Setting up S2Sv3 model

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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 tag_name is the name of the CVS tag of interest. It can be for instance yuri-s2s3-unstable-SLES12.

You will get a directory named GEOSodas.

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 sponsor code id 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 GEOSodas/ 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 Linux/ will be created inside GEOSodas/. The Linux/ 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 GEOSgcm.x exists in the directory GEOSodas/src/Applications/GEOSgcm_App/.

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 GEOSodas/src/Applications/GEOSgcm_App/. 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 gcm_setup, 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 YES.
  • You want to to run the REPLAY DUAL OCEAN Model,
    • Answer YES if you want to have the option of running ODAS.


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 HISTORY.AOGCM.rc.tmpl or HISTORY.S2S.rc.tmpl. All other parameters may be left default. If the `ODAS` configuration is selected, the entire GEOSodas/src/Applications/UMD_Etc/ directory will be copied into the ocean_das directory located in the experiment directory.

When you are asked which history template do you want to use, you may choose HISTORY.AOGCM.rc.tmpl or HISTORY.S2S.rc.tmpl. All other parameters may be left default. If the ODAS configuration is selected, the entire GEOSodas/src/Applications/UMD_Etc/ directory will be copied into the ocean_das 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 gcm_setup 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 ODAS 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 AGCM.rc.with_RECORD_OFF and AGCM.rc.with_RECORD_ON need to be updated.

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

  • CAP.rc: to set the end date.
  • HISTORY.rc: to specify the collections you are interested in.
  • gcm_run.j: to change the requested wallclock time (-l walltime) and the number of tasks (--ntasks).
  • input.nml: to modify the layout settings in the ocean_model_nml section. This is tied to the settings in AGCM.rc.with_RECORD_OFF and AGCM.rc.with_RECORD_ON.


To check out the model: 

cvs co -r tag_name GEOSodas_m7,

where 

tag_name = yuri-s2s3-unstable for SLES11
tag_name = yuri-s2s3-unstable-SLES12 for SLES12

Note: You can use either tag on pfe. They are identical besides different modules.

To build the model: 

cd GEOSodas/src
source g5_modules
setenv ESMADIR path_to_sandbox (GEOSodas)
make install

To build with debug options: 

make BOPT=g install

To set up experiment

cd Applications/GEOSgcm_App
./gcm_setup

When you are asked if you want to run a coupled model, answer 'yes'. Available resolutions are: 

c90x72 atmosphere, 360x200x50 ocean;
c180x72 atmosphere, 720x410x40 ocean;
c180x72 atmosphere, 1440x1080x50 ocean. This is S2Sv3 resolution.

When you are asked which history template do you want to use, you may choose HISTORY.AOGCM.rc.tmpl or HISTORY.S2S.rc.tmpl. All other parameters may be left default.

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