Run Basemodel CLaMS

Namelist Setup

An example namelist setup for a CLaMS standalone run can be found in directory messy/nml/MBM/clams.

There you will find all necessary namelists with detailed descriptions of all parameters, a README with compile and run instructions and the corresponding xmessy_mmd.header.

Example CLaMS standalone run:

• one day clams run starting on 01/01/1979

• all CLaMS submodels (except sedi) are used:
  

  • traj, mix, bmix, dissoc, chem, cirrus, deepconv, tracer
• example ERA5 data (for 2 days) is used

In directory messy/nml/EMAC/LG/CLaMS/base there is an example namelist setup for a coupled CLaMS-EMAC run.

See information on page EMAC-CLaMS

Create Run Script

• Create run script with for Basemodel CLaMS with:

  ./messy/util/xmkr MBM/clams

  Run Script messy/util/xmessy_mmd.MBM-clams is created.
  
  Create run script for CLaMS-EMAC run with:

  ./messy/utils/xmkr EMAC/LG/CLaMS/base

  Run Script messy/util/xmessy_mmd.EMAC-LG-CLaMS-base is created.

Modify Run Script

• 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=clams-esm
  
  

• Set experiment name (used for output filenames):

  EXP_NAME=climtest

• Change working directory, e. g.:

  WORKDIR=/p/scratch/clams-esm/thomas2/messy_out/clams

• On JUWELS/JURECA you have to set BASEDIR, e.g.:

  BASEDIR=/p/project/clams-esm/thomas2/messy-clams

• Set start date and end date:

  START_YEAR=1979
  START_MONTH=01
  START_DAY=01
  START_HOUR=12
  STOP_YEAR=1979
  STOP_MONTH=01
  STOP_DAY=02
  STOP_HOUR=12

• Specify subdirectory with namelist setup
  
  For Basemodel CLaMS:

  NML_SETUP=MBM/clams

  For CLaMS-EMAC:

  NML_SETUP=EMAC/LG/CLaMS/base

• Set MESSy input directory:
  
  On JUWELS:

  INPUTDIR_MESSY=/p/data1/slmet/model_data/MESSy/DATA/MESSy2

  On ICE4 workstations:

  INPUTDIR_MESSY=/usr/nfs/data/meteocloud/data1/model_data/MESSy/DATA/MESSy2

• Select model:
  
  CLaMS run:

  MINSTANCE[1]=clams

  CLaMS-EMAC 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/JUWELS it has to match the number of tasks specified in the first lines of the script (#SBATCH ...).

Change Namelist Setup

The namelist setup in directory messy/nml/MBM/clams should work on IEK7-Cluster and JUWELS without any changes.

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

  • delta_time: model time step in seconds
    

  • IO_RERUN_EV: interval for rerun output, for example write rerun files once a month:

    IO_RERUN_EV = ${RESTART_INTERVAL},'${RESTART_UNIT}','first',0,

  • NO_CYCLES: number of how often rerun files are written without interrupting the simulation
  • RESTART_INTERVAL, RESTART_UNIT and NO_CYCLES were set in messy script

  (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

See detailed description of all namelist parameters in example namelists in directory messy/nml/MBM/clams

Execute

• Create working directory (specified in messy script), e.g.

  mkdir /p/scratch/clams-esm/thomas2/messy_out/clams

• Change to working directory, e.g.

  cd /p/scratch/clams-esm/thomas2/messy_out/clams

• Start run script from working directory
  
  

  • Start run script on workstation cluster, e.g.:

    ~/messy-clams/messy/util/xmessy_mmd.MBM-clams 2>&1 | tee out

  • Start run script on JUWELS/JURECA, e.g.:

    sbatch /p/project/clams-esm/thomas2/juwels/messy-clams/messy/util/xmessy_mmd.MBM-clams 

• 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.