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:

#!/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:

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
(see MESSy CHANNEL User Manual)
qtimer.nml
Set queue time limit
(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
(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]
      Show status of all jobs.
    - scancel <jobid>
      Cancel a job.
    - scontrol show job <jobid>
      Show detailed information about a pending, running or recently completed job.
    - scontrol update job <jobid> set ...
      Update a pending job.
    - scontrol -h
      Show detailed information about scontrol.
    - sacct -j <jobid>
      Query information about old jobs.
    - sprio
      Show job priorities.
    - smap
      Show distribution of jobs. For a graphical interface users are referred to llview.
    - sinfo
      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.
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.