GEOS-5

Regridding restarts for Fortuna 2.2

Revision as of 08:17, 29 November 2010 by Andrew.eichmann (talk | contribs) (→Creating restarts from scratch)

Here are basic instructions on how to regrid restarts, based on a README by Larry Takacs.

Creating restarts from scratch

If you lack a set of restarts for the appropriate date, you can derive yours from MERRA. MERRA restarts are available on the NCCS discover cluster under the following directories: 

/archive/g_proj5/production/GEOSdas-2_1_4/d5_merra_jan79/rs/
/archive/g_proj5/production/GEOSdas-2_1_4/d5_merra_jan89/rs/
/archive/g_proj5/production/GEOSdas-2_1_4/d5_merra_jan98/rs/

Restarts are in subdirectories according to their respective year and month. The are in the form (as an example) d5_merra_jan79.catch_internal_rst.19910128_21z.bin, which you would otherwise know as catch_internal_rst (with the appropriate cap_restart). Be aware that a cp from /archive may appear to hang initially -- sometimes for hours -- while the appropriate tape is queued for mounting.

Required Restarts

A few of the restart files are critical for model function and need to be compatible to the model version, 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_rst
  • landice_internal_rst
  • lake_internal_rst
  • saltwater_internal_rst

Optional (boot-strappable) restarts:

  • pchem_internal_rst
  • gocart_internal_rst
  • solar_internal_rst
  • irrad_internal_rst
  • turb_internal_rst
  • saltwater_import_rst
  • surf_import_rst
  • turb_import_rst
  • moist_import_rst

For DAS runs, you may also interpolate:

  • agcm_import_rst

Note: if the grid dimensions are the same SOME restarts from earlier model versions may be used , while other may not.

  • fvcore_internal_rst and moist_internal_rst may be used directly from earlier versions.
  • catch_internal_rst, lake_internal_rst, landice_internal_rst, and saltwater_internal_rst must be re-gridded due to new land surface tile data
  • All other restarts from earlier versions should be boot-strapped.

Regridding Upper-Air Related Restarts

Within your build, go to the directory: 

 src/GMAO_Shared/GEOS_Util/post

Running make rs_hinterp.x using the same environment for building the model (that is, after running source g5_modules) should produce the executable: 

rs_hinterp.x

Running rs_hinterp.x shows the usage: 

> ./rs_hinterp.x
Usage:

rs_hinterp_$ARCH.x -dyn      DYNRST
                   -moist    MOISTRST
                   -other    OtherRST1 OtherRST2 OtherRST3 ...
                   -topo_old TOPO_OLD
                   -topo_new TOPO_NEW
                   -im       IM_OUT
                   -jm       JM_OUT

where:

  -dyn         DYNRST:  Filename for DYNAMICS_INTERNAL_RESTART
  -moist     MOISTRST:  Filename for    MOIST_INTERNAL_RESTART
  -other     OtherRST:  Filename for Other Flat Binary_RESTART
  -topo_old  TOPO_OLD:  Filename for OLD Topography (associated with INPUT  resolution)
  -topo_new  TOPO_NEW:  Filename for NEW Topography (associated with OUTPUT resolution)
  -im          IM_OUT:  IM Dimension for Output
  -jm          JM_OUT:  JM Dimension for Output


So, as an example, to regrid from an existing 2x2.5-deg set of restarts to 1x1.25-deg, you have: 

rs_hinterp_$ARCH.x -dyn      fvcore_internal_rst
                    -moist    moist_internal_rst
                    -other    pchem_internal_rst  gocart_internal_rst
                    -topo_old TOPO_OLD
                    -topo_new TOPO_NEW
                    -im       288
                    -jm       181

where TOPO_OLD is linked to: 

/discover/nobackup/ltakacs/bcs/Fortuna-2_1/144x91/topo_DYN_ave_144x91_DC.data

and TOPO_NEW is linked to: 

/discover/nobackup/ltakacs/bcs/Fortuna-2_1/288x181/topo_DYN_ave_288x181_DC.data

Topography files for different Fortuna versions can be found under /discover/nobackup/ltakacs/bcs/. Fortuna 2.1 topography files are used regridding restarts for Fortuna 2.2, and Fortuna 1.4 540x361 topography files are used for regridding from MERRA.

Running the above will produce: 

fvcore_internal_rst.0288x0181
moist_internal_rst.0288x0181
pchem_internal_rst.0288x0181
gocart_internal_rst.0288x0181

These are the finished restarts. They will have to be renamed -- truncated after rst -- in order to be recognized by the model in its standard configuration.

Note that even if you have no restarts that fall under the -other option, you still have to include that option (with nothing after it) in the command.

Regridding Land-Surface Related Restarts

Within your build, go to: 

src/GEOSgcs_GridComp/GEOSgcm_GridComp/GEOSagcm_GridComp/GEOSphysics_GridComp/ ...
GEOSsurface_GridComp/GEOSland_GridComp/GEOScatch_GridComp/mk_restarts

At this point it is best to update your directory to the HEAD of CVS to be sure you have the latest datasets: 

cvs upd -A

Under the mk_restarts directory you have the directories: 

InData
OutData

The basic idea is:

  1. Put your existing land-related restarts in the InData directory
  2. Put the appropriate tile file for your current resolution in the InData directory
  3. Put your target resolution tile file and appropriate clsm directory in the OutData directory

Where to find the appropriate tile file depends on the Fortuna versions you are regridding from and to, and is detailed below.

Run mk_Restarts

Your regridded restarts will be produced in the OutData directory.

Old and New Tile Files

There are two possible scenarios for regridding land-surface related restarts:

  1. Converting existing restarts to resolutions: 144x91, 288x181, 540x361, 1080x721 (old tile files for Fortuna 1.4 and earlier)
  2. Converting existing restarts to resolutions: 144x91, 288x181, 576x361, 1152x721 (new tile files for Fortuna 1.5 and later)


The old tile files are currently archived in: 

/discover/nobackup/ltakacs/bcs/Fortuna-1_4/144x91/FV_144x91_DC_360x180_DE.til
/discover/nobackup/ltakacs/bcs/Fortuna-1_4/288x181/FV_288x181_DC_360x180_DE.til
/discover/nobackup/ltakacs/bcs/Fortuna-1_4/540x361/FV_540x361_DC_360x180_DE.til
/discover/nobackup/ltakacs/bcs/Fortuna-1_4/1080x721/FV_1080x721_DC_360x180_DE.til

The new tile files and clsm directories are located in: 

/discover/nobackup/ltakacs/bcs/Fortuna-2_1/144x91/FV_144x91_DC_360x180_DE.til
/discover/nobackup/ltakacs/bcs/Fortuna-2_1/288x181/FV_288x181_DC_360x180_DE.til
/discover/nobackup/ltakacs/bcs/Fortuna-2_1/576x361/FV_576x361_DC_360x180_DE.til
/discover/nobackup/ltakacs/bcs/Fortuna-2_1/1152x721/FV_1152x721_DC_360x180_DE.til

(These work for Fortuna 2.2 as well, and are identical to those in /discover/nobackup/ltakacs/bcs/Fortuna-2_1

Depending on which tile file you are regridding to, there are two procedures:

1) Target tile file is from OLD set (model tags Fortuna-1_4 and earlier)

Since your target tile file is OLD (and not consistent with the new mosaic_veg_typs_fracs data), you have to remove the mosaic_veg_typs_fracs file from the InData direcory (or simply rename it, eg: mosaic_veg_typs_fracs.hold). In its place you have to copy the OLD nirdf.dat, visdf.dat, and lai_grn_clim boundary condition datasets into the InData directory. These can be found in the corresponding /discover/nobackup/ltakacs/bcs/Fortuna-1_4 directories. Note, the names that the Fortran program is looking for are not the same names in our bcs directory. Therefore you need to link the old datasets to the proper names. For example, regridding FROM the old 540x361 resolution (eg. MERRA), you should have:

nirdf.dat -> /discover/nobackup/ltakacs/bcs/Fortuna-1_4/540x361/nirdf_540x361_DC.dat

visdf.dat -> /discover/nobackup/ltakacs/bcs/Fortuna-1_4/540x361/visdf_540x361_DC.dat

lai_grn_clim -> /discover/nobackup/ltakacs/bcs/Fortuna-1_4/540x361/lai_green_clim_540x361_DC.data

2) Target tile file is from NEW set (model tags Fortuna-1_5 and later)

In this case, the target tile files are consistent with the mosaic_veg_typs_fracs dataset which resides in the InData directory. Therefore you do not have link in the old nirdf.dat, visdf.dat, and lai_grn_clim datasets. For Fortuna 2.2 you do have to copy or link the clsm directory in directory with the appropriately-dimensioned tile files.

Bootstrapping for a Complete Set of Restarts

The above procedure produces all the necessary restart files for the model to run, but others are needed for proper function. The model can produce them starting from the minimal set created by the regridding procedure; this requires some modification of the AGCM.rc file in your experiment home directory (probably under your account home directory).

In AGCM.rc -- you probably want to keep a copy of the default version for normal runs -- and using turb_import_rst as an example, comment out the lines referring to RESTART: 

TURBULENCE_IMPORT_RESTART_FILE:         turb_import_rst
TURBULENCE_IMPORT_RESTART_TYPE:         binary 
TURBULENCE_IMPORT_CHECKPOINT_FILE:      turb_import_checkpoint
TURBULENCE_IMPORT_CHECKPOINT_TYPE:      binary

#TURBULENCE_IMPORT_RESTART_FILE:         turb_import_rst
#TURBULENCE_IMPORT_RESTART_TYPE:         binary
TURBULENCE_IMPORT_CHECKPOINT_FILE:      turb_import_checkpoint
TURBULENCE_IMPORT_CHECKPOINT_TYPE:      binary

Running the model for a model day using this modified AGCM.rc will produce a full set of restart files, which can be used with the default model configuration.

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