Regridding Restarts for Jason 3.0
Here are basic instructions on how to create restart files for Jason 3.0. Due to changes in the tiling it is not possible to use restarts from older versions of GEOS-5 without converting them with the regrid.pl script.
Back to GEOS-5 Documentation for Jason 3.0
Using the regrid.pl Script
Restarts can be easily created from MERRA2 data or other model-generated sources using the regrid.pl script in Linux/bin/ (above src/) -- this script is different from, and is specifically a wrapper for, the regrid script used in earlier versions. The regrid.pl script is created when make install is run. The same script can regrid restarts between different versions of Fortuna 1.4 to Jason 3.0 at any resolution.
Running regrid.pl -h (after running source g5_modules) -- with the -h for help -- tells the story:
NAME
regrid.pl
PURPOSE
Wrapper script for programs which regrid GCM restarts
SYNOPSIS
regrid.pl yyyymmdd hr gridID outdir [options]
REQUIRED INPUTS
-----------------------------
as ordered runtime parameters
-----------------------------
yyyymmdd 8-digit date of the restarts being regridded
hr 2-digit hour of the restarts being regridded
grOUT grid ID of the output restarts (see GRID IDENTIFIERS below)
outdir directory location for output restarts
--------------------
or as flagged values
--------------------
-ymd yyyymmdd
-hr hr
-grout grOUT
-outdir outdir
REQUIRED OPTION FOR MERRA INPUTS
-merra (same as -merra1)
-merra1 get input restarts from OPS MERRA-1 data archives
-merra2 get input restarts from OPS MERRA-2 data archives
REQUIRED OPTIONS FOR NON-MERRA INPUTS
-d rstdir location of input restart files
-expid expid experiment ID of input restart files
INTERACTIVE OPTION
-i prompt for inputs that are not supplied
(this is the default if no inputs are supplied)
-np no prompt; take defaults for all prompts;
note: the -np flag takes precedence over the -i flag
OTHER OPTIONS
-levsout levsout number of atmosphere levels in output
-oceanin oceanIN ocean horizontal grid of inputs
=c : 1-deg (360x180); e.g. Reynolds
=e : 1/4-deg (1440x720); e.g. MERRA-2
=f : 1/8-deg (2880x1440); e.g. OSTIA
defaults to 'c'
-oceanout oceanOUT ocean horizontal grid of outputs (see -oceanIN)
-esmabin ESMABIN location of build's scripts and programs; defaults to location
of regrid.pl script
-iceDT dtime datetime for alternate landice rst input if regridding to
'Ganymed-2_0' from earlier tag; dtime should have the
following format: -iceDT yyyymmdd_hh
if dtime is not provided or if no restarts can be found to
match dtime, then script will prompt user from list of
available datetimes.
if dtime eq '0', then alternate landice rst will not be used
-newid newid label to replace expid in output restart names;
defaults to 'n-expid' where n is OUTPUT atmosphere grid ID
-tagin tagIN GCM or DAS tag associated with inputs (see TAGS below);
defaults to Ganymed-4_0
-tagout tagOUT GCM or DAS tag associated with outputs (see TAGS below);
defaults to Ganymed-4_0
-rs flag flag indicating which restarts to regrid
=1 for upper-air restarts only
=2 for land-surface restarts only
=3 for both upper-air and land-surface restarts (default)
-catchcn Create a version of the catch restart which contains carbon values;
Not valid for tags prior to Heracles; Note: This option will add
10-20 minutes to the regrid process.
-route write the route_internal_rst
-[no]bkg copy and rename input bkg + satbang/bias files
-[no]lbl label final restarts with 'tagID.gridID' extension
-[no]lcv create rst.lcv file for final restarts
-gcm gcm mode; equivalent to -nobkg, -lbl, and -nolcv flags
-grpid group id; sponsor code to use for batch job charge
-qos debug use SBATCH --qos=debug directive for batch jobs,
if job meets --qos=debug requirements
-db (debug mode) Do not clean work directory after running programs;
-dbh (debug hash) Show contents of hashes: %IN and %OUT
-v verbose mode
-h[elp] print usage message
GRID IDENTIFIERS
Atmosphere Horizontal Grids
===========================
latlon grids im jm
------------ -- --
a = 4x5 72 46
b = 2x2.5 144 91
c = 1x1.25 288 181
D = 0.5x0.666 540 361
d = 0.5x0.625 572 361
E = 0.25x0.3330 1080 721
e = 0.25x0.3125 1152 721
cubed-sphere grids
------------------
Cn, where n = {24, 48, 90, 180, 360, 500, 720, 1000, 1440, 2000, 2880}
Ocean Horizontal Grids
======================
c = 1-deg (360x180); e.g. Reynolds
e = 1/4-deg (1440x720) ; e.g. MERRA-2
f = 1/8-deg (2880x1440); e.g. OSTIA
TAGS
Use GCM or DAS tag names with -tagin and -tagout flags
Sample GCM tags
---------------
F14 : Fortuna-1_4 ............ Fortuna-1_4_p1
F21 : Fortuna-2_1 ............ Fortuna-2_5_pp2
G10 : Ganymed-1_0 ............ Ganymed-1_0_BETA4
G10p : Ganymed-1_0_p1 ......... Ganymed-1_0_p6
G20 : Ganymed-2_0 ............ Ganymed-2_1_p6
G30 : Ganymed-3_0 ............ Ganymed-3_0_p1
G40 : Ganymed-4_0 ............ Heracles-5_4_p3
HNL : Heracles-NL ............ Heracles-NL
Sample DAS tags
---------------
214 : GEOSdas-2_1_4 .......... GEOSdas-2_1_4-m4
540 : GEOSadas-5_4_0 ......... GEOSadas-5_5_3
561 : GEOSadas-5_6_1 ......... GEOSadas-5_7_3_p2
580 : GEOSadas-5_8_0 ......... GEOSadas-5_9_1
591p : GEOSadas-5_9_1_p1 ...... GEOSadas-5_9_1_p9
5A0 : GEOSadas-5_10_0 ........ GEOSadas-5_10_0_p1
5B0 : GEOSadas-5_10_0_p2 ..... GEOSadas-5_11_0
512 : GEOSadas-5_12_2 ........ GEOSadas-5_16_5
So the following will create restarts in C180 (roughly equivalent to ½-degree lat-lon) resolution, on the ¼-degree ocean from MERRA2 on the first day of 2012 and put them in /discover/nobackup/mathomp4/Regrid:
./regrid.pl -ymd 20120101 -hr 21 -grout C180 -outdir /discover/nobackup/mathomp4/Regrid -merra -tagout Icarus -oceanout e
The above presents the minimum options to get a working set of restarts -- anything lacking will be requested interactively. Your selections will be presented for your review before the script does any heavy lifting. The script may appear to stall while it waits for the relevant MERRA or MERRA-2 files to be retrieved from the /archive filesystem.
For sources other than MERRA/MERRA-2, you will have to specify the location of a regrid resource file that contains the model version, resolution and location of the source restarts, and the resolution of the output restarts. A sample regrid resource file is regrid.rc in the same directory as the regrid script. Note that regrid only works for creating restarts for its model tag, and does not work at all for making restarts for tags before Jason 3.0. Restarts for earlier model tags have to be created "manually".
Renaming Restart Files
At this point you will have restart files with a fair bit of cruft in the filenames. As described above, they will have to be renamed for the model to recognize them. There are a number of scripts with different techniques for completing this tedious chore; here is one example:
#!/usr/bin/env python
import re
import os
# Open file for reading
dirlist = os.listdir(".")
for file in dirlist:
if( re.search(".*rst.*",file) ):
print file
# the concept is to match ??????.something_rst.??????? OR something_rst.????????
# and extract "something_rst"
newfile = re.sub(r'(^.+\.|^)([a-z_]+rst)\..+$',r'\2',file)
print newfile
if cmp(newfile,file):
os.symlink(file,newfile)
It will grab anything in the current working directory resembling the common forms of restart filename generated by the regridding scripts and other utilities and create symbolic links to them in the same directory with the superfluous parts of the filenames stripped. In an experiment directory the links will be overwritten by the model with "fresh" restart files at the end of a run segment. Alternatively, you can easily copy the restart files with cp *rst
Required Restarts
A few of the restart files are critical and need to be present for the model to function, while others can be "bootstrapped": the model is started without them and then it generates the restarts in order to save state for the next restart.
The following restart files are critical and need to be regridded:
fvcore_internal_rst(atmosphere)moist_internal_rst(atmosphere)catch_internal_rst(surface)
The following surface restarts should be regridded, but can be bootstrapped:
vegdyn_internal_rstlandice_internal_rstlake_internal_rstsaltwater_internal_rst
Optional (boot-strappable) restarts:
pchem_internal_rstgocart_internal_rstturb_internal_rstsaltwater_import_rstsurf_import_rstturb_import_rstmoist_import_rst
For DAS runs, you may also interpolate:
agcm_import_rst
The restarts irrad_internal_rst and solar_internal_rst should not be regridded from versions earlier than Fortuna 2.5, as they must be bootstrapped.
Note: if the grid dimensions are the same SOME restarts from earlier model versions may be used , while other may not.
fvcore_internal_rstandmoist_internal_rstmay be used directly from earlier versions.catch_internal_rst,lake_internal_rst,landice_internal_rst, andsaltwater_internal_rstmust be re-gridded due to new land surface tile data- All other restarts from earlier versions should be boot-strapped.