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Running GEOSadas on discover

VERSION 6  Click to view document history
Created on: Mar 1, 2010 12:25 PM by Jules Kouatchou - Last Modified:  Mar 2, 2010 11:09 AM by Jules Kouatchou

This document describes how to obtain, compile and run GEOSadas on discover. It only applies to the tag GEOSadas-5_4_0_p4.

 

Let:

 

     workDir: the working directory where the source code will be located

     runDir:     the directory where the executable will be run. It will be by default /discover/nobackup/userID

 

 

Obtaining the Code

 

Go to your working directory (workDir) and type:

 

 

   cvs -d :ext:userID@progressdirect:/cvsroot/esma co -r GEOSadas-5_4_0_p4 GEOSadas

 

 

You will have the directory GEOSadas.

 

 

Compiling the Code

 

Issue the following commands:

 

   cd GEOSadas/src 
   source g5_modules
   make install >& compileGEOS.log &

 

You can check the compilation progress by typing:

 

   tail -f compileGEOS.log

 

The compilation will automatically create the directory:

 

         workDir/GEOSadas/Linux

 

that will contain the necessary information to set up experiments.

 

Setting Up Experiments

 

This setting assumes that we carry out an experiment starting on September 10, 2009 (20090910) at 2100z and ending on September 12, 2009 (20090912) at 900z. The start-up files are located in:

 

               /archive/u/dao_ops/GEOS-5_pre_ops/GEOSadas-5_4_0_p2/d540_tst_02

 

The above directory contains files for the months of May to December in 2009. Any starting date in those months "should be fine". It is important to set the starting time at 2100z.

 

You need to go to your running directory and type:

 

   workDir/GEOSadas/Linux/bin/fvsetup

 

You will be prompted to answer a series of questions (The red keys are the ones you should enter. You can use default values for the others.):

 

     Executing fvsetup from the following directory: workDir/GEOSadas/Linux/bin

     Is this correct (y/n)? [n] y

 

 

 

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

G5GCM SETTINGS

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

 

     Resolution? [b72] d72

 

 

-----

EXPID

-----

 

 

     EXPID? [u000_d72] d540_tst_02

     EXPDSC? [d540_tst_02,GEOSadas-5_4_0_p2,1st_try]

 

 

------

FVHOME: HOME directory for your fvDAS experiment.

------

 

     DEFAULT: /discover/nobackup/userID/d540_tst_02

     FVHOME? runDir/d540_tst_02

 

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

Analysis Update Frequency

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

 

     Which case of variational analysis ? [1]

     Window of the variational analysis (min)? [360]

 

     FVINPUT? [/discover/nobackup/projects/gmao/share/dao_ops/fvInput_4dvar]

     REAL TIME BCS? [/discover/nobackup/projects/gmao/share/dao_ops/fvInput_4dvar/g5gcm/bcs/SST]

 

     g5chem? [/discover/nobackup/projects/gmao/share/dao_ops/fvInput_4dvar/g5chem]

 

 

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

INITIAL CONDITIONS: Provide the directory where the start-up files are located:

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

 

     FVICS? [/archive/u/dao_ops/GEOS-5.0.1/GEOS-5_beta10p4/d501_apr05_rp] /archive/u/dao_ops/GEOS-5_pre_ops/GEOSadas-5_4_0_p2/d540_tst_02

 

 

     Starting year-month-day? [20061217] 20090910

     Starting hour-min-sec? [210000]

     Name of experiment where ICs come from: [d540_tst_02]

 

 

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

ADM-TLM Defaults

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

 

      Do you want to run model-adjoint-related applications [0]? (0=no, 1=yes)
-----------------------------
Analysis Sensitivity Defaults
-----------------------------
     Do you want to run analysis-sensitivity applications [0]? (0=no, 1=yes)
----------
TIME RANGE
----------
     Ending year-month-day? [20090912]
     Length (in days) of FORECAST run segments? [5]
     Number of one-day DAS segments per PBS job? [1]
     Number of PEs in the zonal direction (NX)? [4] 8
     Number of PEs in the meridional direction (NY)? [16] 8
     Job nickname? [g5das]
     Request Harpertown nodes (y/n) [y]?
     Run in split executable mode (1=yes;0=no)? [1]
     Frequency of background fields (hour-min-sec)? [030000]
------------
GSI SETTINGS
------------
     Triangular spectral truncation? [254]
     Analysis vertical levels (sig))? [72]
     GSI grid resolution? [NA]
     GEOS grid resolution instead? [d]
     Number of procs in the zonal direction (NX)? [12]
     Number of procs in the meridional direction (NY)? [4]
------------------------
OBSERVING SYSTEM CLASSES
------------------------
     Merra obsclass files only (y/n)? [y]
     OBSERVING SYSTEM CLASSES?
-----------------
CHECKING OBSYSTEM
-----------------
     CHECKING OBSYSTEM? [2]
--------------
RADCOR SETTING
--------------
     Which RADCOR option? [NCEP_VAI]
-----------
FORECASTING
-----------
     Frequency (in days) for writing restarts? [0]
------------
FVGCM OUTPUT
------------
          Frequency for PROGNOSTIC fields? [030000]
          Frequency for surface (2D) DIAGNOSTIC fields? [010000]
          Frequency for upper air (3D) DIAGNOSTIC fields? [030000]
          Dimension of output in zonal direction? [576]
          Dimension of output in meridional direction? [361]
  ------------------
  DIAGNOSTICS OUTPUT
  ------------------
          Would you like 2D diagnostics? [y]
          Would you like 3D diagnostics? [y]
          Would you like to compress diagnostics output files? [y]
--------------
GOCART TRACERS
--------------
          Include GOCART tracers (CO,CO2,aerosols,etc) (y/n)? [n]
-------
HISTORY
-------
          Which template? [HISTORY.rc.tmpl]
          Edit COLLECTIONS list in HISTORY.rc.tmpl (y/n)? [n]
          Edit COLLECTIONS list in GCMPROG.rc.tmpl (y/n)? [n]
          select group: yourSponsorCodeAccount
          Cannot find turb_import_rst restart.  BOOTSTRAP this restart (y/n)? [y] n
          Cannot find agcm_internal_rst restart.  Will continue anyway. Hit <cr> ...
-------------------
CERES Configuration
-------------------
          Edit files in run directory for CERES configuration (y/n)? [n]
------
REVIEW
------
          Which? Q

 

 

Editing Scripts

 

Go to the directory runDir/d540_tst_02/run/.
Edit the file lnbcs to replace:

 

          setenv G5GCMBCS $FVBCS/g5gcm/bcs
          setenv G5GRTBCS /discover/nobackup/projects/gmao/share/dao_ops/fvInput_4dvar/g5gcm/bcs/SST

 

wiith

 

     setenv G5GCMBCS /discover/nobackup/projects/gmao/share/dao_ops/fvInput_4dvar/g5gcm/bcs
     setenv G5GRTBCS /discover/nobackup/projects/gmao/share/dao_ops/fvInput_4dvar/g5gcm/bcs/realtime /SST

 

 

Edit the file AGCM.rc.tmpl to comment out the four lines:

 

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

 

 

Edit the file g5das.j to replace:

 

          setenv FVBCS $FVHOME/fvInput

 

with

 

          setenv FVBCS /discover/nobackup/projects/gmao/share/dao_ops/fvInput_4dvar

 

and comment out (or delete) the line:

 

          setenv DAT_OVERRIDE /usr/local/dapl/1.2.12/etc/dat.conf

 

 

Submitting the Job

 

From the directory runDir/d540_tst_02/run/, type:

 

   qsub g5das.j

 

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