2  Getting Started on Hazel

3 01. First steps in Hazel HPC

3.1 Set up an account

Request access from your supervisor and in the mean time read and understand Acceptable Use Policy. Obtain your UnityID credentials and ensure you have VPN access if working off-campus.

3.2 Log in

  1. Web browser (OnDemand): https://servood.hpc.ncsu.edu
  2. Terminal: To connect to the shared HPC login nodes, open a terminal window and type
ssh [UnityID]@login.hpc.ncsu.edu

where user_name is the Unity ID.

To allow Hazel to open a window on a local machine, e.g., for GUI applications, X11 forwarding must be enabled by adding the -X option (i.e. ssh -X user_name@login.hpc.ncsu.edu). On macOS, install XQuartz to use X11 forwarding. When using MobaXterm, X11 is enabled by default.

  1. VSCode: https://hpc.ncsu.edu/Documents/LoginUsingVSCode.php

3.3 Transfer files

3.3.1 OnDemand

Go to OnDemand

  • Under Files, using the Upload or Download buttons to transfer. Make sure you navigate to the destination/source directory on cluster using the Go To button before transferring files.

3.3.2 SCP

For transferring a single file in one direction. Open a terminal on your local machine, and without login into the HPC do:

# Local to HPC
$ scp filename [UnityID]@login.hpc.ncsu.edu:/rs1/researchers/[letter]/[name] local/path/to/stuff

# HPC to local
$ scp [UnityID]@login.hpc.ncsu.edu:/rs1/researchers/[letter]/[name] local/path/to/stuff

3.3.3 SFTP

To transfer multiple files or in multiple directions (local to HPC and viceversa) without needing to re-authenticate, or to be able to navigate the remote file system. From the local machine initiate an SFTP session:

$ sftp [UnityID]@login.hpc.ncsu.edu

At the prompt do:

sftp> cd /path/to/stuff
sftp> put filename
sftp> get filename

3.3.4 Globus

Globus is a point to point file syncing platform. It is very useful for transfering large files or large numbers of small files, since it allows for bacground scheduled transfers. See our Globus-ncsu tutorial to learn more about Globus and how to use it with the NCSU Hazel HPC.

3.4 Useful commands

3.4.1 System and user info

  • Check queues you have access to: $ bqueues -u [UnityID]
  • Check the groups you belong to (first one is your default): $ groups
  • To see what node you are in: $ hostname or $ echo $HOSTNAME

3.4.2 Storage

  • Check size of the directory you are in: $ du -sh . > Important for checking pipeline output size
  • Check size of files in a directory: $ du -sh [pathtodirectory]/*
  • Check how much space is being used in your home directory: $ quota
  • Check space allocations for your group: $ quota -s -g group_name
  • Check files in reversed time order (most recently modified at the end): $ ls -lrt

3.4.3 Software and resource info

  • Find available modules: $ module avail
  • Find path to executable: $ wich [executablename]

3.5 Resources

3.6 Your First Week on Hazel HPC

3.6.1 Before You Start:

3.6.2 Getting Connected: