Hardware and Access

🖥️HPCF3 Cluster Overview

The HPCF3 login node is accessible via SSH using the hostname:

hpcf3.cpos.hku.hk

Click here for more details.

🧰Operating System & Software

All HPCF3 servers run on Rocky Linux 8.
A broad range of commonly used bioinformatics software is preinstalled and available to all users.

⚙️Services

Users submit jobs through OpenPBS, the cluster’s job scheduling system.
Execution is carried out on compute nodes via PBS jobs only.

➡️ Direct login to compute nodes is not permitted.

👤User Account Setup

To request a user account, contact itsupport.cpos@hku.hk.

• All account applications are subject to CPOS approval.
• Approved users receive a Linux account to access the cluster.
• Each account comes with 100 GB default storage; additional quota can be requested (subject to availability and charges).
• Each account is assigned to a named individual — account sharing is strictly prohibited.
• While storage systems are protected by hardware redundancy, users are strongly advised to maintain their own backups regularly.
• Users should be familiar with the Linux/UNIX environment. A reference guide is available from ITS.

🔐Cluster Login

Users may connect remotely via SSH using clients such as PuTTY, available at: http://www.chiark.greenend.org.uk/~sgtatham/putty/ 

Connection Details

To connect to the login node of HPCF3, please use an SSH client to open a SSH terminal session with the following: 

Hostname: hpcf3.cpos.hku.hk
Username:

🔒Network Requirement

For security reasons, HPCF3 servers are accessible only from within the HKU network.

• Off-campus users must first connect through HKUVPN.
  Details: https://its.hku.hk/services/network-connectivity/hkuvpn/

📦Data Transfer

🪟 Windows Users

For Windows users there are several free, GUI-based secure file transfer clients, such as WinSCP or FileZilla. You could use these clients with simply drag and drop files between the cluster front-end node and your desktop or laptop.

🍏 Mac / 🐧 Linux Users

For a Mac or Linux, the command-line scp client is typically installed with the operating system. You can access it through a terminal running on your local machine. For example, suppose you have a Mac, and a local file called myfile on your mac that you want to copy to your home directory on the cluster. 

Example:

 scp myfile userid@hpcf3.cpos.hku.hk:mydir/

This copies myfile into the directory mydir/ under your HPCF3 home directory.

As with any Unix command that takes files or directories as arguments, the file or directory for either the source or destination can be specified as either an absolute path (one that begins with a slash) or a relative path (one that does not). For local files or directories, relative paths are relative to the current working directory. For remote files or directories, relative paths are relative to a home directory on the remote host. 

📡Bulk Data Transfer Guidelines

To avoid impacting campus network performance:

• Transfers larger than 30 GB to/from outside the HKU network should be done outside office hours.
• For transfers exceeding 500 GB, please notify itsupport.cpos@hku.hk in advance so we can coordinate with ITS.

⚠️ Failure to provide notice for large transfers may result in ITS temporarily blocking cluster servers from the Internet.