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Using Linux Command Line Interface

SCINet HPC resources can be used via GUI tools such as Geneious, CLC Workbench, SmartAnalysis, JupyterHub, SCINet Galaxy etc., however users are limited by what these tools provide. One can do much more ssh-ing to a cluster and using Command Line Interface (CLI). If you’re not familiar with CLI, check out the following resources:

  1. Introduction to Unix
  2. Unix Tutorials

Below is a list of basic CLI commands

man command - Show manual for command

pwd - Output the current directory that you are in

ls - List the content of the current directory

ls -a - List all the content, including hidden files

ls -l - List the content and its information

mkdir foldername – Create a new folder foldername

cd foldername – Change the working directory to foldername

cd - Return to $Home directory

cd .. - Go up a directory

cd - - Return to the previous directory

my_quotas - reports storage usage and quota information for home and project directories

emacs, nano, vi – Editors

cp source destination – Copy source to destination

cp -r source destination – Copy a folder recursively from source to destination

mv source destination - Move (or rename) a file from source to destination

rm file - Remove file

rm -r folder - Remove folder and its contents recursively

cat file – Print contents of file on the screen

less file - View and paginate file

head file - Show first 10 lines of file

tail file - Show last 10 lines of file

history – Show list of commands issued earlier

!commandnumber – Reissue command number commandnumber

which command – Shows the full path of command


module avail or module spider – Show all available software modules

module avail swname – Show all modules that have swname in the name

module load modulename – Load module modulename in your environment

module unload modulename - Unload module modulename from your environment

module list – List all modules currently loaded in your environment

module help modulename – Show information about module modulename

module purge – Unload all modules from your environment

module use path – Add path where to search for available modules


salloc -p debug -N 1 -n 2 –mem=7G -t 2:00:00 – Request 2 cores and 7 GB of memory in debug partition for 2 hours

exit – Close session (should be used to close interactive session)

sbatch jobscript – Submit jobscript into queue

squeue – Show all jobs currently running or waiting in the queue

sinfo – Show available partitions (queues)

scancel jobnumber – Cancel job jobnumber

seff jobnumber – Get resource usage information for job jobnumber (use it for jobs that have already finished)