Running ADAS: Difference between revisions

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First, we choose a DAS run to simulate. On NCCS Discover
==ADAS run==


  $ cd ~dao_ops
===Build model===
  $ ls
First, choose a model tag to build. For this example, we choose GEOSadas-5_9_1_p7.


for a list of the various runs. As an example, we choose the run 'e572p5_fp'.
$ cvs co -P -r GEOSadas-5_9_1_p7 -d g591p8 GEOSadas-5_9


  $ cd ~dao_ops/e572p5_fp/run
Not the module name <tt>GEOSadas-5_9</tt>. Unlike AGCM, all ADAS tags have a corresponding module.


1. Checkout and build the model:
$ cd g591p8/src
$ ./parallel_build.csh


For model tag and module name, check with Joe Stassi.
===Setup experiment (Run <tt>fvsetup</tt>)===


  $ cvs co -r GEOSadas-5_7_2_p5_m1 GEOSadas-5_7
Run <tt>fvsetup</tt> from the bin directory (<tt>g591p8/Linux/bin</tt>) with the following options (default value chosen for ones not mentioned):
  $ cd GEOSadas/src
[we choose the default value for the initial conditions (FVICS) as well]
  $ source g5_modules
 
  $ gmake install
AGCM Resolution? [b72]
> C180
OGCM Resolution? [c34]
> f34
EXPID? [u000_C180]
> g591p8
OBSERVING SYSTEM CLASSES?
> "ncep_prep_bufr"
<!--
> "ncep_1bamua_bufr,ncep_1bamub_bufr,ncep_1bhrs2_bufr,ncep_1bhrs3_bufr,
    ncep_1bmsu_bufr,ncep_osbuv_bufr,ncep_prep_bufr,ncep_sptrmm_bufr,
    disc_airs_bufr,disc_amsua_bufr,ncep_mhs_bufr,ncep_1bhrs4_bufr,
    ncep_amsre_bufr,ncep_goesfv_bufr,ncep_mtiasi_bufr,ncep_gpsro_bufr,
    aura_omi_bufr,ncep_satwnd_bufr,ncep_atms_bufr,ncep_sevcsr_bufr"
-->
Do Aerosol Analysis (y/n)? [y]
> n
 
One can, of course, turn on Aerosol Analysis and AOD assimilation here.
 
A pdf of an example <tt>fvsetup</tt> session is provided here: [[Media:Fvsetup_session.pdf|fvsetup_session]].
 
====FVHOME====
FVHOME is the home directory for fvDAS experiment. Resource files, restarts and system output will be stored
under this directory. Usually it contains subdiretories:
 
ana/        first guess/analysis output
anasa/      job script to run stand-alone analysis
daotovs/    daotovs field output
diag/      diagnostic field output
etc/        listings and other odds & ends
fcst/      forecast run directory
fvInput/    process required inputs
obs/        post-analysis ODS files
prog/      prognostic field output
recycle/    latest restart files
rs/        restart files
run/        resource files
 
<tt>$FVHOME/.FVROOT</tt> gives the location of the installation <tt>bin</tt> directory.
 
Some of these directories (<tt>ana/</tt>, <tt>chem/</tt>, <tt>diag/</tt>, <tt>etc/</tt>, <tt>obs/</tt>, <tt>rs/</tt>) are stored in the archive. After completing the experiment, look in <tt>$ARCHIVE/g591p8</tt> (where <tt>g591p8</tt> is the experiment ID).
 
====Run directory====
$ cd $FVHOME/run
 
<tt>g5das.j</tt> is the job submission script. The number of cpus etc. can be changed here (if they haven't already been changed during setup). Also, if you want to run a single cycle of <tt>GSIsa.x</tt> & <tt>GEOSgcm.x</tt> add <tt>exit</tt> right before 'PART IV'.
<!--
To simulate the OPS run d591_fpit, we make a few changes:
# NX, NY in AGCM.rc.tmpl and AGCM.BOOTSTRAP.rc.tmpl have the same values (8, 48) as in the OPS run
# Copy HISTORY.rc.tmpl over from the OPS run
# Copy obsys.rc over from the OPT run
# NX, NY in GSI_GridComp.rc.tmpl should match those from the OPS run (6, 36)
# Set NUM_SGMT to 1 in CAP.rc.tmpl
# <tt>g5das.j</tt>
## PBS -l select=32
## <tt>setenv NCPUS    384</tt>
## <tt>setenv NCPUS_GSI 216</tt>
## '''One cycle''': To run one segment each of GSIsa.x and GEOSgcm.x add '<tt>exit</tt>' before 'PART IV'
-->
 
===Data Assimilation===
 
$ cd $FVHOME/run
$ qsub g5das.j
 
<tt>g5das</tt> creates a scratch directory <tt>$NOBACKUP/fvwork.xxxx</tt> and runs the experiment there. After the initial setup, <tt>GSIsa.x</tt> is run with output written to <tt>ana.log</tt> followed by <tt>GEOSgcm.x</tt> which writes its output to <tt>stdout</tt> and <tt>fvpsas.log</tt>.
 
===Forecast===
 
==Simulating OPS run==
<!--EVERYTHING BELOW IS COMMENTED OUT
 
==Simulating DAS forecast run==
 
The DAS forecast run can be simulated using the corresponding AGCM tag.
 
====Checkout and build the model====


Or, one can checkout the corresponding AGCM model Fortuna-2_5_p6 (module
Grab the corresponding AGCM tag (Check out <tt>GEOSadas-5_9_1_p4</tt> and look for <tt>GCM</tt> in the file <tt>src/Applications/GEOSdas_App/ChangeLog</tt>).
Fortuna) and build it.


  $ cvs co -r Ganymed-1_0_p3 Ganymed
  $ cd GEOSagcm/src
  $ source g5_modules
  $ ./parallel_build.csh


2. Experiment setup:
====Experiment setup====


To simulate a forecast run we can use gcm_setup to setup our experiment
To simulate a forecast run we can use gcm_setup to setup our experiment
Line 28: Line 113:
   $ cd Applications/GEOSgcm_App/
   $ cd Applications/GEOSgcm_App/
   $ ./gcm_setup
   $ ./gcm_setup
        GOCART: yes
        GOCART Emission Files to use: OPS
        AERO_PROVIDER: GOCART
        HISTORY: Current


Cubed-sphere was not fully implemented in this model. Choose Lat/Lon with
=====Edit files=====
resolution 1152x721x72 for the 'e'-run. The other options are
======AGCM.rc, CAP.rc, HISTORY.rc======
GOCART -> yes
GOCART Emission Files to use -> OPS
AERO_PROVIDER-> GOCART
HISTORY-> Current
 
3. AGCM.rc, CAP.rc, HISTORY.rc


Edit these files to match with the corresponding .tmpl files in
Edit these files to match with the corresponding .tmpl files in
   ~dao_ops/e572p5_fp/run
   ~dao_ops/e572p5_fp/run


4. gcm_run.j
Then, change the restart reading behavior to pbinary:
 
  $ sed -i -e '/RESTART_TYPE:/ s/binary/pbinary/' AGCM.rc
 
======gcm_run.j======


Ensure that the correct boundary datasets are linked to. Compare the links in
Ensure that the correct boundary datasets are linked to. Compare the links in
Line 48: Line 135:
   ~dao_ops/e572p5_fp/run/lnbcs
   ~dao_ops/e572p5_fp/run/lnbcs


4. RC files
Also, be sure to add an "exit" after you run the executable (if, say, you want to run one segment).
 
=====RC files=====


Copy the .rc files over
Copy the .rc files over
Line 54: Line 143:
   $ find ~dao_ops/e572p5_fp/run -name "*.rc" -exec cp {} /path/to/home/dir/RC \;
   $ find ~dao_ops/e572p5_fp/run -name "*.rc" -exec cp {} /path/to/home/dir/RC \;


5. restart files
=====Restart files=====


Locate the dir containing restarts by querying FVARCH in FVDAS_Run_Config
Locate the dir containing restarts by querying FVARCH in FVDAS_Run_Config


   $ grep FVARCH ~dao_ops/e572p5_fp/run/FVDAS_Run_Config
   $ grep ATAG ~dao_ops/e572p5_fp/run/FVDAS_Run_Config
    setenv FVARCH  /archive/u/gmao_ops/GEOS-5.7.2/${ATAG}/ #include trailing colon


  $ grep ATAG ~dao_ops/e572p5_fp/run/FVDAS_Run_Config
     setenv ATAG    GEOSadas-5_7_2_p5_m1
     setenv ATAG    GEOSadas-5_7_2_p5_m1
     setenv ATAG    $GTAG
     setenv ATAG    $GTAG
     setenv FVARCH  /archive/u/gmao_ops/GEOS-5.7.2/${ATAG}/ #include trailing colon
     setenv FVARCH  /archive/u/gmao_ops/GEOS-5.7.2/${ATAG}/ #include trailing colon
  $ cd /archive/u/gmao_ops/GEOS-5.7.2/GEOSadas-5_7_2_p5_m1
  $ cd e572p5_fp


Pick a date and time: say 2012/05/15, 21z
Pick a date and time: say 2012/05/15, 21z
Line 74: Line 158:
   $ ls *_rst.20120515_21z.bin
   $ ls *_rst.20120515_21z.bin


Copy these files over from ARCHIVE to experiment directory.
Copy these files over from ARCHIVE to experiment directory and the rename them:
 
  $ cd /path/to/experiment
  $ rename _rst.20120515_21z.bin _rst *_rst.20120515_21z.bin
<nowiki> $ rename e572p5_fp. '' *rst</nowiki>
 
Also, create a cap_restart file:
 
  $ echo '20120515 210000' > cap_restart


6. Run job
====Run job====
    
    
   $ qsub gcm_run.j
   $ qsub gcm_run.j
-->
[[Category:SI Team]]
[[Category:Running the Model]]

Latest revision as of 09:38, 29 March 2013

ADAS run

Build model

First, choose a model tag to build. For this example, we choose GEOSadas-5_9_1_p7. 

$ cvs co -P -r GEOSadas-5_9_1_p7 -d g591p8 GEOSadas-5_9

Not the module name GEOSadas-5_9. Unlike AGCM, all ADAS tags have a corresponding module. 

$ cd g591p8/src
$ ./parallel_build.csh

Setup experiment (Run fvsetup)

Run fvsetup from the bin directory (g591p8/Linux/bin) with the following options (default value chosen for ones not mentioned): [we choose the default value for the initial conditions (FVICS) as well] 

AGCM Resolution? [b72]
> C180

OGCM Resolution? [c34]
> f34

EXPID? [u000_C180]
> g591p8

OBSERVING SYSTEM CLASSES?
> "ncep_prep_bufr"

Do Aerosol Analysis (y/n)? [y]
> n

One can, of course, turn on Aerosol Analysis and AOD assimilation here.

A pdf of an example fvsetup session is provided here: fvsetup_session.

FVHOME

FVHOME is the home directory for fvDAS experiment. Resource files, restarts and system output will be stored under this directory. Usually it contains subdiretories: 

ana/        first guess/analysis output
anasa/      job script to run stand-alone analysis
daotovs/    daotovs field output
diag/       diagnostic field output
etc/        listings and other odds & ends
fcst/       forecast run directory
fvInput/    process required inputs
obs/        post-analysis ODS files
prog/       prognostic field output
recycle/    latest restart files
rs/         restart files
run/        resource files

$FVHOME/.FVROOT gives the location of the installation bin directory.

Some of these directories (ana/, chem/, diag/, etc/, obs/, rs/) are stored in the archive. After completing the experiment, look in $ARCHIVE/g591p8 (where g591p8 is the experiment ID).

Run directory

$ cd $FVHOME/run

g5das.j is the job submission script. The number of cpus etc. can be changed here (if they haven't already been changed during setup). Also, if you want to run a single cycle of GSIsa.x & GEOSgcm.x add exit right before 'PART IV'.

Data Assimilation

$ cd $FVHOME/run
$ qsub g5das.j

g5das creates a scratch directory $NOBACKUP/fvwork.xxxx and runs the experiment there. After the initial setup, GSIsa.x is run with output written to ana.log followed by GEOSgcm.x which writes its output to stdout and fvpsas.log.

Forecast

Simulating OPS run

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