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Quick start guide to running a job on Klone

See the "Running a job" instructions for a more detailed description of how set up and run a job on Klone.

  1. SSH into Klone:

  2. ssh <UW_NetID>@klone.hyak.uw.edu

    • You'll need to replace <UW_NetID> (including the < and >) with your UW NetID.

  3. Create a SLURM script (e.g. 20240917-cgig-ncbi-blastx.sh) with the following commands (these come after the SLURM header):

    module load apptainer


apptainer exec \
--home $PWD \
--bind /mmfs1/home/ \
--bind /mmfs1/gscratch/ \
/gscratch/srlab/containers/srlab-bioinformatics-container-<git_commit_hash>.sif \
<commands-script.sh>
    • You'll need to replace anything in <> (including the < and >) with your specific requirements.
    • <commands-script.sh> is a Bash script containing all of the commands/programs you wan to run.

  4. Submit job to SLURM scheduler (i.e. start your job):

    • sbatch <slurm_script_name.sh>

      • You'll need to replace anything in <> (including the < and >) with your specific requirements.

For more information, check out the following: