4. Using the command line

Run the following command to print help and check that it runs: cis --help

The following should be displayed:

usage: cis [-h] [-v | -q] [--force-overwrite]
           {plot,info,col,aggregate,subset,eval,stats,version} ...

positional arguments:
    plot                Create plots
    info                Get information about a file
    col                 Perform collocation
    aggregate           Perform aggregation
    subset              Perform subsetting
    eval                Evaluate a numeric expression
    stats               Perform statistical comparison of two datasets
    version             Display the CIS version number

optional arguments:
  -h, --help            Show this help message and exit
  -v, --verbose         Increase the level of logging information output to
                        screen to include 'Info' statements
  -vv                   All log messages will be output to the screen including 'Debug' statements
  -q, --quiet           Suppress all output to the screen, only 'Error'
                        messages will be displayed (which are always fatal).
  --force-overwrite     Do not prompt when an output file already exists -
                        always overwrite. This can also be set by setting the
                        'CIS_FORCE_OVERWRITE' environment variable to 'TRUE'

There are 8 commands the program can execute:

  • plot which is used to plot the data
  • info which prints information about a given input file
  • col which is used to perform collocation on data
  • aggregate which is used to perform aggregation along coordinates in the data
  • subset which is used to perform subsetting of the data
  • eval which is used to evaluate a numeric expression on data
  • stats which is used to perform a statistical comparison of two datasets
  • version which is used to display the version number of CIS

If an error occurs while running any of these commands, you may wish to increase the level of output using the verbose option, or check the log file ‘cis.log’; the default location for this is the current user’s home directory.

4.1. LSF Batch Job Submission

CIS jobs may be submitted to an LSF type batch submission system (e.g. the JASMIN environment) by using the command cis.lsf instead of cis. In this case the job will be sent to the batch system and any output will be written to the log file.