KAUST Supercomputing Laboratory Newsletter 10th September 2020

In this newsletter:

  • Shaheen 101 training: September 17th, 2020
  • RCAC meeting
  • KAUST supercomputer Shaheen II joins the fight against COVID-19
  • Tip of the Week: Reduce the I/O wait time with IOBUF
  • Follow us on Twitter
  • Previous Announcements
  • Previous Tips


Shaheen 101 Training: September 17th, 2020

KAUST Supercomputing Lab invites you to attend the “HPC 101 Shaheen II Training”, which will be held on Thursday, September 17th, 2020 online via Zoom: https://kaust.zoom.us/j/92335642776

The aim of this course is to give users of Shaheen II, Cray XC40 supercomputer, an introductory overview of the system and its usage, and to help them make efficient use of their allocated resources. Changes and new features on Shaheen will be also discussed.

The workshop agenda is as follows and the slides are here attached:

  • 10:00 am           Welcome
  • 10:05 am           Overview of Shaheen and Neser Architecture
  • 10:15 am            How to get an account and access to Shaheen
  • 10:25 am            Running environment and Job Scheduling
  • 10:50 am            Running HPC workflow on Shaheen: VASP example
  • 11:05 am            Applications software example: CFD example
  • 11:20 am            Programming environment, debugging and profiling, Best practices and tips
  • 11:40 am            Questions and open discussions with KSL team

Please register at  https://hpc.kaust.link/Shaheen101_Fall2020


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


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: Reduce the I/O wait time with IOBUF

You can reduce the I/O wait time for programs that read or write large files sequentially by using IOBUF.

IOBUF is an I/O buffering library that intercepts I/O system calls and adds a layer of buffering to improve program performance by enabling asynchronous prefetching and caching of file data. It can also gather runtime statistics on the I/O activity for each file.

No program source changes are needeed, all you need is to just load the IOBUF module and relink your program binary.

module load iobuf

Set the IOBUF_PARAMS environment variable in your job script using:

export IOBUF_PARAMS='*:verbose'

More information are available in the man page accessible using: man iobuf


Follow us on Twitter

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

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