KAUST Supercomputing Laboratory Newsletter 3rd September 2020

In this newsletter:

  • RCAC meeting
  • KAUST Research Team Wins Best Paper Award at EuroPar'2020
  • KAUST supercomputer Shaheen II joins the fight against COVID-19
  • Tip of the Week: Parsing the jobid for dependencies
  • Follow us on Twitter
  • Previous Announcements
  • Previous Tips

 

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 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 Research Team Wins Best Paper Award at EuroPar'2020

Congratulations to our colleagues at ECRC (Tariq Alturkestani, Hatem Ltaief, and David Keyes) for winning the Best Paper Award at EuroPar'2020, entitled Maximizing I/O Bandwidth for Reverse Time Migration on Heterogeneous Large-Scale Systems.

The reverse time migration (RTM) method is critical in seismic imaging for oil and gas industries. The team demonstrated the effectiveness of  Multilayer Buffer System (MLBS) framework developed by Tariq Alturkestani on Shaheen-2 and Summit supercomputers. MLBS achieves up to 2.5X and 1.4X performance speedups compared to the reference RTM implementation for a large 3D solution grid on Shaheen-2 and Summit, respectively using 2048 nodes.

More information is available here:

https://cemse.kaust.edu.sa/hicma/news/tariq-receives-his-best-paper-award-europar2020

 

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: Parsing the jobid for dependencies

To simplify your workflow with job dependencies to construct complex pipelines or chain together long simulations requiring multiple steps, you can use  the --parsable option to sbatch. This command outputs only the job id number. Check the example below:

jobid1=$(sbatch --parsable submit_job1.sh )
jobid2=$(sbatch --parsable --dependency=afterany:$jobid1 submit_job2.sh)
jobid3=$(sbatch --parsable --dependency=afterany:$jobid1 submit_job3.sh)
sbatch --dependency=afterok:$jobid2,afterok:$jobid3 submit_finaljob.sh

 

Follow us on Twitter

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

Previous Announcements

http://www.hpc.kaust.edu.sa/announcements/

Previous Tips

http://www.hpc.kaust.edu.sa/tip/