KAUST Supercomputing Laboratory Newsletter 29th July 2020

In this newsletter:

  • System Maintenance
  • Application License Server Maintenance by IT
  • EID Holiday
  • RCAC meeting
  • KAUST supercomputer Shaheen II joins the fight against COVID-19
  • Tip of the Week: Filtering jobs in squeue
  • Follow us on Twitter
  • Previous Announcements
  • Previous Tips

 

System Maintenance

We would like to announce that our next maintenance session on Shaheen will be on Tuesday the 11th of August 2020. We will send another reminder and more details closer to the date. Please get in touch with us at help@hpc.kaust.edu.sa, should this cause any concerns.

 

Application License Server Maintenance by IT on Thursday, 30th July 2020, 8.00 PM to 4:00 AM 31st July

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.

 

EID Holiday

KAUST will be on holiday from 30th July until 8th August (inclusive) due to the EID Al-Adha Holiday. Please do not expect to receive replies to support requests during this period.

 

RCAC meeting

The project submission deadline for the next RCAC meeting is 31st July 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: Filtering jobs in squeue

The latest version of SLURM installed on Shaheen during the last maintenance session introduced a new option for squeue. Compact and easy to remember, if you want to filter your own jobs in the queue, run:

squeue --me

    JOBID  PARTITION         NAME     USER    STATE       TIME TIME_LIMI  NODES NODELIST(REASON)
14185711     workq     my_jobName  kortass  RUNNING      43:53   2:00:00      1         nid00312

Similar commands filters jobs:

squeue --nodelist=f16n35,f16n37  Show Jobs Running on Compute Nodes
squeue --user=xxxx Show Jobs for user xxxx
squeue --start Show the Estimated Start Time

 

squeue -j jobid Show Job jobid

Looking for other tips?  Check this page for more than 90 previous tips covering a wide range of domains: job management, compilers, code debugging, use of highly tuned libraries, MPI, performance monitoring & tuning, filesystems and even domain specific topics such as CFD and Numerical Analysis. 

 

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/