Run CyTRACK

How do I run CyTRACK?

To run CyTRACK, create a file with the following code (could be run_cytrack.py)

import numpy as np
 import cytrack

 args = cytrack.read_args()
 if args.cytrack_help:
    cytrack.help()
 elif args.get_template:
    cytrack.get_cytrack_inputs_template()
 else:
    cytrack.get_cytrack_main(args.parameterfile)

Once this code is created, CyTRACK can be run as follows:

On a Linux computer

mpirun -n N_proc python run_cytrack.py  -pf input_file

e.g:  mpirun -np 4 python run_cytrack.py  -pf test_case.cfg

On a HPC with Linux

Create a bash script (run_cytrack.sh). This example is valid for FINESTARRAE III cluster at the Galician Supercomputing Center.

#!/bin/bash -l

#SBATCH --mem=64GB
#SBATCH -N 1
#SBATCH -n 40
#SBATCH -t 7-00:00:00

module --purge
module load cesga/2020
module load miniconda3/4.9.2
conda activate envname


srun -n $SLURM_NTASKS  --mpi=pmi2 python run_cytrack.py -pf input_file

Input and help

You can also get the input file template and help by using the run_cytrack.py script created above.

For input file template:

python run_cytrack.py -gt t

For help on the input file:

python run_cytrack.py -cth t

Note

CyTRACK could run under Windows if you have installed the Anaconda distribution. This case has not been tested yet. If you have any problem, please contact us.