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Submitting A Batch Job

Batch Scripts

  • When we want to run a script on the Tufts HPC cluster we need to submit it as a batch script.
  • Here is an example of a batch script called sbatch.sh:

sbatch.sh

#!/bin/bash
#SBATCH --job-name=job            # job name is "job"
#SBATCH --nodes=1                 # 1 nodes #for many shared-memory programs,please leave -N as 1.
#SBATCH -n 2                      # 2 tasks total and 1 cpu per task, that gives you 2 cpu cores for this job
#SBATCH --partition=batch         # running on "batch" partition/queue
#SBATCH --reservation=bioworkshop # running on a reservation, named "bioworkshop", if no access to reservation, omit this line
#SBATCH --mem=8Gb                 # requesting 8GB of RAM total for the number of cpus you requested
#SBATCH --time=0-24:00:00         # requested time (DD-HH:MM:SS) 24 hours
#SBATCH --output=%j.out           # saving standard output to file, %j=JOBID
#SBATCH --error=%j.err            # saving standard error to file, %j=JOBID
#SBATCH --mail-type=ALL           # email optitions
#SBATCH --mail-user=Your_Tufts_Email@tufts.edu  # use your own Tufts email address

# [this is a comment]
# The order of the "#SBATCH" options doesn't matter

#[commands_you_would_like_to_exe_on_the_compute_nodes]
# for example, running blast 
# load the module so the correct version of blast is available to you

module load blast-plus/2.11.0

# running blast
blastp -query mm-second.faa -db zebrafish.1.protein.faa -out mm-second.x.zebrafish.tsv -outfmt 6

Submitting a Batch Job

  • Submit the job using the following command from command line interface:
sbatch sbatch.sh

Looking for a sample batch script?

Sample Scripts including R, conda, matlab, gaussian, etc. can be found here:

/cluster/tufts/hpc/tools/slurm_scripts