abcunit-cmip5-stats

Processing Framework for calculating temporal statistics from CMIP5 (using ABCUnit).

Overview

The name ABCunit corresponds to the 4 layers the workflow is split in to:

1. A - all
2. B - batch
3. C - chunk
4. The Unit

These scripts are an example of using the ABCUnit structure on CMIP5 data. This provides a repteable and efficient workflow.

The statistics that can be calculated are the maximum, minimum and mean.

The models, ensembles and variables available can be found in lib/defaults.py

Structure

1. Run all script = run_all.py

• Calculates given statistic for chosen models, ensembles and variables
• These are given as arguments on the command line
• Statistic must be specified as an argument at the command line
• Defaults to running for all models, ensembles and variables
• For each model it runs the batch script

2. Run batch script = run_batch.py

• Calculates the statistic over one chosen model and chosen ensembles and variables
• Defaults to all ensembles and variables
• Statistic and model must be specified when run at the command line
• Calls each ensemble as an argument for the chunk script
• The chunk script is submitted to LOTUS via bsub

3. Run chunk script = run_chunk.py

• Typically run on lotus but can be run from the command line
• Calculates the statstic for the specified model, ensemble and variables
• Statistic, model and ensemble must all be specified if run from the command line
• Defaults to all variables
• For each variable it:
  • Ignores if already calculated
  • Finds the necessary files
  • Checks the date range specified is valid
  • Calculates the statistic and writes to output file
  • Checks output file exists

Example usage

Log in to a JASMIN sci server:

ssh <user-id>@jasmin-sci5.ceda.ac.uk

Edit these files to match your setup:

• SETTINGS.py
• setup-env.sh

Clone this repositroy and make sure you are in the top level abcunit-cmip5-stats directory:

• https://github.com/cedadev/abcunit-cmip5-stats.git
• cd abcunit-cmip5-stats

First run the setup-env.sh script to setup up your environment.

Options for models, ensembles and variables can be found in lib/defaults.py. Note that the model is defined by its institute/model combination.

Running the top level 'run all' script at the command line:

python run_all.py -s mean

Running the 'run batch' script:

python run_batch.py -s mean -m MOHC/HadGEM2-ES

Running the 'run chunk' script locally, instead of using LOTUS, which is how it is invoked in the batch script:

python run_chunk.py -s mean -m MOHC/HadGEM2-ES -e r1i1p1

In each example, all other arguments are optional and can be included. For example, to calculate the mean of only 2 variables for in one model and ensemble:

python run_chunk.py -s mean -m MOHC/HadGEM2-ES -e r1i1p1 -v rh ra

Log Handling and Outputs

Currently the system supports two different ways to log successes and failures of jobs, output to the file system or using a database. One of these methods can be chosen in the settings file with the BACKEND variable.

File system logs

If using the file system log handler, log files will be outputted in the following way. Each job will result in a file with a success path or failure path in the following formats:

<current-directory>/logs/success/<stat>/<model>/<ensemble>/<var_id>

<current-directory>/logs/failure/<failure-type>/<stat>/<model>/<ensemble>/<var_id>

• current-directory is the directory you are in when running the python scripts.
• failure-type can be one of:
  • bad_data - Empty file produced when no netCDF files could be found for the chosen arguments.
  • bad_num - Empty file produced when the chosen date range is invalid for the chosen files.
  • no_output - Empty file produced when the output file could not be generated.

Database logs

If using the database log handler, success / failure logs will be output into a relation (named 'results' by default) in the following format:

id	result
mean.MOHC.HadGEM2-ES.r1i1p1.shrubFrac	success
mean.MOHC.HadGEM2-ES.r1i1p1.tran	bad_data
mean.MOHC.HadGEM2-ES.r1i1p1.treeFrac	success

To use this handler you will need to do the following setup:

1. Contact the JASMIN help desk and ask for a postgresql database to be made for you
2. Create an environment variable called ABCUNIT_DB_SETTINGS which stores a connection string for psycopg2, for example:
   • export ABCUNIT_DB_SETTINGS="dbname=<database_name> user=<user_name> host=<host_name> password=<database_password>"

Its useful to setup the variable in a script separate from your public code.

Outputs

Lotus outputs are in the following format:

<current-directory>/logs/lotus-outputs/<stat>/<model>/<ensemble>.out or <ensemble>.err

If a job is successful, its corresponding netcdf4 file will be output to:

<gws>/<user>/abcunit-outputs/<var_id>.nc

Where gws is a path to a group workspace and user is your username. Netcdf4 files are output to a group workspace to more effectivley use storage space.