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,info,col,aggregate,subset,eval,stats,version}
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 datainfo
which prints information about a given input filecol
which is used to perform collocation on dataaggregate
which is used to perform aggregation along coordinates in the datasubset
which is used to perform subsetting of the dataeval
which is used to evaluate a numeric expression on datastats
which is used to perform a statistical comparison of two datasetsversion
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.