batch.md

Batch Script Helper

ai2-kit tool batch --help

A toolkit to generate batch scripts.

Usage

ai2-kit tool batch map_path --help
ai2-kit tool batch run_cmd --help
ai2-kit tool batch gen_batches --help

Examples

Generate batch scripts to run CP2K tasks

Suppose you want to run new CP2K tasks based on the previous runs, whose work directories can be found with ./old/iters*/label-cp2k/tasks/*, and the new CP2K config file is in ./new/cp2k.inp, then you can do the following steps:

1. Create new tasks directories by linking to (or copying) the old ones

ai2-kit tool batch map_path ./old/iters*/label-cp2k/tasks/* --target "new/task-{i:04d}"

The command above will create new directories new/task-0000, new/task-0001, etc. and link the old tasks directories to them. If you want to copy the old tasks directories instead of linking them, you can use --copy option.

2. Generate batch scripts

Suppose you are using SLURM as your job scheduler, then you need to prepare a header file for your batch scripts. For example, you can create a file named header.sh with the following content:

#!/bin/bash
#SBATCH --job-name=cp2k
#SBATCH --nodes=4
#SBATCH --ntasks-per-node=32

module load intel/2019.5
module load cp2k/7.1

Suppose the command you want to run in each task directory is mpirun cp2k.popt -i ../cp2k.inp &> output (note that the command is run in the task directory, so the input file is at ../cp2k.inp), then you can generate batch scripts with the following command:

ai2-kit tool batch gen_batches new/task-* --header_file header.sh --cmd "mpirun cp2k.popt -i ../cp2k.inp &> output" \
    --out_script "new/cp2k-{i}.sbatch" --concurrency 5

The above command will generate 5 batch scripts named new/cp2k-0.sbatch, new/cp2k-1.sbatch, etc. and each batch script will run part of the tasks in new/task-* directory.

3. Submit batch scripts to your job scheduler

You can submit the batch scripts to your job scheduler with sbatch and xargs commands.

ls -1 new/cp2k-*.sbatch | xargs -I {} sbatch {}

Tips

• You can use the write_each_frames in ase tool to generate multiple input files, then use the above command to generate batch scripts for each input file.