Running Coupled Ocean: Difference between revisions

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Steps to run AOGCM

~~__FORCETOC__~~

==Checkout==

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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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$ ./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

===Edit some files===

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$ cd /path/to/exp/dir

~~Need to ensure the following:~~

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

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

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

Need to ensure:

OGCM_NX = NX = 8

OGCM_NY = NY = 10

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

layout = 8,10,

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

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

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

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

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'RUNOFF' , 'SURFACE' ,

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

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

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

(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. Several new restarts are needed but these can be bootstrapped ~~(according to Yury)~~. The new ones are orad_import, seaice_import, and seaice_internal.

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 .

'cap_restart' may need to edited as well 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~~, the~~ only ~~one of which is required is~~ ocean_temp_salt.res.nc~~. The~~ rest can be bootstrapped.

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/

===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 (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 (<tt>gcm_run.j</tt>).

==Run job==

@@ Line 1: / Line 1: @@
+{{rightTOC}}
 Steps to run AOGCM
-__FORCETOC__
 ==Checkout==
@@ Line 11: / Line 12: @@
   $ cd GEOSagcm/src
+ $ cvs up -r Ganymed-2_0_UNSTABLE g5_modules
   $ source g5_modules
@@ Line 33: / 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 53: / 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
 ===Edit some files===
@@ Line 71: / Line 73: @@
   $ cd /path/to/exp/dir
-Need to ensure the following:
+=====CAP.rc=====
+To run a 1 day experiment etc. Also <tt>timers</tt> and <tt>memutils</tt> can be enabled here.
 =====AGCM.rc=====
+Need to ensure:
   OGCM_NX = NX = 8
   OGCM_NY = NY = 10
@@ Line 80: / Line 85: @@
 =====input.nml=====
   layout = 8,10,
-=====gcm_run.j=====
- #PBS -l select=7:ncpus=12:mpiprocs=12
-(need 80 cpus, hence 7 nodes)
 =====HISTORY.rc=====
@@ Line 89: / Line 90: @@
   'RUNOFF'    , 'SURFACE'       ,
 in geosgcm_surf.fields (model crashes with this option).
+=====gcm_run.j=====
+ #PBS -l select=7:ncpus=12:mpiprocs=12
+(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. Several new restarts are needed but these can be bootstrapped (according to Yury). The new ones are orad_import, seaice_import, and seaice_internal.
+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 .
-'cap_restart' may need to edited as well 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, the only one of which is required is ocean_temp_salt.res.nc. The rest can be bootstrapped.
+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/
 ===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 (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 (<tt>gcm_run.j</tt>).
 ==Run job==