KAUST Supercomputing Laboratory Newsletter 2nd July 2020

In this newsletter:

  • RCAC meeting
  • KAUST supercomputer Shaheen II joins the fight against COVID-19
  • Tip of the Week: Detecting memory leaks and errors with Valgrind4hpc tool
  • Follow us on Twitter
  • Previous Announcements
  • Previous Tips


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: Detecting memory leaks and errors with Valgrind4hpc tool

Valgrind4hpc debugging tool helps in the detection of memory leaks and errors in parallel applications. It's similar to valgrind, which is designed for serial applications.

Compile and link with  -g option , then allocate and follow the steps shown bellow. This is an example using one node with 2 tasks.

salloc -N 1
module unload darshan xalt
module load valgrind4hpc
export CTI_WLM_IMPL=slurm
valgrind4hpc -n2 --launcher-args="--hint=nomultithread --ntasks=2" --valgrind-args="--track-origins=yes --leak-check=full" ./my_exe

Here is a clean output. Otherwise, follow the instructions to detect the memory leaks:

RANKS: <0,1>
  in use at exit: 0 bytes in 0 blocks
All heap blocks were freed -- no leaks are possible
ERROR SUMMARY: 0 errors from 0 contexts (suppressed 19)

To run your program and debug it across multiple nodes, allocate the desired number of nodes and then update accordingly the parameters in the launcher-args similar to the option for the srun/sbatch script.

Note that valgrind4hpc and target program arguments should be seperated by two dashes, --

More information is available in the man pages of valgrind and valgrind4hpc.


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