Check time series continuity

To produce smaller files, the NetCDF files are splitted over the time period. Consequently, the different archives designs include the period dates into the filename. This scheme of chunked files in projects is not fixed and depends on several parameters (the institute, the model, the time frequency, etc.). These different schemes lead to unnecessary overlapping files with a more complex folder reading and wasting disk space. In addition, errors in the data production or publication workflows can lead to broken time series.

nctcck is designed to easily highlight broken time series or chunked NetCDF files producing overlaps in a time series. It is able to delete all chunked overlapping files in your variable directories in order to save disk space.

Detects overlaps or time gaps

$> nctcck /PATH/TO/SCAN/

By default, nctcck consider a time serie as broken when time gaps exist between netCDF time period. Following the CMIP Data Request, some data can be asked only for sub-periods in the time serie, thus time gaps are expected. To check compare broken time series against CMIP DR nctcck is able to use DR2XML files patterns to deduce if a time gap is expected or not. To activate this just submit the directory including both your config.card and run.card provided by the libIGCM framework:

$> nctcck /PATH/TO/SCAN/ --card /PATH/TO/SUBMISSION/DIRECTORY

Warning

This option is only available if you run your simulation within the IPSL libICM framework.

Remove overlapping files

$> nctcck /PATH/TO/SCAN/ {-r,--resolve}

Warning

We highly recommend to activate --resolve after a first dry-checking. This will potentially remove and/or rename files. Be careful to activate --resolve when you are sure about errors.

Remove full overlapping files only

$> nctcck /PATH/TO/SCAN/ --resolve --full-only

Define starting and/or ending period time stamps

Default is to consider the start (end) of the period, respectively, as the minimum (maximum) of the filename timestamps for each dataset. This could hide some missing files at the start or the end of the time period to cover. You can specify the start and end dates of the period to cover by using respectively –start and –end flags.

$> nctxck /PATH/TO/SCAN/ --start YYYYMMDD --end YYYYMMDD

Note

The submitted time stamp will be completed to 14 digits. We highly recommend to submit a digit as most precise as possible for the first date of the time axis.

Warning

Be careful this new submitted time stamp will be use to rebuilt time axis of all the file scanned.

Note

Both flags can be used independently.