= MESSy/CLaMS: Running the model =


You have to adjust the run script and the namelist setup


== Changes in run script (e.g. messy-dir/messy/util/xmessy_mmd.climtest) ==

 * On '''JUWELS/JURECA''' set SBATCH commands in the first lines of the run script:
 {{{#!highlight ksh numbers=disable
#!/bin/bash -e
#SBATCH --nodes=2
#SBATCH --ntasks=48
#SBATCH --ntasks-per-node=24
#SBATCH --output=mpi-out.%j
#SBATCH --error=mpi-err.%j
#SBATCH --time=00:30:00
#SBATCH --partition=batch
#SBATCH --account=jicg11
}}}

 * Change working directory, e. g.:
 {{{
WORKDIR=/private/icg112/messy_out/climtest
 }}}

 * Set experiment name (used for output filenames):
 {{{
EXP_NAME=climtest
 }}}


 * On '''JUWELS/JURECA''' you have to set BASEDIR:
 {{{
BASEDIR=/p/project/clams-esm/thomas2/messy-clams
 }}}

 * Set start date and end date:
 {{{
START_YEAR=1988
START_MONTH=01
START_DAY=01
START_HOUR=12
STOP_YEAR=1988
STOP_MONTH=01
STOP_DAY=04
STOP_HOUR=12
 }}}

 * Specify subdirectory with namelist setup:
 {{{
NML_SETUP=MBM/clams_clim
 }}}

 * Select model: <<BR>><<BR>>

 CLaMS run:
 {{{
MINSTANCE[1]=clams
 }}}

 ECHAM5/CLaMS run:  
 {{{
MINSTANCE[1]=ECHAM5
 }}}

 * Set NPX[1] and NPY[1]:
 {{{
NPY[1]=6   # => NPROCA for ECHAM5
NPX[1]=8   # => NPROCB for ECHAM5
 }}}
 NPX[1]*NPY[1] number of cores are used. On JURECA it has to match the number of tasks specified in the first lines of the script (#SBATCH ...).

== Change namelist setup (e.g.  messy-dir/messy/nml/MBM/clams_clim) ==


==== Messy setup ====

 * channel.nml

 This file includes entries to control the output and restart handling for all channels and channel object <<BR>>
 (see ''MESSy CHANNEL User Manual'')

 * qtimer.nml

 Set queue time limit <<BR>>
 (see ''Restarts'' and ''Development Cycle 2 of the Modular Earth Submodel System'')

 * switch.nml
  * Clams submodels (traj, chem, mix, bmix and cirrus) can be switch on or off
  * USE_CLAMS must be TRUE for all clams runs
  * If USE_CLAMSCHEM is TRUE, USE_DISSOC has to be TRUE too

 * timer.nml
  * IO_RERUN_EV: interval for rerun output, for example write rerun files once a month:
  {{{
IO_RERUN_EV = 1,'months','first',0,
 }}}
  * NO_CYCLES: number of how often rerun files are written without interrupting the simulation
  * delta_time: model time step in seconds <<BR>>
 (see ''MESSy TIMER User Manual'')

==== Setup for clams submodels ====

 * clams.nml
 * clamstraj.nml
 * clamschem.nml
 * dissoc.nml
 * clamsmix.nml
 * clamsbmix.nml
 * clamscirrus.nml
 * clamssedi.nml

== Execute program ==

 * Create working directory (specified in run script), e.g. 
 {{{
mkdir /private/icg112/messy_out/climtest
 }}}

 * Change to working directory:
 {{{
cd /private/icg112/messy_out/climtest
 }}}

 * Running the model:


  * Start run script on workstation cluster:
  {{{
~/messy-dir/messy/util/xmessy_mmd.climtest 2>&1 | tee out
 }}}

  * Submit run script on '''JUWELS/JURECA'''
  {{{
sbatch ~/messy-dir/messy/util/xmessy_mmd.climtest
}}}
   * On success, sbatch writes the job ID to standard out.

   * Other Slurm Commands
    * ''squeue   [-u userid]'' <<BR>> 
    Show status of all jobs.
    * ''scancel <jobid>'' <<BR>>   
    Cancel a job.
    * ''scontrol show job <jobid> '' <<BR>> 
    Show detailed information about a pending, running or recently completed job.
    * ''scontrol update job <jobid> set ...'' <<BR>> 
    Update a pending job.
    * ''scontrol -h''	<<BR>> 
    Show detailed information about scontrol.
    * ''sacct -j <jobid>'' <<BR>>
    Query information about old jobs.
    * ''sprio''   <<BR>> 
    Show job priorities.
    * ''smap''	<<BR>> 
    Show distribution of jobs. For a graphical interface users are referred to '''llview'''.
    * '' sinfo'' <<BR>> 
    View information about nodes and partitions.


 * The executable and the namelist setup is copied to the working directory

 * All output and restart files are created in the working directory

 * File MSH_NO is created for automatic reruns. <<BR>>
 If MSH_NO is in the working directory, the model is started in rerun-mode. MSH_NO contains the number of the last chain-element.
 If you want run the example again from the beginning, '''remove file MSH_NO''' before starting the run script.