Posts by Gina Sitaraman

AMD Collaboration with the University of Michigan offers High Performance Open-Source Solutions to the Bioinformatics Community

16 May 2024

Long read DNA sequencing technology is revolutionizing genetic diagnostics and precision medicine by helping us discover structural variants and assemble whole genomes. It also helps us study evolutionary relationships. Lower sequencing costs and high-throughput portable long read sequencers are revolutionizing precision medicine today. Long read sequencers from the top manufacturers including Oxford Nanopore (ONT) and PacBio, can produce reads that are much longer than previous generations of sequencers. However, long reads vary in length and are significantly more error prone than short reads. Sequence alignment (on CPUs) is one of the main bottlenecks in long read processing workflows.

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Application portability with HIP

26 April 2024

Many scientific applications run on AMD-equipped computing platforms and supercomputers, including Frontier, the first Exascale system in the world. These applications, coming from a myriad of science domains, were ported to run on AMD GPUs using the Heterogeneous-compute Interface for Portability (HIP) abstraction layer. HIP enables these High-Performance Computing (HPC) facilities to transition their CUDA codes to run and take advantage of the latest AMD GPUs. The effort involved in porting these scientific applications varies from a few hours to a few weeks and largely depends on the complexity of the original source code. Figure 1 shows several examples of applications that have been ported and the corresponding porting effort.

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Affinity part 2 - System topology and controlling affinity

16 April 2024

In Part 1 of the Affinity blog series, we looked at the importance of setting affinity for High Performance Computing (HPC) workloads. In this blog post, our goals are the following:

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Affinity part 1 - Affinity, placement, and order

16 April 2024

Modern hardware architectures are increasingly complex with multiple sockets, many cores in each Central Processing Unit (CPU), Graphical Processing Units (GPUs), memory controllers, Network Interface Cards (NICs), etc. Peripherals such as GPUs or memory controllers will often be local to a CPU socket. Such designs present interesting challenges in optimizing memory access times, data transfer times, etc. Depending on how the system is built, hardware components are connected, and the workload being run, it may be advantageous to use the resources of the system in a specific way. In this article, we will discuss the role of affinity, placement, and order in improving performance for High Performance Computing (HPC) workloads. A short case study is also presented to familiarize you with performance considerations on a node in the Frontier supercomputer. In a follow-up article, we also aim to equip you with the tools you need to understand your system’s hardware topology and set up affinity for your application accordingly.

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