4 Linux Shell

Shell

Shell is the traditional method for interacting with HPC and Linux

• Even with ondmand you will need to understand how linux commands work
• You will probably need to learn linux on your own as you increase your usage of HPC
• Tons of resources online, just google it.

Review https://ubuntu.com/tutorials/command-line-for-beginners#1-overview

TASK: Lets open a linux shell in multiple ways.

• Ondemand Shell srun -p quick -w compute146 -t 1:00:00 --pty bash -i
• Linux Desktop
• SSH (using a company laptop at work or with VPN)

VAI has many software tools installed

• Using modules

module avail
module load VARI/slurmPretty
slurmnodez
R --version
module load bbc2/R/R-4.4.0
R --version

• Submitting jobs

TASK: Lets resubmit the previous Job

#!/bin/bash
#SBATCH -n 1
#SBATCH -p quick
#SBATCH --job-name=zacks_job
#SBATCH --time=1:01:00

cd /varidata/researchtemp/hpctmp/your.name/hpc_workshop
gzip -v -d /varidata/researchtemp/hpctmp/hpc_workshop/mybigfile.dat.gz

Best practices for submit node and HPC

• No actual Work should be done on the submit node!
• dont just leave your interactive jobs idling too long, especially on bigmem and gpu

Manual VPN and SSH.

• Connecting from home