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README.agcm
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README.agcm
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This file contains information on checking-out, building, and running the GMAO GEOS-5 AGCM.
MODEL_TAG : Fortuna-2_5_p1
MODEL_MODULE: Fortuna
Date: 04Oct2011
#######################################################################
# NEW FEATURES
# (For additional information, see the AGCM ChangeLog)
#######################################################################
NEW FEATURES from Fortuna-2_2
-----------------------------
a) Added options for running with GOCART/CMIP aerosol emission files.
b) Added plot.rc to control monthly mean plotting options.
c) Added option to run PERPETUAL cases (perpetual year, perpetual month, perpetual day).
NEW FEATURES from Fortuna-2_1
-----------------------------
a) Changed default behavior of HISTORY attribute: duration. The NEW default is: duration = frequency
This means that the default behavior will produce 1 time-record per file.
This creates a more robust environment (using gcm_setup) for the post-processing to correctly compute monthly means.
Choosing durations other than the output frequency can create problems for the monthly mean scripts.
#######################################################################
# Basic Build and Run Procedures
#######################################################################
1) Checking out and building the GMAO GEOS-5 AGCM from CVS
----------------------------------------------------------
Set Environment Variables:
--------------------------
setenv CVS_RSH ssh
setenv CVSROOT :ext:$LOGNAME@progressdirect:/cvsroot/esma
Create a directory in your scratch area with the name of the model tag:
eg) mkdir /discover/nobackup/$LOGNAME/MODEL_TAG
cd /discover/nobackup/$LOGNAME/MODEL_TAG
Within that directory, use the cvs "co" command to check-out the model with the syntax:
cvs co -r MODEL_TAG MODEL_MODULE
This will create a directory tree containing the GEOS-5 AGCM.
Go to the model's source directory and issue the commands:
cd /discover/nobackup/$LOGNAME/MODEL_TAG/GEOSagcm/src
source g5_modules
gmake install
This "source" command will install the proper operating system modules and libraries for compilation.
The "gmake" command will perform the model build.
When completed, a model executable (GEOSgcm.x) will be created.
A copy can be found in:
... /MODEL_TAG/GEOSagcm/src/Applications/GEOSgcm_App
2) Running the GMAO GEOS-5 AGCM
-------------------------------
Go to the GCM applications directory:
cd ... /MODEL_TAG/GEOSagcm/src/Applications/GEOSgcm_App
Type the command: gcm_setup
You will be prompted to answer a few questions:
a) Enter the Experiment ID:
b) Enter a 1-line Experiment Description:
c) Enter the Model Horizontal Resolution:
d) Enter the Model Vertical Resolution:
e) Option to run Coupled Ocean/Atmosphere:
f1) Option to run GOCART:
f2) If GOCART, Choose Emission Files:
g) Enter the AERO_PROVIDER:
h) Enter the Desired HISTORY File to use:
i) Enter the Desired Location for HOME Directory:
j) Enter the Desired Location for EXPERIMENT Directory:
k) Enter the BUILD Location:
l) Enter your GROUP ID:
Details:
--------
a) The Experiment ID should be an easily identifiable name representing each individual experiment
you create. One possibility is your initials followed by a 3-digit number: eg) abc001
b) The Experiment Description should be a concise statement describing the relevant nature of your experiment.
c) Model Horizontal Resolution Options:
72 46 (~ 4 -deg)
144 91 (~ 2 -deg)
288 181 (~ 1 -deg)
576 361 (~1/2-deg)
1152 721 (~1/4-deg)
d) Model Vertical Resolution Options:
72
e) Coupled Ocean/Atmosphere Options:
NO
f1) GOCART Options:
YES, NO (Default)
f2) GOCART Emission File Options:
CMIP, MERRA2, NR, PIESA (Default), OPS
g) The AERO PROVIDER describes the Chemistry Component to be used for Radiatively Active Aerosols.
PCHEM is the default used for most AMIP-style Climate Runs.
h) The default HISTORY.rc will be included in the TAG. Users can replace this with their own HISTORY.rc
i) The HOME directory will contain your run scripts and primary resource (rc) files.
j) The EXPERIMENT directory will contain your restarts and model output.
The HOME and EXPERIMENT directories can be the same, eg) /discover/nobackup/$LOGNAME/abc001
k) The BUILD directory to locate GEOSgcm.x in addition to various model utilities.
l) Your GROUP ID is your charge code used for NCCS accounting.
3) The GEOS-5 AGCM HOME Directory
---------------------------------
Within the HOME directory you will find the gcm run and regression scripts, and the primary resource files:
scripts
-------
gcm_run.j (For Forecasts and AMIP-Style Climate Runs)
gcm_regress.j (For developer's regression testing)
resource files
--------------
CAP.rc
AGCM.rc
HISTORY.rc
4) The GEOS-5 AGCM EXPERIMENT Directory
---------------------------------------
Within the EXPERIMENT directory you will find the model executable and four additional directories for use in post-processing,
plotting, and archiving:
executable
----------
GEOSgcm.x
directories
-----------
RC (contains additional resource files, primarily for GOCART Chemistry)
post (contains gcm_post.j to run post-processing jobs)
plot (contains gcm_plot.j plot.rc to run plotting jobs)
archive (contains gcm_archive.j to run archiving jobs)
Within this EXPERIMENT directory the user must provide a set of initial conditions for the model.
The complete set includes:
Critical Restarts
-----------------
cap_restart (ascii file containing Date and Time: YYYYMMDD HHMMSS)
fvcore_internal_rst
moist_internal_rst
catch_internal_rst
lake_internal_rst
landice_internal_rst
saltwater_internal_rst
Boot-strapable Restarts
-----------------------
pchem_internal_rst
solar_internal_rst
irrad_internal_rst
turb_internal_rst
saltwater_import_rst
surf_import_rst
turb_import_rst
moist_import_rst
Notice that these restart filenames are generic in the sense that they do not contain date and time information.
The date and time information is simply kept in the ascii file: cap_restart
This generic naming is essential for proper use of the run scripts.
Creating and/or Regridding Restarts
-----------------------------------
A simple utility exists which will create the critical restarts needed starting from the MERRA Re-Analysis.
The utility "regrid" can be found in your build under:
.../src/GMAO_Shared/GEOS_Util/post
To create restarts from MERRA, simply type:
regrid -nymd YYYYMMDD
-im IM
-jm JM
-out DIRECTORY
where: YYYYMMDD is the desired Date from the MERRA Re-Analysis
IM is the desired Zonal Dimension for ReGridding
JM is the desired Meridional Dimension for ReGridding
DIRECTORY is the full pathname of the desired OUTPUT location
The utility will fetch the restarts from the MERRA Re-Analysis and properly regrid them to the user-supplied
resolution IM,JM. The resulting restarts will be placed in the user-supplied output directory.
An alternative method for creating restarts is to regrid them from an existing set at another resolution.
To do this, the "regrid" utility may again be used:
regrid -rc REGRIDRC
-out DIRECTORY
where: REGRIDRC is the full pathname of a user-defined regrid.rc file
DIRECTORY is the full pathname of the desired OUTPUT location
The regrid.rc file contains all the necessary information needed to properly regrid a set of restarts.
A template for this file can be found under:
.../src/GMAO_Shared/GEOS_Util/post
The user simply needs to fill in the full pathname locations and resolution of the existing restart files, and the
desired output resolution. In addition, the Boundary Condition Tag needs to be identified. This tag will generally be
the one associated with the latest Boundary Condition version (Fortuna-2_1) or the one associated with MERRA (Fortuna-1_4).