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.
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.
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:
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.
Introduction to profiling tools for AMD hardware
- 12 April 2023
Getting a code to be functionally correct is not always enough. In many industries, it is also required that applications and their complex software stack run as efficiently as possible to meet operational demands. This is particularly challenging as hardware continues to evolve over time, and as a result codes may require further tuning. In practice, many application developers construct benchmarks, which are carefully designed to measure the performance, such as execution time, of a particular code within an operational-like setting. In other words: a good benchmark should be representative of the real work that needs to be done. These benchmarks are useful in that they provide insight into the characteristics of the application, and enables one to discover potential bottlenecks that could result in performance degradation during operational settings.
AMD Instinct™ MI200 GPU memory space overview
- 09 March 2023
The HIP API supports a wide variety of allocation methods for host and device memory on accelerated systems. In this post, we will:
AMD matrix cores
- 14 November 2022
Matrix multiplication is a fundamental aspect of linear algebra and it is an ubiquitous computation within High Performance Computing (HPC) Applications. Since the introduction of AMD’s CDNA Architecture, Generalized Matrix Multiplication (GEMM) computations are now hardware-accelerated through Matrix Core Processing Units. Matrix Core accelerated GEMM kernels lie at the heart of BLAS libraries like rocBLAS but they can also be programmed directly by developers. Applications that are throughput bound by GEMM computation can achieve additional speedups by utilizing Matrix Cores.