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Drone Upscaling

Installation

To ensure a consistent environment for all users, this project uses a Conda environment defined in a requirements.yml file. Follow these steps to set up your environment:

1. Install Conda: If you do not have Conda installed, download and install Miniconda or Anaconda.

2. Dependencies: You need to install sudo apt-get install build-essentials build-essential libgdal-dev. You need to match the libgdal version with gdal pip package version.

3. Create the Conda Environment: Navigate to the root of the project directory and run the following command to create a new environment from the requirements.yml file:

   conda env create -f requirements.yml

4. Activate the Environment: Once the environment is created, activate it using:

   conda activate drone_upscaling_env

5. Troubleshooting: If ImportError: /home/bioeos/miniconda3/envs/drone_upscaling_env/bin/../lib/libstdc++.so.6: version 'GLIBCXX_3.4.30' not found (required by /lib/x86_64-linux-gnu/libgdal.so.34)

Use:

sudo find / -name libstdc++.so.6 to find your local file.

strings /usr/lib/x86_64-linux-gnu/libstdc++.so.6 | grep GLIBCXX to check if the version 'GLIBCXX_3.4.32' is present.

Then:

ln -sf /usr/lib/x86_64-linux-gnu/libstdc++.so.6 /home/bioeos/miniconda3/envs/drone_upscaling_env/lib/libstdc++.so
ln -sf /usr/lib/x86_64-linux-gnu/libstdc++.so.6 /home/bioeos/miniconda3/envs/drone_upscaling_env/lib/libstdc++.so.6

Docker

The goal of this docker image is to be a ready-made environment to easily run scripts.

Build command :

docker build -f Dockerfile -t drone-upscaling:latest .

Run command :

docker run --user 1000 --rm \
  -v ./config/:/home/seatizen/app/config \
  -v /mnt/disk_victorlebos/qgis_projects/2023_upscaling_drone/layers/:/home/seatizen/app/layers \
 --name drone-upscaling drone-upscaling:latest -c --config_path ./config/config_stleu.json

Build singularity container

module load singularity/3.6.4

singularity build -f drone_upscaling.sif docker://seatizendoi/drone-upscaling:latest

PBS

#!/bin/bash

#PBS -l select=1:ncpus=32:mem=40g
#PBS -l walltime=2:00:00
#PBS -N drone_upscaling
#PBS -q omp
#PBS -S /bin/bash

signal_handler() {
        pkill --parent "${$}"
}
trap signal_handler EXIT
cd /home1/datahome/villien/PBS/drone_upscaling/

module load singularity/3.6.4


singularity run --pwd /home/seatizen/app/ \
--bind /home1/datahome/villien/PBS/drone_upscaling/config:/home/seatizen/app/config \
--bind /home1/datawork/villien/drone_upscaling_data:/home/seatizen/app/data \
drone_upscaling.sif -c --config_path ./config/config_stleu.json

qstat -f $PBS_JOBID