Slurm Submission

vibes can submit jobs on cluster using the slurm submission system. The configuration goes via the task input file by adding a [slurm] section. A template can be generated via

vibes template slurm >> your_input.in

Task input file with [slurm] section

...
[slurm]
name:         test
tag:          vibes
mail_type:    all
mail_address: your@mail.com
nodes:        1
cores:        32
queue:        express
timeout:      30

Submit a job

A job is submitted by using vibes submit instead of vibes run. For example, you would run vibes submit md md.in on a cluster to submit the calculation to the queue instead of running vibes run md md.in locally. vibes submit will submit the job to the cluster according to the specification it finds in the [slurm] section, see below.

The command will do the following:

• Write a submit.sh script according to the specifications found in the [slurm] section,
• submit the job to the queue via sbatch submit.sh, and
• log the time of submission and the job ID to a file called .submit.log.

Restart a job

vibes supports automatic restarts if the job will take longer than the available walltime, which is often the case during ab initio molecular dynamics simulations. Restarts can be requested by adding

...
[restart]
command: the command to restart the calculation, e.g., `vibes submit md md.in`

to your task input file. This will run the command specified here shortly before the walltime is over.

The [slurm] section

name

str: The name of the job.

tag

str: A common tag added to the job name to cluster sets of jobs.

mail_type

str: The slurm mail type usually specified via --mail-type

mail_address

str: The mail address that slurm will send notifications to.

nodes

int: The number of nodes to be used for the job (job dependent).

cores

int: The number of cores per node to be used for the job (machine dependent!).

queue

str: The name of the queue to be submitted to.

timeout

int: Walltime for the job in minute. Queue and cluster dependent!