This is the command ro run the generation process.
python zar_to_png_tiles.py <zarr_folder> <output_folder> <zoom_levels> <processes> [<fixed_date_index>]
Where zoom_levels should be in the format: <from>-<to>, where from and to are integers and from <= to.
A typical value would be "0-13".
processes indicates the number of parallel processes to use for tiling to speed up the computation.
When the optional fixed_date_index is specified, only the date with the specified index in zarr (0-based) is processed.
After SSH login at submit.unibe.ch this is the command that can be used to schedule a job for execution.
sbatch zarr_to_png_tiles.sh
Once the computational resource is allocated successfully, the console output of the job can be found at slurm-<job_id>.out, where job_id is shown by the previous command.
At the link https://hpc-unibe-ch.github.io/, there is more information about how to use UBELIX.
To host the files with nginx, use the vegetation-anomalies.conf config file from here and put it at /etc/nginx/conf.d. This file has some configurations missing, which should be set according to the place where the server will be used. In the file they are commented out. Make sure that the main config file of nginx, nginx.conf (typically located at /etc/nginx), includes the configs from conf.d.
The web application files should be put at /var/www/<web_application_name>. They are produced by the following command:
npm run build
If npm is not installed, install it.
This will create the build folder in the root folder of the project. Before running the command, make sure that the .env.production file has the parameter REACT_APP_ANOMALIES_MAPS_API_URL, which points to the web URL with the tiles.
To be able to set up GDAL without relying on the libraries installed at the OS level a Conda environment has to be used.
To install Miniconda - the more light-weight Conda environment - use the following commands. Change the path
~/miniconda3 to a different one, if you prefer to have the installation in a different location.
mkdir ~/miniconda3
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh
bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3
rm ~/miniconda3/miniconda.sh
To activate Miniconda in the current shell use the following command:
source ~/miniconda3/bin/activate
To deactivate it run
conda deactivate
Install gdal dependency separately.
conda install -y -c conda-forge gdal zarr
Go to the python directory of the project and install the needed requirements using
pip install -r requirements.txt
To be able to develop with nginx locally a docker image can be used.
To install docker and the required plugin run
sudo apt install docker.io docker-buildx
Look up if your container is running
docker ps
If it is the case, stop the existing container with the command
docker stop <conatiner name>
If needed, the image can be built from the Dockerfile recipe:
docker build docker/tiles_server --tag tiles-server
To start the dockerized server use the following command (change the path of the local mounted directory if needed):
docker run -p 8080:80 --mount type=bind,source=./data/cubes_demo_output,target=/usr/share/nginx/html,readonly --name tiles-server tiles-server &
Press Enter at the end to exit to the shell. The server will be running in the background. If you want to keep the server process attached to see the output, remove the symbol '&' at the end.
To stop a running container use the command:
docker stop tiles-server
docker rm tiles-server
Note that the container does not have to be removed, unless the corresponding image has changed.
If you want to remove the created image in the future, use the command:
docker rmi tiles-server
Note that the image does not have to be removed, if no changed have been made in Dockerfile.
Install the npm package manager. In Debian based Linux it is done with the following command:
sudo apt install npm
The application assumes, the tiles server is running on 'localhost:8080', so make sure to start the server before starting the web application.
When running the application for the first time and when adding/updating the dependencies run the following command:
npm install
From the 'python' directory run the following command.
npm run start
This command will open the web application in the browser.
Run the following command.
npm run build
It will deploy all necessary files in the build folder. This folder can be copied to the production server.