KAUST Supercomputing Laboratory Newsletter 30th April 2020

In this newsletter:

  • KAUST supercomputer Shaheen II joins the fight against COVID-19
  • System Maintenance
  • RCAC Meeting
  • Tip of the Week: Launching Containers on Shaheen
  • Follow us on Twitter
  • Previous Announcements
  • Previous Tips


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.


System Maintenance

The next maintenance session will take place from 08:00 on Monday 11th May until 17:00 on Wednesday 13th May. There will be no access to the system during this period.


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


Tip of the Week: Launching Containers on Shaheen

The Singularity container platform, the preferred platform for HPC centers supporting containerized workloads, is installed on Shaheen.

If you have a pre-existing Docker image you can convert it to a Singularity image file by running the following command:

module load singularity
singularity pull docker://Image_name:tag

which produces a single image File or .sif file in your current working directory. Here Image_name:tag is the name of the image and the tag of your desired image you wish to pull from the Dockerhub repository.

To run a container from this image you can include the following in your jobscript or in an interactive session:

srun -n 1 singularity exec image_name_tag.sif /path/to/application/inside/container/application.exe

There are several useful Singularity commands not covered here. We would love to hear from you if you have a containerized workflow and would like to run it on Shaheen. Please email us  at help@hpc.kaust.edu.sa


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