tkarna / nemodriver

nemodriver

Scripts to run NEMO ocean model simulations

Monthly driver

Scripts are found under monthly_driver subdirectory.

• run_month.sh: creates a run directory for a 1-month run and submits it in the queue
• run_all.sh: queues a sequence of 1-month runs as defined in the env_path.sh file
• env_path.sh: environment variables to define a NEMO run configuration and dates

Typical usage:

Execute a single 1-month simulation

Define parameters in the env_path.sh for the model configuration.

./run_month.sh -s 2014-10

Execute ./run_month.sh -h for more options.

This creates a directory for the NEMO run, $RUN_ROOT_DIR/run_2014-10, where RUN_ROOT_DIR is a user-defined directory, e.g. ../../run01. It copies binary input files from the directory CFG_TEMPLATE_DIR to the run directory. It also generates NEMO namelists based on the user-defined namelist template. The template is defined by NMLCONFIG and the template namelist files are located under template/namelist/$NMLCONFIG directory.

By default, the system uses the slurm queue manager. The template for the job submission script is monthly_driver/job_nemo.slurm. The system also queues a post-processing job that is run after the NEMO run has (successfully) finished; the template is monthly_driver/job_postproc.slurm.

Queue a sequence of 1-month runs

./run_all.sh

This runs a sequence of 1-month runs, as defined by the start_date and end_date environment variables. If the start_date coincides with init_date, the simulation will be initialsed from a cold start (HOTSTART=0) or from restart files (HOTSTART=1, restart files sought under HOTSTART_DIR). Otherwise, the simulation will be hotstarted from the previous month.

Environment variables in env_path.sh

• RUNTAG: a short human-readable name for the simulation, e.g. run01. Should not contain spaces or underscores.
• RUN_ROOT_DIR: directory under which the monthly subdiretories will be created. Default: ../../$RUNTAG
• RUNDIR_PREFIX: prefix to be used in run directory names. The monthly subdirectories are called ${RUNDIR_PREFIX}_2016-06. Default: run.
• CFG_TEMPLATE_DIR: directory that contains all the binary etc files necessary for running the simulation. This includes netCDF files, forcing files, *.xml files, as well as NEMO and XIOS binaries. NOTE: the Fortran namelist files should not be in this directory.
• NMLCONFIG: name of the namelist template to use. The actual template namelist file are stored in template/namelist/$NMLCONFIG directory.
• start_date, end_date: Dates defining the first/last months of the simulation, e.g. 2014-10-01 and 2015-03-01 defines a 6 month run. NOTE: the day digit has no effect, i.e. only year and month counts.
• init_date: Defines the date for cold/hot start.
• HOTSTART: if 1 will use hot start from restart files.
• HOTSTART_DIR: directory where restart files are sought
• MASTER_PARENT_JOB: Slurm job ID. If defined, will wait for this job to finish before starting the first run.
• SINGLE_NML: If 1 will use a single namelist file for NEMO, i.e. the namelist_cfg files will be empty and all the parameters are defined in namelist_ref
• QUEUE_MANAGER: chooses the queue manager for the computing cluster, either slurm or pbs.
• FLAG_WAVE etc: additional namelist parameters that will be substituted to the nameslist files.

Namelist templates

Templates are defined in template/namelist/$NMLCONFIG directory. It contains files:

• namelist_ref
• namelist_ice_ref
• namelist_cfg
• namelist_ice_cfg

The namelist files contain the parameters for the said configuration.

Some parameters can be set dynamically. Those parameters contain tags identified with double underscores:

   nn_itend    = __NTIMESTEP__ !  last  time step (std 29760)
   nn_date0    = __INITDATE__ !  date at nit_0000 (format yyyymmdd) used if ln_rstart=F or (ln_rstart=T and nn_rstctl=0 or 1)

These values will be substituted by the run_month.sh script.

If SINGLE_NML is 1, the *_cfg files are empty and all substitutions are made to the *_ref files directly. If not, the replacements are made to the *_cfg files.