KAUST Supercomputing Laboratory Newsletter 22nd September 2020

In this newsletter:

  • Saudi National Day
  • RCAC meeting
  • Application License Server Maintenance by IT on Thursday, 1st October 2020, 8.00 PM to 4:00 AM 2nd October
  • KAUST supercomputer Shaheen II joins the fight against COVID-19
  • Tip of the week: Customising ssh
  • Follow us on Twitter
  • Previous Announcements
  • Previous Tips


Saudi National Day

The 23rd and 24th September are KAUST holidays to celebrate Saudi National Day. We will be back to work on 27th September.


RCAC meeting

The project submission deadline for the next RCAC meeting is 30th September 2020. Please note that the RCAC meetings are held once per month. Projects received on or before the submission


Application License Server Maintenance by IT on Thursday, 1st October 2020, 8.00 PM to 4:00 AM 2nd October

Due to a scheduled maintenance of the Application License Server by IT on Thursday, 30th July 2020, 8.00 PM to 4:00 AM next day, access to the below applications will be impacted on Shaheen and Neser: 

Ansys, AtomistixToolKit (ATK), Converge, Eclipse, Intel Compilers, Material Studio, Mathematica, MATLAB, Tecplot and Totalview.

During these maintenance windows, you may face issues with Intel at compilation and error with the application at runtime.


KAUST supercomputer Shaheen II joins the fight against COVID-19

King Abdullah University of Science and Technology (KAUST) invites researchers from across the Kingdom to submit proposals for COVID-19-related research. Recognizing the urgency to address global challenges related to the COVID-19 pandemic through scientific discovery and innovation, the University’s Supercomputing Core Laboratory (KSL) is making computing resources—including the flagship Shaheen II supercomputer and its expert scientists—available to support research projects.

Topics may include but are not limited to: understanding the virus on a molecular level; understanding its fluid-dynamical transport; evaluating the repurposing of existing drugs; forecasting how the disease spreads; and finding ways to stop or slow down the pandemic.

Accepted proposals can access the following resources: (1) Shaheen II, a Cray XC-40 supercomputer based on Intel Haswell processors with nearly 200,000 compute cores tightly connected with Aries high-speed interconnect; (2) Ibex cluster, a high throughput computer system with about 500 computing nodes using Intel Skylake and Cascade Lake CPUs and Nvidia V100 GPUs; and (3) KSL staff scientists, who will provide support, training and consultancy to maximize impact. Through 30 June 2020, up to 15% of these resources will be reserved for fast-tracking competitive COVID-19 proposals through the KAUST Research Computing Allocation Committee.  Thereafter, such proposals remain welcome and will be considered in the standard process.

Applicants can apply for computing allocations using the COVID-19 Project Proposal form. Please submit the form to projects@hpc.kaust.edu.sa. Submitted proposals will be fast-tracked for processing.

Please contact help@hpc.kaust.edu.sa with any inquiries.


Tip of the week: Customising ssh

Tired of typing the full address of shaheen when connecting via ssh? Using aliases and configuring your ssh client is the solution!

The default behavior of ssh can be configured by modifying the $HOME/.ssh/config file.  Each configuration in your config file is initiated by the keyword Host followed by an alias name you wil be now able use instead of  the full machine name.

Following this line, you have to define the configuration option you desire for this machine in particular. The most common SSH configuration options are:

  • HostName: the hostname or IP address of the machine to connect. 
  • User: the connection username.
  • Port: the port where the machine is expecting your connection (usually 22)

other interesting options are

  • Compression: a useful option for (very) slow connections.
  • ServerAliveInterval: to avoid having your session closed due to SSH timeouts. you can use this option to know if your unreliable connection is still alive.
  • StrictHostKeyChecking: this option is used to configure whether SSH automatically adds hosts to the ~/.ssh/known_hosts file. 
  • ForwardX11 yes: to systematically allow the forwarding of graphical window, without having to add -X or -Y when calling ssh
  • IdentityFile ~/.ssh/<my_ssh_key.rsa> to use a specific ssh key
  • ControlMaster
  • ControlPath  : these three Control options allow you to use ssh multiplexing, so that you only need to login with authentication once, as long as your first session remains open.
  • ControlPersist


An example $HOME/.ssh/config file entry for connecting to Shaheen is as follows:

Host shaheen
    HostName shaheen.hpc.kaust.edu.sa
    User my_login_name_on_shaheen
    ForwardX11 yes
    ServerAliveInterval 240
    ControlMaster auto
    ControlPath ~/.ssh/master-%r@%h:%p
    ControlPersist 4h

Instead of

ssh -X my_login_name_on_shaheen@shaheen.hpc.kaust.edu.sa

I now type

ssh shaheen

One last thing - to work properly,  permissions on $HOME/.ssh, as well as on $HOME/.ssh/config have to be restricted to your user only. To grant the correct permission on these files, run the following command once:

chmod 700 $HOME/.ssh

chmod 600 $HOME/.ssh/config


Follow us on Twitter

Follow all the latest news on HPC within the Supercomputing Lab and at KAUST, on Twitter @KAUST_HPC.

Previous Announcements


Previous Tips