Fortuna 2.5 User's Guide: Difference between revisions

(19 intermediate revisions by the same user not shown)

Line 87:

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

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

Hit ENTER to use Default Tag/Location: (~~Fortuna-2_5~~)

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

</pre>

Line 103:

<pre>

Enter Desired Location for ~~EXP~~ Directory (to contain model output and restart files)

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

Hit ENTER to use Default Location:

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

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Hit ENTER to use Default Location:

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

Default: /discover/nobackup/aeichman/Fortuna-~~2_5~~

Default: /discover/nobackup/aeichman/Fortuna-2_5_p6

</pre>

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<pre>

~~-----------------------------------~~

~~building~~ file list ~~... done~~

sending incremental file list

GEOSgcm.x

sent ~~50117242~~ bytes received 42 bytes ~~33411522~~.67 bytes/sec

sent 50848492 bytes received 31 bytes 33899015.33 bytes/sec

total size is ~~50110997~~ speedup is 1.00

total size is 50842191 speedup is 1.00

Creating gcm_run.j for Experiment myexp42 ...

Creating gcm_post.j for Experiment myexp42 ...

Creating gcm_plot.j for Experiment myexp42 ...

Creating gcm_plot.tmpl for Experiment myexp42 ...

Creating gcm_archive.j for Experiment myexp42 ...

Creating gcm_regress.j for Experiment myexp42 ...

Line 148:

-----

Build Directory: /discover/nobackup/aeichman/Fortuna-~~2_5~~

Build Directory: /discover/nobackup/aeichman/Fortuna-2_5_p6

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

Line 154:

The following executable has been placed in your Experiment Directory:

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

/discover/nobackup/aeichman/Fortuna-~~2_5~~/Linux/bin/GEOSgcm.x

/discover/nobackup/aeichman/Fortuna-2_5_p6/Linux/bin/GEOSgcm.x

You must now copy your ~~AGCM~~ Initial Conditions into:

You must now copy your Initial Conditions into:

~~-----~~-----------------------------------------------

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

/discover/nobackup/aeichman/myexp42

discover28: /discover/nobackup/aeichman/Fortuna-2_5_p6/src/Applications/GEOSgcm_App >

</pre>

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Failing the above sources, you can convert restarts from different resolutions and model versions, including MERRA, as described in [[Regridding Restarts for Fortuna 2.5]].

== What Happens During a Run ==

When the script <code>gcm_run.j</code> starts running, it creates a directory called <code>scratch</code> and copies or links into it the model executable, rc files, restarts and boundary conditions necessary to run the model. It also creates a directory for each of the output collections (in the default setup with the suffix <code>geosgcm_</code>) in the directory <code>holding</code> for before post-processing, and in the experiment directory for after post-processing. It also tars the restarts and moves the tarball to the <code>restarts</code> directory.

Then the executable <code>GEOSgcm.x</code> is run in the <code>scratch</code> directory, starting with the date in <code>cap_restart</code> and running for the length of a segment. A segment is the length of model time that the model integrates before returning, letting <code>gcm_run.j</code> do some housekeeping and then running another segment. A model job will typically run a number of segments before trying to resubmit itself, hopefully before the allotted wallclock time of the job runs out.

The processing that the various batch jobs perform is illustrated below:

[[Image:F2.5-job-diagram002.png]]

Each time a segment ends, <code>gcm_run.j</code> submits a post-processing job before starting a new segment or exiting. The post-processing job moves the model output from the <code>scratch</code> directory to the respective collection directory under <code>holding</code>. Then it determines whether there is a enough output to create a monthly or seasonal mean, and if so, creates them and moves them to the collection directories in the experiment directory, and then tars up the daily output and submits an archiving job. The archiving job tries to move the tarred daily output, the monthly and seasonal means and any tarred restarts to the user's space in <code>archive</code> filesystem. The post-processing script also determines (assuming the default settings) whether enough output exists to create plots; if so, a plotting job is submitted to the queue. The plotting script produces a number of pre-determined plots as <code>.gif</code> files in the <code>plot_CLIM</code> directory in the experiment directory.

As explained above, the contents of the <code>cap_restart</code> file determine the start of the model run in model time, which determines boundary conditions and the times stamps of the output. The end time may be set in <code>CAP.rc</code> with the property <code>END_DATE</code> (format ''YYYYMMDD HHMMSS'', with a space), though integration is usually leisurely enough that one can just kill the job or rename the run script <code>gcm_run.j</code> so that it is not resubmitted to the job queue.

===Tuning a run===

Most of the other properties in <code>CAP.rc</code> are discussed elsewhere, but two that are important for understanding how the batch jobs work are <code>JOB_SGMT</code>, the length of the segment, and <code>NUM_SGMT</code>, the number of segments that the job tries to run before resubmitting itself and exiting. <code>JOB_SGMT</code> is in the format of ''YYYYMMDD HHMMSS'' (but usually expressed in days) and <code>NUM_SGMT</code> as an integer, so the multiple of the two is the total model time that a job will attempt to run. It may be tempting to just run one long segment, but much housekeeping is done between segments, such as saving state in the form of restarts and spawning archiving jobs that keep your account from running over disk quota. So to tune for the maximum number of segments in a job, it is usually best to manipulate <code>JOB_SGMT</code>.

== Determining Output: <code>HISTORY.rc</code> ==

The contents of the the file <code>HISTORY.rc</code> (in your experiment <code>HOME</code> directory) tell the model what and how to output its state and diagnostic fields. The default <code>HISTORY.rc</code> provides many fields as is, but you may want to modify it to suit your needs.

===File format===

The top of a default <code>HISTORY.rc</code> will look something like this:

<pre>

EXPID: myexp42

EXPDSC: this_is_my_experiment

COLLECTIONS: 'geosgcm_prog'

'geosgcm_surf'

'geosgcm_moist'

'geosgcm_turb'

</pre>

[....]

The attribute <code>EXPID</code> must match the name of the experiment <code>HOME</code> directory; this is only an issue if you copy the <code>HISTORY.rc</code> from a different experiment. The <code>EXPDSC</code> attribute is used to label the plots. The <code>COLLECTIONS</code> attribute contains list of strings indicating the output collections to be created. The content of the individual collections are determined after this list. Individual collections can be "turned off" by commenting the relevant line with a <code>#</code>.

The following is an example of a collection specification:

<pre>

geosgcm_prog.template: '%y4%m2%d2_%h2%n2z.nc4',

geosgcm_prog.archive: '%c/Y%y4',

geosgcm_prog.format: 'CFIO',

geosgcm_prog.frequency: 060000,

geosgcm_prog.resolution: 144 91,

geosgcm_prog.vscale: 100.0,

geosgcm_prog.vunit: 'hPa',

geosgcm_prog.vvars: 'log(PLE)' , 'DYN' ,

geosgcm_prog.levels: 1000 975 950 925 900 875 850 825 800 775 750 725 700 650 600 550 500 450 400 350 300 250 200 150 100 70 50 40 30 20 10 7 5 4 3 2 1 0.7 0.5 0.4 0.3 0.2

0.1 0.07 0.05 0.04 0.03 0.02,

geosgcm_prog.fields: 'PHIS' , 'AGCM' ,

'T' , 'DYN' ,

'PS' , 'DYN' ,

'ZLE' , 'DYN' , 'H' ,

'OMEGA' , 'DYN' ,

'Q' , 'MOIST' , 'QV' ,

::

</pre>

The individual collection attributes are described below, but what users modify the most are the <code>fields</code> attribute. This determines which exports are saved in the collection. Each field record is a string with the name of an export from the model followed by a string with the name of the gridded component which exports it, separated by a comma. The entries with a third column determine the name by which that export in saved in the collection file when the name is different from that of the export.

===What exports are available?===

To add export fields to the <code>HISTORY.rc</code> you will need to know what fields the model provides, which gridded component provides them, and their name. The most straightforward way to do this is to use <code>PRINTSPEC</code>. The setting for <code>PRINTSPEC</code> is in the file <code>CAP.rc</code>. By default the line looks like so:

PRINTSPEC: 0 # (0: OFF, 1: IMPORT & EXPORT, 2: IMPORT, 3: EXPORT)

Setting <code>PRINTSPEC</code> to 3 will make the model send to standard output a list of exports available to <code>HISTORY.rc</code> in the model's current configuration, and then exit without integrating. The list includes each export's gridded component and short name (both necessary to include in <code>HISTORY.rc</code>), long (descriptive) name, units, and number of dimensions. Note that run-time options can affect the exports available, so see to it that you have those set as you intend. The other <code>PRINTSPEC</code> values are useful for debugging.

While you can set <code>PRINTSPEC</code>, submit <code>qsub gcm_run.j</code>, and get the export list as part of PBS standard output, there are quicker ways of obtaining the list. One way is to run it as a single column model on a single processor, as explained in [[Fortuna 2.5 Single Column Model]]. Another way is to run it in an existing experiment. In the <code>scratch</code> directory of an experiment that has already run, change <code>PRINTSPEC</code> in <code>CAP.rc</code> as above. Then, in the file <code>AGCM.rc</code>, change the values of <code>NX</code> and <code>NY</code> (near the beginning of the file) to 1. Then, from an interactive job (one processor will suffice), run the executable <code>GEOSgcm.x</code> in <code>scratch</code>. You will need to run <code>source src/g5_modules</code> in the model's build tree to set up the environment. The model executable will simply output the export list to <code>stdout</code>.

== Special Requirements ==

=== Perpetual ("Groundhog Day") mode ===

GEOS-5 Fortuna 2.5 and later can be run in "perpetual mode", automatically running with the same forcings for a time period delineated as a calendar year, month or day. The time period desired is set in <code>CAP.rc</code> with the parameters <code>PERPETUAL_YEAR</code>, <code>PERPETUAL_MONTH</code> and <code>PERPETUAL_DAY</code>. Set all three to run with the forcings for a particular day, and <code>NUM_SGMT</code> to how many times you wish to run it -- the history collection files will be appended with dates starting with the one in <code>cap_restart</code> and generally incrementing for the number of days in <code>NUM_SGMT</code>.

=== Saving restarts during a segment ===

=== post.rc ===

@@ Line 87: / Line 87: @@
 (To use HISTORY.AGCM.rc.tmpl from current build, Type:  Current         )
 -------------------------------------------------------------------------
-Hit ENTER to use Default Tag/Location: (Fortuna-2_5)
+Hit ENTER to use Default Tag/Location: (Current)
 </pre>
@@ Line 103: / Line 103: @@
 <pre>
-Enter Desired Location for EXP Directory (to contain model output and restart files)
+Enter Desired Location for EXPERIMENT Directory (to contain model output and restart files)
 Hit ENTER to use Default Location:
 ----------------------------------
@@ Line 115: / Line 115: @@
 Hit ENTER to use Default Location:
 ----------------------------------
-Default:  /discover/nobackup/aeichman/Fortuna-2_5
+Default:  /discover/nobackup/aeichman/Fortuna-2_5_p6
 </pre>
@@ Line 128: / Line 128: @@
 <pre>
------------------------------------
-building file list ... done
+sending incremental file list
 GEOSgcm.x
-sent 50117242 bytes  received 42 bytes  33411522.67 bytes/sec
+sent 50848492 bytes  received 31 bytes  33899015.33 bytes/sec
-total size is 50110997  speedup is 1.00
+total size is 50842191  speedup is 1.00
 Creating gcm_run.j for Experiment myexp42 ...
 Creating gcm_post.j for Experiment myexp42 ...
-Creating gcm_plot.j for Experiment myexp42 ...
+Creating gcm_plot.tmpl for Experiment myexp42 ...
 Creating gcm_archive.j for Experiment myexp42 ...
 Creating gcm_regress.j for Experiment myexp42 ...
@@ Line 148: / Line 148: @@
 -----
-Build Directory: /discover/nobackup/aeichman/Fortuna-2_5
+Build Directory: /discover/nobackup/aeichman/Fortuna-2_5_p6
 ----------------
@@ Line 154: / Line 154: @@
 The following executable has been placed in your Experiment Directory:
 ----------------------------------------------------------------------
-/discover/nobackup/aeichman/Fortuna-2_5/Linux/bin/GEOSgcm.x
+/discover/nobackup/aeichman/Fortuna-2_5_p6/Linux/bin/GEOSgcm.x
-You must now copy your AGCM Initial Conditions into:
+You must now copy your Initial Conditions into:
-----------------------------------------------------
+-----------------------------------------------
 /discover/nobackup/aeichman/myexp42
+discover28: /discover/nobackup/aeichman/Fortuna-2_5_p6/src/Applications/GEOSgcm_App >
 </pre>
@@ Line 176: / Line 178: @@
 Failing the above sources, you can convert restarts from different resolutions and model versions, including MERRA, as described in  [[Regridding Restarts for Fortuna 2.5]].
+== What Happens During a Run ==
+When the script <code>gcm_run.j</code> starts running, it creates a directory called  <code>scratch</code> and copies or links into it the model executable, rc files, restarts and boundary conditions necessary to run the model.  It also creates a directory for each of the output collections (in the default setup with the suffix <code>geosgcm_</code>) in the directory <code>holding</code> for before post-processing, and in the experiment directory for after post-processing.  It also tars the restarts and moves the tarball to the <code>restarts</code> directory.
+Then the executable  <code>GEOSgcm.x</code> is run in the <code>scratch</code> directory, starting with the date in  <code>cap_restart</code> and running for the length of a segment.  A segment is the length of model time that the model integrates before returning, letting <code>gcm_run.j</code> do some housekeeping and then running another segment.  A model job will typically run a number of segments before trying to resubmit itself, hopefully before the allotted wallclock time of the job runs out.
+The processing that the various batch jobs perform is illustrated below:
+[[Image:F2.5-job-diagram002.png]]
+Each time a segment ends, <code>gcm_run.j</code> submits a post-processing job before starting a new segment or exiting.  The post-processing job moves the model output from the  <code>scratch</code> directory to the respective collection directory under  <code>holding</code>.  Then it determines whether there is a enough output to create a monthly or seasonal mean, and if so, creates them and moves them to the collection directories in the experiment directory, and then tars up the daily output and submits an archiving job.  The archiving job tries to move the tarred daily output, the monthly and seasonal means and any tarred restarts to the user's space in <code>archive</code> filesystem.  The post-processing script also determines (assuming the default settings) whether enough output exists to create plots; if so, a plotting job is submitted to the queue.  The plotting script produces a number of pre-determined plots as <code>.gif</code> files in the <code>plot_CLIM</code> directory in the experiment directory.
+As explained above, the contents of the <code>cap_restart</code> file determine the start of the model run in model time, which determines boundary conditions and the times stamps of the output.  The end time may be set in <code>CAP.rc</code> with the property <code>END_DATE</code>  (format ''YYYYMMDD HHMMSS'', with a space), though integration is usually leisurely enough that one can just kill the job or rename the run script <code>gcm_run.j</code> so that it is not resubmitted to the job queue.
+===Tuning a run===
+Most of the other properties in <code>CAP.rc</code> are discussed elsewhere, but two that are important for understanding how the batch jobs work are <code>JOB_SGMT</code>, the length of the segment, and <code>NUM_SGMT</code>, the number of segments that the job tries to run before resubmitting itself and exiting.  <code>JOB_SGMT</code> is in the format of ''YYYYMMDD HHMMSS'' (but usually expressed in days) and <code>NUM_SGMT</code> as an integer, so the multiple of the two is the total model time that a job will attempt to run.  It may be tempting to just run one long segment, but much housekeeping is done between segments, such as saving state in the form of restarts and spawning archiving jobs that keep your account from running over disk quota.  So to tune for the maximum number of segments in a job, it is usually best to manipulate <code>JOB_SGMT</code>.
+== Determining Output: <code>HISTORY.rc</code> ==
+The contents of the the file <code>HISTORY.rc</code> (in your experiment <code>HOME</code> directory) tell the model what and how to output its state and diagnostic fields.  The default <code>HISTORY.rc</code> provides many fields as is, but you may want to modify it to suit your needs.
+===File format===
+The top of a default <code>HISTORY.rc</code> will look something like this:
+<pre>
+EXPID:  myexp42
+EXPDSC: this_is_my_experiment
+COLLECTIONS: 'geosgcm_prog'
+             'geosgcm_surf'
+             'geosgcm_moist'
+             'geosgcm_turb'
+</pre>
+[....]
+The attribute <code>EXPID</code> must match the name of the experiment <code>HOME</code> directory; this is only an issue if you copy the  <code>HISTORY.rc</code> from a different experiment.  The <code>EXPDSC</code> attribute is used to label the plots.  The <code>COLLECTIONS</code> attribute contains list of strings indicating the output collections to be created.  The content of the individual collections are determined after this list.  Individual collections can be "turned off" by commenting the relevant line with a <code>#</code>.
+The following is an example of a collection specification:
+<pre>
+  geosgcm_prog.template:  '%y4%m2%d2_%h2%n2z.nc4',
+  geosgcm_prog.archive:   '%c/Y%y4',
+  geosgcm_prog.format:    'CFIO',
+  geosgcm_prog.frequency:  060000,
+  geosgcm_prog.resolution: 144 91,
+  geosgcm_prog.vscale:     100.0,
+  geosgcm_prog.vunit:     'hPa',
+  geosgcm_prog.vvars:     'log(PLE)' , 'DYN'          ,
+  geosgcm_prog.levels:     1000 975 950 925 900 875 850 825 800 775 750 725 700 650 600 550 500 450 400 350 300 250 200 150 100 70 50 40 30 20 10 7 5 4 3 2 1 0.7 0.5 0.4 0.3 0.2
+.1 0.07 0.05 0.04 0.03 0.02,
+  geosgcm_prog.fields:    'PHIS'     , 'AGCM'         ,
+                          'T'        , 'DYN'          ,
+                          'PS'       , 'DYN'          ,
+                          'ZLE'      , 'DYN'          , 'H'   ,
+                          'OMEGA'    , 'DYN'          ,
+                          'Q'        , 'MOIST'        , 'QV'  ,
+                          ::
+</pre>
+The individual collection attributes are described below, but what users modify the most are the <code>fields</code> attribute.  This determines which exports are saved in the collection.  Each field record is a string with the name of an export from the model followed by a string with the name of the gridded component which exports it, separated by a comma.  The entries with a third column determine the name by which that export in saved in the collection file when the name is different from that of the export.
+===What exports are available?===
+To add export fields to the <code>HISTORY.rc</code> you will need to know what fields the model provides, which gridded component provides them, and their name.  The most straightforward way to do this is to use <code>PRINTSPEC</code>.  The setting for  <code>PRINTSPEC</code> is in the file <code>CAP.rc</code>.  By default the line looks like so:
+ PRINTSPEC: 0  # (0: OFF, 1: IMPORT & EXPORT, 2: IMPORT, 3: EXPORT)
+Setting <code>PRINTSPEC</code> to  3 will make the model send to standard output a list of exports available to <code>HISTORY.rc</code> in the model's current configuration, and then exit without integrating. The list includes each export's gridded component and short name (both necessary to include in <code>HISTORY.rc</code>), long (descriptive) name, units, and number of dimensions.  Note that run-time options can affect the exports available, so see to it that you have those set as you intend.  The other <code>PRINTSPEC</code> values are useful for debugging.
+While you can set  <code>PRINTSPEC</code>, submit <code>qsub gcm_run.j</code>, and get the export list as part of PBS standard output, there are quicker ways of obtaining the list.  One way is to run it as a single column model on a single processor, as explained in [[Fortuna 2.5 Single Column Model]].  Another way is to run it in an existing experiment.  In the <code>scratch</code> directory of an experiment that has already run, change <code>PRINTSPEC</code> in  <code>CAP.rc</code> as above.  Then, in the file <code>AGCM.rc</code>, change the values of <code>NX</code> and <code>NY</code> (near the beginning of the file) to 1.  Then, from an interactive job (one processor will suffice), run the executable <code>GEOSgcm.x</code> in <code>scratch</code>.  You will need to run <code>source src/g5_modules</code> in the model's build tree to set up the environment.  The model executable will simply output the export list to <code>stdout</code>.
+== Special Requirements ==
+=== Perpetual ("Groundhog Day") mode  ===
+GEOS-5 Fortuna 2.5 and later can be run in "perpetual mode", automatically running with the same forcings for a time period delineated as a calendar year, month or day.  The time period desired is set in <code>CAP.rc</code> with the parameters <code>PERPETUAL_YEAR</code>, <code>PERPETUAL_MONTH</code> and <code>PERPETUAL_DAY</code>.  Set all three to run with the forcings for a particular day, and <code>NUM_SGMT</code> to how many times you wish to run it -- the history collection files will be appended with dates starting with the one in <code>cap_restart</code> and generally incrementing for the number of days in <code>NUM_SGMT</code>.
+=== Saving restarts during a segment ===
+=== post.rc ===