Running Coupled Ocean: Difference between revisions

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Steps to run AOGCM

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$ cd GEOSagcm/src

$ cvs up -r Ganymed-2_0_UNSTABLE g5_modules

$ source g5_modules

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OGCM_NY = NYGLOB/BLCKY (= 10 in our example)

[I had tried with NXGLOB = 360, BLCKX = 40 => OGCM_NX = 9. It didn't work. Apparently, odd numbered processes don't.]

[I had tried with NXGLOB = 360, BLCKX = 40 => OGCM_NX = 9. It didn't work. Apparently, odd numbered processes don't. ''Update'': I could get it to work on 1x1 layout.]

Since the resolution/layout are specified at compile time (really!), the model needs to be compiled for a new resolution/layout combination.

Since the resolution/layout are specified at compile time (really!), the model needs to be re-compiled for a new resolution/layout combination.

Finally, compile:

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==Setup experiment==

===gcm_setup===

$ cd Applications/GEOSgcm_App

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$ ./gcm_setup

Experiment ID:

Experiment ID: Choose

Experiement Description:

Experiement Description: Choose

Atmospheric Horizontal Resolution: 144 91

Atmospheric Vertical Resolution: Default

COUPLED Ocean/Sea-Ice Model: YES

Ocean Lat/Lon Horizontal Resolution: Default

Ocean Model Vertical Resolution: Default

GOCART: Default

HISTORY template: HISTORY_COUPLED.rc.tmpl

HOME directory:

HOME directory: Choose

EXPERIMENT directory:

EXPERIMENT directory: Same as HOME

BUILD directory:

BUILD directory: Default

GROUP ID:

GROUP ID: Default

$ mv /path/to/exp/dir

===Edit some files===

$ cd /path/to/exp/dir

=====CAP.rc=====

To run a 1 day experiment etc. Also <tt>timers</tt> and <tt>memutils</tt> can be enabled here.

Need to ensure ~~the following~~:

=====AGCM.rc=====

Need to ensure:

~~In AGCM.rc:~~

OGCM_NX = NX = 8

OGCM_NY = NY = 10

CICE_NPROCS = 80

In input.nml:

=====input.nml=====

layout = 8,10,

~~In gcm_run.j:~~

=====HISTORY.rc=====

~~#PBS -l select~~=~~7:ncpus~~=~~12:mpiprocs~~=12

Comment out the line

~~(need 80 cpus, hence 7 nodes)~~

In HISTORY.rc~~: comment~~ out the line

'RUNOFF' , 'SURFACE' ,

in geosgcm_surf.fields (model crashes with this option).

~~Next, we edit CAP.rc and~~ gcm_run.j (~~to run a 1-day simulation~~).

=====gcm_run.j=====

#PBS -l select=7:ncpus=12:mpiprocs=12

~~Copy restarts (example restarts can be found in ~yvikhlia~~/~~geos5~~/~~test180/expdir). Several new restarts are needed but these can be bootstrapped according to Yuri. The new ones are orad_import, seaice_import,~~ and ~~seaice_internal~~.

(need 80 cpus, hence 7 nodes)

Also commenting out the 2 <tt>qsub</tt> lines prevents <tt>gcm_run.j</tt> from running post processing and re-submitting jobs.

===Copy restarts===

Example restarts can be found in ~yvikhlia/geos5/test180/expdir (for atmosphere resolution of 144x91 and ocean resolution of 360x200). Several new restarts are needed but these can be bootstrapped. The new ones are orad_import, seaice_import, and seaice_internal. [The required restarts are <tt>fvcore_internal_rst</tt>, <tt>lake_internal_rst</tt>, <tt>landice_internal_rst</tt>, <tt>catch_internal_rst</tt>, <tt>moist_internal_rst</tt>, <tt>saltwater_internal_rst</tt>, <tt>seaice_internal_rst</tt>, <tt>seaice_import_rst</tt>, <tt>orad_import_rst</tt>. If using GOCART, then <tt>gocart_internal_rst</tt>, <tt>carma_internal_rst</tt>, <tt>stratchem_internal_rst</tt>, <tt>gmichem_internal_rst</tt> as well.]

$ cp ~yvikhlia/geos5/test180/expdir/*_rst .

$ cp ~yvikhlia/geos5/test180/expdir/cap_restart .

We may need to ~~edit cap_restart~~ to specify a particular year (no changes in month, day or time).

'''<tt>cap_restart</tt> may need to edited''' as well to specify a particular year (no changes in month, day or time).

When the experiment directory is created (by gcm_setup) a new directory is now there called RESTART. Inside are restart files [only <tt>ocean_temp_salt.res.nc</tt> is required, rest can be bootstrapped].

$ cp ~yvikhlia/geos5/test180/expdir/RESTART/* RESTART/

~~When the experiment directory is created (by gcm_setup)~~ a ~~new directory is now there called RESTART~~. ~~Inside~~ are ~~restart files,~~ the ~~only one of which is required is ocean_temp_salt~~.~~res.nc. The rest can be bootstrapped~~.

===Boundary conditions===

We need ocean grid_spec, ice grid, KPAR data and river routing file during a run. They are all in directory pointed to by $GRIDDIR in the runscript (<tt>gcm_run.j</tt>).

$ ~~cp ~yvikhlia/geos5/test180/expdir/RESTART/* RESTART/~~

==Run job==

$ qsub gcm_run.j

~~We need ocean grid_spec, ice grid, KPAR data and river routing file during a run. They are all in directory pointed to by $GRIDDIR in~~ the ~~runscript (gcm_run.j).~~

[[Category:SI Team]]

[[Category:Running the Model]]

@@ Line 1: / Line 1: @@
+{{rightTOC}}
 Steps to run AOGCM
@@ Line 10: / Line 12: @@
   $ cd GEOSagcm/src
+ $ cvs up -r Ganymed-2_0_UNSTABLE g5_modules
   $ source g5_modules
@@ Line 32: / Line 35: @@
   OGCM_NY = NYGLOB/BLCKY (= 10 in our example)
-[I had tried with NXGLOB = 360, BLCKX = 40 => OGCM_NX = 9. It didn't work. Apparently, odd numbered processes don't.]
+[I had tried with NXGLOB = 360, BLCKX = 40 => OGCM_NX = 9. It didn't work. Apparently, odd numbered processes don't. ''Update'': I could get it to work on 1x1 layout.]
-Since the resolution/layout are specified at compile time (really!), the model needs to be compiled for a new resolution/layout combination.
+Since the resolution/layout are specified at compile time (really!), the model needs to be re-compiled for a new resolution/layout combination.
 Finally, compile:
@@ Line 42: / Line 45: @@
 ==Setup experiment==
+===gcm_setup===
   $ cd Applications/GEOSgcm_App
@@ Line 51: / Line 55: @@
   $ ./gcm_setup
-         Experiment ID:
+         Experiment ID:                                     Choose
-         Experiement Description:
+         Experiement Description:                           Choose
-         Atmospheric Horizontal Resolution: 144 91
+         Atmospheric Horizontal Resolution:                 144 91
-         Atmospheric Vertical Resolution: Default
+         Atmospheric Vertical Resolution:                   Default
-         COUPLED Ocean/Sea-Ice Model: YES
+         COUPLED Ocean/Sea-Ice Model:                       YES
-         Ocean Lat/Lon Horizontal Resolution: Default
+         Ocean Lat/Lon Horizontal Resolution:               Default
-         Ocean Model Vertical Resolution: Default
+         Ocean Model Vertical Resolution:                   Default
-         GOCART: Default
+         GOCART:                                            Default
-         HISTORY template: HISTORY_COUPLED.rc.tmpl
+         HISTORY template:                                  HISTORY_COUPLED.rc.tmpl
-         HOME directory:
+         HOME directory:                                    Choose
-         EXPERIMENT directory:
+         EXPERIMENT directory:                              Same as HOME
-         BUILD directory:
+         BUILD directory:                                   Default
-         GROUP ID:
+         GROUP ID:                                          Default
-  $ mv /path/to/exp/dir
+===Edit some files===
+  $ cd /path/to/exp/dir
+=====CAP.rc=====
+To run a 1 day experiment etc. Also <tt>timers</tt> and <tt>memutils</tt> can be enabled here.
-Need to ensure the following:
+=====AGCM.rc=====
+Need to ensure:
-In AGCM.rc:
   OGCM_NX = NX = 8
   OGCM_NY = NY = 10
   CICE_NPROCS = 80
-In input.nml:
+=====input.nml=====
   layout = 8,10,
-In gcm_run.j:
+=====HISTORY.rc=====
- #PBS -l select=7:ncpus=12:mpiprocs=12
+Comment out the line
-(need 80 cpus, hence 7 nodes)
-In HISTORY.rc: comment out the line
   'RUNOFF'    , 'SURFACE'       ,
 in geosgcm_surf.fields (model crashes with this option).
-Next, we edit CAP.rc and gcm_run.j (to run a 1-day simulation).
+=====gcm_run.j=====
+ #PBS -l select=7:ncpus=12:mpiprocs=12
-Copy restarts (example restarts can be found in ~yvikhlia/geos5/test180/expdir). Several new restarts are needed but these can be bootstrapped according to Yuri. The new ones are orad_import, seaice_import, and seaice_internal.
+(need 80 cpus, hence 7 nodes)
+Also commenting out the 2 <tt>qsub</tt> lines prevents <tt>gcm_run.j</tt> from running post processing and re-submitting jobs.
+===Copy restarts===
+Example restarts can be found in ~yvikhlia/geos5/test180/expdir (for atmosphere resolution of 144x91 and ocean resolution of 360x200). Several new restarts are needed but these can be bootstrapped. The new ones are orad_import, seaice_import, and seaice_internal. [The required restarts are <tt>fvcore_internal_rst</tt>, <tt>lake_internal_rst</tt>, <tt>landice_internal_rst</tt>, <tt>catch_internal_rst</tt>, <tt>moist_internal_rst</tt>, <tt>saltwater_internal_rst</tt>, <tt>seaice_internal_rst</tt>, <tt>seaice_import_rst</tt>, <tt>orad_import_rst</tt>. If using GOCART, then <tt>gocart_internal_rst</tt>, <tt>carma_internal_rst</tt>, <tt>stratchem_internal_rst</tt>, <tt>gmichem_internal_rst</tt> as well.]
   $ cp ~yvikhlia/geos5/test180/expdir/*_rst .
   $ cp ~yvikhlia/geos5/test180/expdir/cap_restart .
-We may need to edit cap_restart to specify a particular year (no changes in month, day or time).
+'''<tt>cap_restart</tt> may need to edited''' as well to specify a particular year (no changes in month, day or time).
+When the experiment directory is created (by gcm_setup) a new directory is now there called RESTART. Inside are restart files [only <tt>ocean_temp_salt.res.nc</tt> is required, rest can be bootstrapped].
+ $ cp ~yvikhlia/geos5/test180/expdir/RESTART/* RESTART/
-When the experiment directory is created (by gcm_setup) a new directory is now there called RESTART. Inside are restart files, the only one of which is required is ocean_temp_salt.res.nc. The rest can be bootstrapped.
+===Boundary conditions===
+We need ocean grid_spec, ice grid, KPAR data and river routing file during a run. They are all in directory pointed to by $GRIDDIR in the runscript (<tt>gcm_run.j</tt>).
-    $ cp ~yvikhlia/geos5/test180/expdir/RESTART/* RESTART/
+==Run job==
+ $ qsub gcm_run.j
-We need ocean grid_spec, ice grid, KPAR data and river routing file during a run. They are all in directory pointed to by $GRIDDIR in the runscript (gcm_run.j).
+[[Category:SI Team]]
+[[Category:Running the Model]]