Running

The Fractional Cover application works in 2 parts:

1. Creating the task list

2. Check for unexpected existing files - these were most likely created during an run that did not successfully finish.

3. Submit the job to gadi.

To run fractional cover:

$ module use /g/data/v10/public/modules/modulefiles/
$ module load dea

This will list the available app configs:

$ datacube-fc list
ls5_fc_albers.yaml
ls7_fc_albers.yaml
ls8_fc_albers.yaml

To submit the job to gadi, the datacube-fc app has a the datacube-fc submit command: This command kick off two stage PBS job

Stage 1 (Generate task file):

The task-app machinery loads a config file, from a path specified on the command line, into a dict.

If dry is enabled, a dummy DatasetType is created for tasks generation without indexing the product in the database. If dry run is disabled, generate tasks into file and queue PBS job to process them.

Stage 2 (Run):

During normal run, following are performed:

1. Tasks (loadables (nbart,ps,dsm) + output targets) shall be yielded for dispatch to workers.

2. Load data

3. Run FC algorithm

4. Attach metadata

5. Write output files and

6. Finally index the newly created FC output files

If dry run is enabled, application only prepares a list of output files to be created and does not record anything in the database.

Tracking progress

$ qstat -u $USER

$ qcat 7517348.gadi-pbs | head

$ qcat 7517348.gadi-pbs | tail

$ qps 7517348.gadi-pbs

File locations

The config file (eg. ls5_fc_albers.yaml) specifies the app settings, and is found in the module.

You will need to check the folder of the latest dea module:

ls /g/data/v10/public/modules/dea/<YYYYMMDD>/lib/python3.6/site-packages/fc/config

The config file lists the output location and file_path_template``, as shown in this snippet:

source_type: ls5_nbar_albers
output_type: ls5_fc_albers

description: Landsat 5 Fractional Cover 25 metre, 100km tile, Australian Albers Equal Area projection (EPSG:3577)
product_type: fractional_cover

location: '/g/data/fk4/datacube/002/'
file_path_template: 'LS5_TM_FC/{tile_index[0]}_{tile_index[1]}/LS5_TM_FC_3577_{tile_index[0]}_{tile_index[1]}_{start_time}_v{version}.nc'

So here the output files are saved to /g/data/fk4/datacube/002/FC/LS5_TM_FC/<tile_index>/*.nc

License

This repository is licensed under the Apache License 2.0. See the LICENSE file in this repository for details.

Contacts

Geoscience Australia developers:

Joshua Sixsmith joshua.sixsmith@ga.gov.au

Jeremy Hooke jeremy.hooke@ga.gov.au

Damien Ayers damien.ayers@ga.gov.au

Duncan Gray duncan.gray@ga.gov.au

Algorithm developer:

Peter Scarth peter.scarth@qld.gov.au