KAUST Supercomputing Laboratory Newsletter 14th May 2020

In this newsletter:

  • RCAC Meeting
  • KAUST supercomputer Shaheen II joins the fight against COVID-19
  • Tip of the Week:Creating & controling your module environment
  • Follow us on Twitter
  • Previous Announcements
  • Previous Tips


RCAC Meeting

The project submission deadline for the next RCAC meeting is 31st May 2020. Please note that the RCAC meetings are held once per month. Projects received on or before the submission deadline will be included in the agenda for the subsequent RCAC meeting. The detailed procedures, updated templates and forms are available here: https://www.hpc.kaust.edu.sa/account-applications


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:  Creating & Controlling your module environment

KSL systems share the same $HOME regardless of the platform (Shaheen, Neser, Ibex). There are 2 options to customize your environment for each platform, either by customising startup files or by using the module snapshot.

Option1: updating your .bashrc (for example)

Specify the host of the system, otherwise it will cause issues depending on the platform you are accessing, since the module path and default enviroment variables are not the same. Here is an example for Shaheen and Neser within $HOME/.bashrc


case "$KSL_HOST" in
        : # settings for Shaheen
        export My_Env="Path of Shaheen env"
         module swap PrgEnv-cray PrgEnv-intel
        : # settings for Neser
        export My_Env="Path of Neser env"
         module load intel

Option2: Using module snapshots

The basic idea is that you take a snapshot of your environment and save it with a name.

  • swap and load modules to your desired configuration
  • save the "snapshot" with  module snapshot <snapshot-filename>

When you want to restore the environment, there is no need to manually load all the modules, it can be done with module restore <snapshot-filename>.

Also, you can create and install your own modules in your project directory and share with other team members. It can be made visible to the module command by module use /path/to/customized/modulefiles.


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