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:
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)