Getting started with RAAD2

Introduction

We have two primary HPC systems, one called "raad2" and the other "hazeem".

Raad2 is a Linux based system from the vendor Cray (now HPE) and has a total of 4,128 traditional CPU cores of the Intel Haswell architecture. Each of its 172 compute nodes contains 24 physical CPU cores -- 2 processor sockets with 12 cores per socket -- and 128GB of RAM. The interconnect is comprised of the Cray Aries network, which is employed both for MPI as well as storage traffic. Raad2 runs SLURM as its workload manager, and is paired with a storage system from the vendor DDN that uses the parallel filesystem Lustre, providing about 800TB of usable disk capacity accessible from all nodes.

Hazeem too is a Linux based system from the same vendor and it has a total of 4,840 traditional CPU cores of the Intel Broadwell architecture. Each of its 121 compute nodes contains 40 physical CPU cores -- 2 processor sockets with 20 cores per socket -- and 192GB of RAM. The interconnect is comprised of the Cray Aries network, which is employed both for MPI as well as storage traffic. Hazeem also runs SLURM as its workload manager, and is paired with a Cray Sonexion storage system that uses the parallel filesystem Lustre, providing about 1PB of usable disk capacity accessible from all nodes.

Once your account is approved, you will receive an email notification containing temporary login credentials and basic guidance to access the system of your choice (Raad2 or Hazeem).

Raad2

Reaching Raad2 on the network

Note that raad2 started its life as an asset of Texas A&M University at Qatar (TAMUQ) but with mutual agreement this asset was transferred into the ownership of HBKU in 2025. Raad2 currently resides on a network administered by the Qatar Biomedical Research Institute (QBRI), which is isolated from the core HBKU network administered by HBKU IT. Practically, this means there are two ways to access the system: (a) via a VPN connection into the QBRI network, or (b) via a wifi network called "QBRI_Network" available in select buildings (currently LAS and RDC).

Please follow guidance from this page to reach this system.

Login to Raad2

You may login to the system using any SSH client but make sure to VPN into the QBRI network first if you are accessing the machine from outside HBKU.

% ssh <user_name>@raad2.biolab.local

In the case of raad2, note that the system login nodes are actually named "raad2a" and "raad2b" and you will automatically be directed to one or the other; it does not matter which login node you land on, or if you land on a different one in different login sessions -- both are configured identically and you may treat them as one and the same, even though they are two distinct physical servers.

Importantly, do note that the fully qualified domain names of these login nodes end in ".biolab.local". This is an unfortunate artifact of the QBRI network architecture, but we have accepted this naming scheme for now as it is not intended to be a permanent arrangement.

Hazeem

Reaching Hazeem on the network

Unlike raad2, Hazeem resides on the core HBKU network administered by HBKU IT (also known as University Technology Services, or UTS). As long as you are on the HBKU network, you may simply initiate a ssh connection to one of its two login nodes "xc50-1" or "xc50-2". Being "on the HBKU network" generally means you are joined to the HBKU-STAFF or HBKU-STUDENT wifi network or have a wired Ethernet connection to your device in a building operated by HBKU. You can establish a ssh connection with any ssh client program, but we commonly recommend MobaXterm. You will only ever need HBKU VPN to reach hazeem if you are away from HBKU (at home or traveling).

Please follow the guidance from this page to remotely access the system.

Login to Hazeem

You may login to the system using any SSH client but make sure to VPN into the HBKU network first if you are accessing the machine from outside HBKU.

% ssh <user_name>@hazeem.hbku.edu.qa

Change your initial password

You will be prompted to change your initial password on your first login to raad2 and hazeem. If this does not happen on its own please change it yourself by entering the command passwd in your terminal window. Note that your hazeem and raad2 account passwords are NOT linked to your domain account, although you may choose to set your password string to be identical to that other password. In order to change your initial password, as you type your current password and new password, you will notice the cursor doesn't move; this is normal and you may continue to enter your password string and proceed to hit enter thereafter.

Your home directory location

Your home directory location on raad2 is /ddn/home/<user_name> and for hazeem it is /lustre/home/<username>. When you login to the machine, by default you land in this location.

mustarif63@raad2b:~> pwd
/ddn/home/mustarif63
mustarif63@raad2b:~>

Applications available on the system

There are multiple software packages (applications, compilers & development tools, libraries, etc) which came bundled with the base software stack on the system. There are also others we installed on the system upon user request. All these can be listed for perusal using the command below:

mustarif63@raad2b:~> module avail

To setup the environment to access any specific software from your shell, you can issue...

mustarif63@raad2b:~> module load <module_name>

The commands above are shown to be executed on raad2 but they apply on hazeem as well.