payu 0.1

Initialization

If you have access to the v45 project on raijin, then add the v45 modules to your environment and load the payu module:

module use /projects/v45/modules
module load payu

You may want to include these lines in your .login (for tcsh) or .profile (for bash) scripts.

To see a list of supported climate models, type:

payu list

While not currently supported, the following command will eventually compile the model and set up the laboratory:

payu init $model_name

Setting up the experiment

Until ``payu init`` is properly configured, users will have to manually setup their experiments by following the steps below. We are working on automating these steps.

1. Create a laboratory path, usually somewhere in /short:

   mkdir -p /short/${PROJECT}/${USER}/${MODEL}

   where ${MODEL} is one of the models supported by payu.

2. Inside this directory (which we call ${LAB}), create directories for your executables and input fields:

   mkdir ${LAB}/bin
   mkdir ${LAB}/input

3. Either compile or copy an executable into the ${LAB}/bin directory:

   cp /path/to/model/exec ${LAB}/bin/

4. Create a directory relevant to your experiment, and copy any binary input files into this directory:

   mkdir ${LAB}/input/my_data
   cp /some/data/file ${LAB}/input/my_data/

5. Return to the home directory and create a control directory:

   cd ~
   mkdir -p ${MODEL}/my_expt
   cd ${MODEL}/my_expt

6. Copy any configuration files into this directory, such as namelists or other input text files:

   cp /path/to/namelists ~/${MODEL}/my_expt

7. Create a config.yaml file inside the directory, such as the one shown below for MOM:

   # Submission settings
   queue: normal
   project: v45
   ncpus: 1
   walltime: 1:00:00
   jobname: bowl1
   # Model settings
   model: mom
   shortpath: /short/v45
   exe: fms_MOM_solo.x
   input: bowl1
   # Collation
   collate_walltime: 10:00
   collate_mem: 1GB

   See the (as yet unwritten) section on config.yaml creation for more details.

After completing these steps, the model is ready for submission.

Running the Model

Once the experiment has been set up (see the next section), the model is run from the control directory by typing the following:

payu run

This will run the model once, and save the output to the archive directory.

If you type payu run again, then the model will continue from the end of the previous run.

To run the model N times in succession, type the following:

payu run -n N

If there are no archived runs, the model will start from initialization. If there is an existing run, it will start from the last run and do N additional runs.

If you ever need to start from a particular run, say K, then type the following:

payu run -i K -n N

Note that numbering is 0-based, so that the first run is 0, the second run is 1, and so on. In general, one should not expect to use the -i flag outside of testing.

Running jobs are stored in a work directory, which can be accessed by a symbolic link work created inside the control directory. Completed runs are stored in the archive directory, accessible by an equivalent archive symbolic link.