diff --git a/manual/cluster_job_GPU_processing_template.job b/manual/cluster_job_GPU_processing_template.job new file mode 100644 index 0000000000000000000000000000000000000000..37ddc92b311745b7b34ea94429bcf8e3974b691c --- /dev/null +++ b/manual/cluster_job_GPU_processing_template.job @@ -0,0 +1,98 @@ +#!/usr/bin/zsh + +############################################## +##### Batch script for the MRCNN processing #### +############################################## + +#### CREATE SBATCH ENTRIES #### +#### Paths and parameters must be adapted accordingly. + +#### job name +#SBATCH --job-name=<JobName> + +#### Path and name of the output file of the job execution +#SBATCH --output=/home/<UserID>/.../<JobOutputFolderName>/%x_%J_output.txt + +#### Job runtime +#SBATCH --time=0-00:00:00 + +#### Memory requirement per GPU . +#### For example: if value is 5GB --> --mem-per-gpu=5G +#SBATCH --mem-per-gpu=5G + +#### E-mail address +#SBATCH --mail-user=<EmailAdress> + +#### E-mails to be received +#SBATCH --mail-type=ALL + +#### Number of tasks to be performed +#SBATCH --ntasks=1 + +#### Number of GPUs required per node +#SBATCH --gres=gpu:1 + +#### Definition of the job array starting at 0. ### +#### This parameter is only required if you want to perform several jobs in parallel +#### from one job script, e.g. processing one testing image set with several MRCNN models (epochs) +#### In this example we process one testing image set with 10 MRCNN models (= 10 epochs). +#### Thus, we will run 10 jobs in parallel from one job script --> array=0-9 +#SBATCH --array=0-9 + +#### CREATE TERMINAL ENTRIES #### +#### Paths and parameters must be adapted accordingly + +#### Definition of the job parameter, which is varied +#### if several jobs are executed in parallel from one job script. +#### This job parameter is only required if you have specified the #SBATCH parameter --array above. +#### In this example, we process one testing image set with 10 MRCNN models. +#### Thus, we will run 10 jobs in parallel from one job script: +#### the parameter model corresponds to the model of the current processing, +#### which is varied for each job. +model="$SLURM_ARRAY_TASK_ID" + +#### Loading the Cuda module +module load cuda/10.0 + +#### Export path in which Anaconda is located +export PATH=$PATH:/home/<UserID>/anaconda3/bin + +#### Activate environment +source activate env_mrcnn_gpu + +#### Navigate to the path where the droplet.py script is located +cd /home/<UserID>/.../samples/droplet/ + +#### Run the process_automated_droplet.py script. +#### These are the required processing parameters to be specified +#### with additional parameters required for the execution of parallel jobs from one job script. +#### In this example, we process one testing image set with 10 MRCNN models. +#### Thus, 10 jobs are executed in parallel (#SBATCH --array=0-9). +#### In each job the job parameter model is varied, starting with 0 and ending with 9. +#### The model names are model_00 to model_09. +#### First, we specify the processing parameter weights_name (--weights_name=model_0"$model"). +#### Moreover, we specify output folder and Excel output file names +#### defined by the processing parameters save_path and name_result_file, since we need 10 of them. +#### Optional processing parameters can be found below. +#### Description/default settings of all processing parameters see manual. +python process_automated_droplet.py --dataset_path=<InputFolderName> --save_path=<OutputFolderName>_0"$model" --name_result_file=<ExcelFileName>_0"$model" --weights_path=<WeightsFolderName> --weights_name=model_0"$model" --file_format=<FileFormat> --device=<Boolean> --pixelsize=<Double> --image_max=<Integer> + +#### Optional processing parameters: +#### --masks +#### --save_nth_image +#### --image_crop +#### --images_gpu +#### --confidence +#### --detect_reflections +#### --detect_oval_droplets +#### --min_aspect_ratio +#### --detect_adhesive_droplets +#### --save_coordinates +#### --min_velocity +#### --min_size_diff +#### --n_images_compared +#### --n_adhesive_high +#### --n_adhesive_low +#### --low_distance_threshold +#### --edge_tolerance +#### --contrast \ No newline at end of file