Running Coupled Ocean: Difference between revisions

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Line 85:

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

layout = 8,10,

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

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

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

~~Also, if running a 1 day experiment, comment out <tt>qsub</tt> lines.~~

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

Line 95:

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. [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>moist_import_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.]

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 .

Line 103:

'''<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 85: / Line 85: @@
 =====input.nml=====
   layout = 8,10,
-=====gcm_run.j=====
- #PBS -l select=7:ncpus=12:mpiprocs=12
-(need 80 cpus, hence 7 nodes)
-Also, if running a 1 day experiment, comment out <tt>qsub</tt> lines.
 =====HISTORY.rc=====
@@ Line 95: / 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. [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>moist_import_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.]
+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 .
@@ Line 103: / Line 103: @@
 '''<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==