set of restarts and the corresponding <code>cap_restart</code> in its experiment directory.  Another source is <code>/archive/u/aeichman/restarts</code>.  Restarts are also left during runs in date-labeled tarballs in the <code>restarts</code> directory under the experiment directory before being transferred to the user's <code>/archive</code> space.  You may have to create the <code>cap_restart</code>, which is simply one line of text with the date of the restart files in the format ''YYYYMMDD HHMMSS'' (with a space).
-Failing the above sources, you can convert restarts from different resolutions and model versions, including MERRA, as described in  [[Regridding Restarts for Ganymed 1.0]].
+Failing the above sources, you can convert restarts from different resolutions and model versions, including MERRA, as described in  [[Regridding Restarts for Ganymed 4.0]].
 == What Happens During a Run ==