Setting up S2Sv3 model: Difference between revisions

Line 1:

== ~~Coupled~~ model build ~~instructions~~ ==

= Coupled Model Build Instructions =

This document describes the basic step to obtain, compile and execute the GEOS couple Ocean model.

=== Obtain the Code ===

The code is in a CVS repository. To obtain it, issue the command:

cvs co -P -r tag_name GEOSodas_m7

where <code>tag_name</code> is the name of the CVS tag of interest. It can be for instance <code>yuri-s2s3-unstable-SLES12</code>.

You will get a directory named <code>GEOSodas</code>.

=== Compile the Code ===

To compile the code, issue the following commands:

cd GEOSodas/src

source g5_modules

./parallel_build.csh

In the last command, you might be asked to provide a <code>sponsor code id</code> is if you have more than one on the platform you are using.

An alternative method to compile the code is use a simple script (C-shell here) for a serial build. It assumes that that the script is located at the same level as the <code>GEOSodas/</code> directory.

#!/bin/csh -f

source /usr/share/modules/init/csh

set curDIR = `pwd`

setenv ESMADIR ${curDIR}/GEOSodas

cd $ESMADIR/src

module purge

source g5_modules

set CLEAN = 0

set MAKEALL = 1

set MAKEALLDEBUG = 0

if ($CLEAN) gmake realclean

if ($MAKEALLDEBUG) gmake install BOPT=g

if ($MAKEALL) gmake pinstall

Regardless the method that you use to build the code, a directory named <code>Linux/</code> will be created inside <code>GEOSodas/</code>. The <code>Linux/</code> directory contains temporary files, libraries and executables created during the compilation process. To make sure that the code was successfully compiled, check that the file <code>GEOSgcm.x</code> exists in the directory <code>GEOSodas/src/Applications/GEOSgcm_App/</code>.

=== Create the Experiment Directory ===

After building the executable, we need to create an experiment directory. The code comes with a tool that allows you to do that. We recommend that you always go through this process whenever to start a new experiment.

The first step is to go to the directory <code>GEOSodas/src/Applications/GEOSgcm_App/</code>. Then check that the following files are available:

AGCM.rc.tmpl GAAS_GridComp.rc.tmpl GEOSgcm.x gcm_run.j gcm_setup ocean_das_config.tmpl

There are many other files in the directory but the above ones play an important role in setting the experiment directory and driving the model.

The script <code>gcm_setup</code>, when executed, asks a series of questions to determine a set of parameters and input files needed to run the model.

Issue the command:

./gcm_setup

and provide the information requested. When you are asked if:

* You want to run the COUPLED Ocean/Sea-Ice Model, answer <code>YES</code>.

* You want to to run the REPLAY DUAL OCEAN Model, answer

** <code>YES</code> is you intend to run <code>ODAS</code>.

** <code>NO</code> otherwise.

The available resolutions are:

| Atmosphere | Ocean |

| ---------- | ------------------------------- |

| c90x72 | 360x200x50 |

| c180x72 | 720x410x40 |

| c180x72 | 1440x1080x50 (S2Sv3 resolution) |

When you are asked which history template do you want to use, you may choose <code>HISTORY.AOGCM.rc.tmpl</code> or <code>HISTORY.S2S.rc.tmpl</code>. All other parameters may be left default. If the `ODAS` configuration is selected, the entire <code>GEOSodas/src/Applications/UMD_Etc/</code> directory will be copied into the <code>ocean_das</code> directory located in the experiment directory.

When you are asked which history template do you want to use, you may choose <code>HISTORY.AOGCM.rc.tmpl</code> or <code>HISTORY.S2S.rc.tmpl</code>. All other parameters may be left default. If the <code>ODAS</code> configuration is selected, the entire <code>GEOSodas/src/Applications/UMD_Etc/</code> directory will be copied into the <code>ocean_das</code> directory located in the experiment directory.

Here, we provide a sample dialogue:

Enter the Experiment ID:

test_odas

Enter a 1-line Experiment Description:

Test ODAS

Do you wish to CLONE an old experiment? (Default: NO or FALSE)

NO

Enter the Atmospheric Horizontal Resolution code:

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

Lat/Lon Cubed-Sphere

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

b -- 2 deg c48 -- 2 deg

c -- 1 deg c90 -- 1 deg

d -- 1/2 deg c180 -- 1/2 deg (56-km)

e -- 1/4 deg (35-km) c360 -- 1/4 deg (28-km)

c720 -- 1/8 deg (14-km)

c1440 - 1/16 deg ( 7-km)

DYAMOND Grids

c768 -- 1/8 deg (12-km)

c1536 - 1/16 deg ( 6-km)

c3072 - 1/32 deg ( 3-km)

c180

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

72

Do you wish to run the COUPLED Ocean/Sea-Ice Model? (Default: NO or FALSE)

Yes

Enter the Ocean Lat/Lon Horizontal Resolution: IM JM (Default: 360 200)

1440 1080

Enter the Ocean Model Vertical Resolution: LM (Default: 50)

50

Do you wish to run the REPLAY DUAL OCEAN Model? (Default: NO or FALSE)

YES

Do you wish to run the AODAS Model? (Default: NO or FALSE)

YES

Enter the choice of Restart Record Parameters: Frequency (hhmmss): (Default: 240000)

240000

Enter the choice of Restart Record Parameters: Reference Date (YYYYMMDD): (Default: 19800101)

19800101

Enter the choice of Restart Record Parameters: Reference Time (hhmmss): (Default: 210000)

210000

Enter the choice of Land Surface Model: use 1 (Default: Catchment Model), 2 (CatchmentCN Model)

1

Do you wish to run the Runoff Routing Model? (Default: NO or FALSE)

NO

Do you wish to run GOCART with Actual or Climatological Aerosols? (Enter: A (Default) or C)

A

Enter the GOCART Emission Files to use: MERRA2 (Default), PIESA, CMIP, NR, MERRA2-DD or OPS:

MERRA2

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: (/discover/nobackup/jkouatch/GEOS_OCEAN/yuri-s2s3-unstable-SLES12/GEOSodas/src/Applications/GEOSgcm_App)

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

Hit ENTER to use Default Location:

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

Default: /gpfsm/dnb32/jkouatch/GEOS_OCEAN/yuri-s2s3-unstable-SLES12/test_odas

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

Hit ENTER to use Default Location:

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

Default: /gpfsm/dnb32/jkouatch/GEOS_OCEAN/yuri-s2s3-unstable-SLES12/test_odas

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

Hit ENTER to use Default Location:

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

Default: /discover/nobackup/jkouatch/GEOS_OCEAN/yuri-s2s3-unstable-SLES12/GEOSodas

Current GROUPS: k3002 a930b s0942 s1043 m2val j1008

Enter your GROUP ID for Current EXP: (Default: s1043)

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

sending incremental file list

GEOSgcm.x

sent 140,652,369 bytes received 35 bytes 93,768,269.33 bytes/sec

total size is 140,617,928 speedup is 1.00

Creating gcm_run.j for Experiment: test_odas

Creating gcm_archive.j for Experiment: test_odas

Creating gcm_regress.j for Experiment: test_odas

Creating gcm_convert.j for Experiment: test_odas

Creating gcm_plot.tmpl for Experiment: test_odas

Creating gcm_quickplot.csh for Experiment: test_odas

Creating gcm_moveplot.j for Experiment: test_odas

Creating gcm_stats.j for Experiment: test_odas

Creating gcm_forecast.tmpl for Experiment: test_odas

Creating gcm_forecast.setup for Experiment: test_odas

Creating gcm_emip.setup for Experiment: test_odas

Creating CAP.rc.tmpl for Experiment: test_odas

Creating AGCM.rc.tmpl for Experiment: test_odas

Creating GAAS_GridComp.rc.tmpl for Experiment: test_odas

Creating ocean_das_config.tmpl for Experiment: test_odas

Creating HISTORY.rc.tmpl for Experiment: test_odas

Creating input.nml for Experiment: test_odas

Creating diag_table for Experiment: test_odas

Creating field_table for Experiment: test_odas

Creating plotocn.j for Experiment: test_odas

Creating __init__.py for Experiment: test_odas

Creating fvcore_layout.rc for Experiment: test_odas

/bin/mv: '/gpfsm/dnb32/jkouatch/GEOS_OCEAN/yuri-s2s3-unstable-SLES12/test_odas/GAAS_GridComp.rc.tmpl' and '/gpfsm/dnb32/jkouatch/GEOS_OCEAN/yuri-s2s3-unstable-SLES12/test_odas/GAAS_GridComp.rc.tmpl' are the same file

Done!

-----

Build Directory: /discover/nobackup/jkouatch/GEOS_OCEAN/yuri-s2s3-unstable-SLES12/GEOSodas

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

The following executable has been placed in your Experiment Directory:

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

/discover/nobackup/jkouatch/GEOS_OCEAN/yuri-s2s3-unstable-SLES12/GEOSodas/Linux/bin/GEOSgcm.x

You must now copy your Initial Conditions into:

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

/gpfsm/dnb32/jkouatch/GEOS_OCEAN/yuri-s2s3-unstable-SLES12/test_odas

Copying Sandbox Source Code (including non-committed files) into /gpfsm/dnb32/jkouatch/GEOS_OCEAN/yuri-s2s3-unstable-SLES12/test_odas/src/GEOSagcm/src ...

Enter CVS Tag to COMMIT this Experiment (Default: test_odas__jkouatch)

Enter q or quit to QUIT or SKIP the CVS COMMIT:

q

=== Running the Code ===

After running the <code>gcm_setup</code> script, an experiment directory will be created.

Depending on your settings, you will have (among others) the following files (in the experiment directory) that are critical in running the <code>ODAS</code> configuration:

AGCM.rc.with_RECORD_OFF

AGCM.rc.with_RECORD_ON

GAAS_GridComp.rc.tmpl

ocean_das_config

You do not need to edit any of the above files unless you change the processor decomposition. In that case, the files <code>AGCM.rc.with_RECORD_OFF</code> and <code>AGCM.rc.with_RECORD_ON</code> need to be updated.

To run the code, you will need to create the <code>cap_restart</code> file. You may also need to edit the following files:

* <code>CAP.rc</code>: to set the end date.

* <code>HISTORY.rc</code>: to specify the collections you are interested in.

* <code>gcm_run.j</code>: to change the requested wallclock time (<code>-l walltime</code>) and the number of tasks (<code>--ntasks</code>).

* <code>input.nml</code>: to modify the <code>layout</code> settings in the <code>ocean_model_nml</code> section. This is tied to the settings in <code>AGCM.rc.with_RECORD_OFF</code> and <code>AGCM.rc.with_RECORD_ON</code>.

---------

To check out the model:

cvs co -r tag_name GEOSodas_m7,

@@ Line 1: / Line 1: @@
-== Coupled model build instructions ==
+= Coupled Model Build Instructions =
+This document describes the basic step to obtain, compile and execute the GEOS couple Ocean model.
+=== Obtain the Code ===
+The code is in a CVS repository. To obtain it, issue the command:
+    cvs co -P -r tag_name GEOSodas_m7
+where <code>tag_name</code> is the name of the CVS tag of interest. It can be for instance <code>yuri-s2s3-unstable-SLES12</code>.
+You will get a directory named <code>GEOSodas</code>.
+=== Compile the Code ===
+To compile the code, issue the following commands:
+     cd GEOSodas/src
+     source g5_modules
+     ./parallel_build.csh
+In the last command, you might be asked to provide a <code>sponsor code id</code> is if you have more than one on the platform you are using.
+An alternative method to compile the code is use a simple script (C-shell here) for a serial build. It assumes that that the script is located at the same level as the <code>GEOSodas/</code> directory.
+     #!/bin/csh -f
+     source /usr/share/modules/init/csh
+     set curDIR = `pwd`
+     setenv ESMADIR ${curDIR}/GEOSodas
+     cd $ESMADIR/src
+     module purge
+     source g5_modules
+     set CLEAN = 0
+     set MAKEALL = 1
+     set MAKEALLDEBUG = 0
+     if ($CLEAN) gmake realclean
+     if ($MAKEALLDEBUG) gmake install BOPT=g
+     if ($MAKEALL) gmake pinstall
+Regardless the method that you use to build the code, a directory named <code>Linux/</code> will be created inside <code>GEOSodas/</code>. The <code>Linux/</code> directory contains temporary files, libraries and executables created during the compilation process. To make sure that the code was successfully compiled, check that the file <code>GEOSgcm.x</code> exists in the directory <code>GEOSodas/src/Applications/GEOSgcm_App/</code>.
+=== Create the Experiment Directory ===
+After building the executable, we need to create an experiment directory. The code comes with a tool that allows you to do that. We recommend that you always go through this process whenever to start a new experiment.
+The first step is to go to the directory <code>GEOSodas/src/Applications/GEOSgcm_App/</code>. Then check that the following files are available:
+   AGCM.rc.tmpl GAAS_GridComp.rc.tmpl GEOSgcm.x gcm_run.j gcm_setup ocean_das_config.tmpl
+There are many other files in the directory but the above ones play an important role in setting the experiment directory and driving the model.
+The script <code>gcm_setup</code>, when executed, asks a series of questions to determine a set of parameters and input files needed to run the model.
+Issue the command:
+      ./gcm_setup
+and provide the information requested. When you are asked if:
+* You want to run the COUPLED Ocean/Sea-Ice Model, answer <code>YES</code>.
+* You want to to run the REPLAY DUAL OCEAN Model, answer
+** <code>YES</code> is you intend to run <code>ODAS</code>.
+** <code>NO</code> otherwise.
+The available resolutions are:
+ | Atmosphere | Ocean                           |
+ | ---------- | ------------------------------- |
+  | c90x72     | 360x200x50                      |
+ | c180x72    | 720x410x40                      |
+ | c180x72    | 1440x1080x50 (S2Sv3 resolution) |
+When you are asked which history template do you want to use, you may choose <code>HISTORY.AOGCM.rc.tmpl</code> or <code>HISTORY.S2S.rc.tmpl</code>. All other parameters may be left default. If the `ODAS` configuration is selected, the entire <code>GEOSodas/src/Applications/UMD_Etc/</code> directory will be copied into the <code>ocean_das</code> directory located in the experiment directory.
+When you are asked which history template do you want to use, you may choose <code>HISTORY.AOGCM.rc.tmpl</code> or <code>HISTORY.S2S.rc.tmpl</code>. All other parameters may be left default. If the <code>ODAS</code> configuration is selected, the entire <code>GEOSodas/src/Applications/UMD_Etc/</code> directory will be copied into the <code>ocean_das</code> directory located in the experiment directory.
+Here, we provide a sample dialogue:
+     Enter the Experiment ID:
+          test_odas
+     Enter a 1-line Experiment Description:
+          Test ODAS
+     Do you wish to CLONE an old experiment? (Default: NO or FALSE)
+          NO
+     Enter the Atmospheric Horizontal Resolution code:
+     -----------------------------------------------------------
+     Lat/Lon                     Cubed-Sphere
+     -----------------------------------------------------------
+        b --  2  deg                c48  --  2   deg
+        c --  1  deg                c90  --  1   deg
+        d -- 1/2 deg                c180 -- 1/2  deg (56-km)
+        e -- 1/4 deg (35-km)        c360 -- 1/4  deg (28-km)
+                                    c720 -- 1/8  deg (14-km)
+                                    c1440 - 1/16 deg ( 7-km)
+                                              DYAMOND Grids
+                                    c768 -- 1/8  deg (12-km)
+                                    c1536 - 1/16 deg ( 6-km)
+                                    c3072 - 1/32 deg ( 3-km)
+          c180
+     Enter the Atmospheric Model Vertical Resolution: LM (Default: 72)
+     Do you wish to run the COUPLED Ocean/Sea-Ice Model? (Default: NO or FALSE)
+          Yes
+     Enter the Ocean Lat/Lon Horizontal Resolution: IM JM (Default: 360 200)
+1080
+     Enter the Ocean Model Vertical Resolution: LM (Default: 50)
+     Do you wish to run the REPLAY DUAL OCEAN Model? (Default: NO or FALSE)
+          YES
+     Do you wish to run the AODAS Model? (Default: NO or FALSE)
+          YES
+     Enter the choice of  Restart Record Parameters: Frequency (hhmmss): (Default: 240000)
+     Enter the choice of  Restart Record Parameters: Reference Date (YYYYMMDD): (Default: 19800101)
+          19800101
+     Enter the choice of  Restart Record Parameters: Reference Time (hhmmss): (Default: 210000)
+     Enter the choice of  Land Surface Model: use 1 (Default: Catchment Model), 2 (CatchmentCN Model)
+     Do you wish to run  the Runoff Routing Model? (Default: NO or FALSE)
+          NO
+     Do you wish to run GOCART with Actual or Climatological Aerosols? (Enter: A (Default) or C)
+          A
+     Enter the GOCART Emission Files to use: MERRA2 (Default), PIESA, CMIP, NR, MERRA2-DD or OPS:
+          MERRA2
+     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: (/discover/nobackup/jkouatch/GEOS_OCEAN/yuri-s2s3-unstable-SLES12/GEOSodas/src/Applications/GEOSgcm_App)
+     Enter Desired Location for the HOME Directory (to contain scripts and RC files)
+     Hit ENTER to use Default Location:
+     ----------------------------------
+     Default:  /gpfsm/dnb32/jkouatch/GEOS_OCEAN/yuri-s2s3-unstable-SLES12/test_odas
+     Enter Desired Location for the EXPERIMENT Directory (to contain model output and restart files)
+     Hit ENTER to use Default Location:
+     ----------------------------------
+     Default:  /gpfsm/dnb32/jkouatch/GEOS_OCEAN/yuri-s2s3-unstable-SLES12/test_odas
+     Enter Location for Build directory containing:  src/ Linux/ etc...
+     Hit ENTER to use Default Location:
+     ----------------------------------
+     Default:  /discover/nobackup/jkouatch/GEOS_OCEAN/yuri-s2s3-unstable-SLES12/GEOSodas
+     Current GROUPS: k3002 a930b s0942 s1043 m2val j1008
+     Enter your GROUP ID for Current EXP: (Default: s1043)
+     -----------------------------------
+     sending incremental file list
+     GEOSgcm.x
+     sent 140,652,369 bytes  received 35 bytes  93,768,269.33 bytes/sec
+     total size is 140,617,928  speedup is 1.00
+     Creating gcm_run.j for Experiment: test_odas
+     Creating gcm_archive.j for Experiment: test_odas
+     Creating gcm_regress.j for Experiment: test_odas
+     Creating gcm_convert.j for Experiment: test_odas
+     Creating gcm_plot.tmpl for Experiment: test_odas
+     Creating gcm_quickplot.csh for Experiment: test_odas
+     Creating gcm_moveplot.j for Experiment: test_odas
+     Creating gcm_stats.j for Experiment: test_odas
+     Creating gcm_forecast.tmpl for Experiment: test_odas
+     Creating gcm_forecast.setup for Experiment: test_odas
+     Creating gcm_emip.setup for Experiment: test_odas
+     Creating CAP.rc.tmpl for Experiment: test_odas
+     Creating AGCM.rc.tmpl for Experiment: test_odas
+     Creating GAAS_GridComp.rc.tmpl for Experiment: test_odas
+     Creating ocean_das_config.tmpl for Experiment: test_odas
+     Creating HISTORY.rc.tmpl for Experiment: test_odas
+     Creating input.nml for Experiment: test_odas
+     Creating diag_table for Experiment: test_odas
+     Creating field_table for Experiment: test_odas
+     Creating plotocn.j for Experiment: test_odas
+     Creating __init__.py for Experiment: test_odas
+     Creating fvcore_layout.rc for Experiment: test_odas
+     /bin/mv: '/gpfsm/dnb32/jkouatch/GEOS_OCEAN/yuri-s2s3-unstable-SLES12/test_odas/GAAS_GridComp.rc.tmpl' and '/gpfsm/dnb32/jkouatch/GEOS_OCEAN/yuri-s2s3-unstable-SLES12/test_odas/GAAS_GridComp.rc.tmpl' are the same file
+     Done!
+     -----
+     Build Directory: /discover/nobackup/jkouatch/GEOS_OCEAN/yuri-s2s3-unstable-SLES12/GEOSodas
+     ----------------
+     The following executable has been placed in your Experiment Directory:
+     ----------------------------------------------------------------------
+     /discover/nobackup/jkouatch/GEOS_OCEAN/yuri-s2s3-unstable-SLES12/GEOSodas/Linux/bin/GEOSgcm.x
+     You must now copy your Initial Conditions into:
+     -----------------------------------------------
+     /gpfsm/dnb32/jkouatch/GEOS_OCEAN/yuri-s2s3-unstable-SLES12/test_odas
+     Copying Sandbox Source Code (including non-committed files) into /gpfsm/dnb32/jkouatch/GEOS_OCEAN/yuri-s2s3-unstable-SLES12/test_odas/src/GEOSagcm/src ...
+     Enter CVS Tag to COMMIT this Experiment (Default: test_odas__jkouatch)
+     Enter q or quit to QUIT or SKIP the CVS COMMIT:
+          q
+=== Running the Code ===
+After running the <code>gcm_setup</code> script, an experiment directory will be created.
+Depending on your settings, you will have (among others) the following files (in the experiment directory) that are critical in running the <code>ODAS</code> configuration:
+    AGCM.rc.with_RECORD_OFF
+    AGCM.rc.with_RECORD_ON
+    GAAS_GridComp.rc.tmpl
+    ocean_das_config
+You do not need to edit any of the above files unless you change the processor decomposition. In that case, the files <code>AGCM.rc.with_RECORD_OFF</code> and <code>AGCM.rc.with_RECORD_ON</code> need to be updated.
+To run the code, you will need to create the <code>cap_restart</code> file. You may also need to edit the following files:
+* <code>CAP.rc</code>: to set the end date.
+* <code>HISTORY.rc</code>: to specify the collections you are interested in.
+* <code>gcm_run.j</code>: to change the requested wallclock time (<code>-l walltime</code>) and the number of tasks (<code>--ntasks</code>).
+* <code>input.nml</code>: to modify the <code>layout</code> settings in the <code>ocean_model_nml</code> section. This is tied to the settings in <code>AGCM.rc.with_RECORD_OFF</code> and <code>AGCM.rc.with_RECORD_ON</code>.
+---------
+---------
 To check out the model:
   cvs co -r tag_name GEOSodas_m7,