rosesnip

A set of python scripts to automatically generate rose configuration files for parallel execution

Overview

Postprocessing of climate data often involves computing averages and other statistical measures of diagnostic fields across models and for many simulation years. Afterburner is a Python application that performs these tasks. Currently, afterburner only runs on a single processor, which can make postprocessing slow.

Rosesnip takes the same input as afterburner - a rose configuration file - and splits the job into many jobs that can run concurrently. The jobs are split across diagnostic fields, models and, if start and end dates are provided, across chunks of years. The reduction in turn around time can be significant, depending on the number of diagnostics, models and the number of years.

Initial setup

Rosesnip requires:

• Python 3.x
• Iris 2.x
• Afterburner
• Cylc 7.8.x

Edit rosesnip.rc and adapt the configuration for your environment. For instance

    [afterburner]
    abrun_exec = /nesi/nobackup/nesi99999/pletzera/niwa00013/nesi/turbofan/pletzer/bin/abrun.sh
    python_exec = /opt/nesi/CS500_centos7_skl/Anaconda2/2019.10-GCC-7.1.0/bin/python
    ...
    [slurm]
     account = nesi99999
    ...

How to use rosesnip

Running rosesnip involves three steps:

1. prepare the rose configuration files for parallel execution
2. generate the cylc suite.rc file
3. run the suite

Prepare the rose configuration files

python rsn_prepare.py -d my_res_dir -c rose-app-expanded.conf

This will create directory my_res_dir and split file rose-app-expanded.conf into many small rose configureation files, each running a subset of tasks.

Generate the cylc suite file

python rsn_create-cylc-suite.py -d my_res_dir -s

This will create file suite.rc. Use option -s option to create SLURM jobs.

Submit the rosesnip job with cylc

Once suite.rc has been created, register the suite and submit the suite for execution:

cylc register rosesnip_1 /path/to/suite.rc
gcylc rosesnip_1 &

Upon completion, you will find netCDF files under my_res_dir/nc and plots under my_res_dir/images. It is also possible to create the plots interactively by executing

python rsn_plot.py -d my_res_dir -I