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Analyzing the Performance Portability of SYCL across CPUs, GPUs, and Hybrid Systems with Protein Database Search

Manuel Costanzo, Enzo Rucci, Carlos García-Sánchez, Marcelo Naiouf, Manuel Prieto-Matías

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Tags: AMD Radeon RX 6700 XT, AMD Radeon RX Vega 6, ATI, Bioinformatics, Biology, Computer science, CUDA, Databases, Heterogeneous systems, HPC, Intel, Intel Arc A770, Intel UHD 630, Intel UHD 770, nVidia, nVidia GeForce GTX 1080, nVidia GeForce GTX 980, nVidia GeForce RTX 2070, nVidia GeForce RTX 3070, nVidia GeForce RTX 3090, oneAPI, Package, performance portability, SYCL, Tesla V100

December 15, 2024 by hgpu

gpuPairHMM: High-speed Pair-HMM Forward Algorithm for DNA Variant Calling on GPUs

Bertil Schmidt, Felix Kallenborn, Alexander Wichmann, Alejandro Chacon, Christian Hundt

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Tags: Bioinformatics, Biology, Computer science, CUDA, FPGA, Genomics, nVidia, nVidia A100, nVidia H100, nVidia L4, nVidia L40s, nVidia V100, Package

November 24, 2024 by hgpu

Assessing opportunities of SYCL for biological sequence alignment on GPU-based systems

Manuel Costanzo, Enzo Rucci, Carlos García-Sanchez, Marcelo Naiouf, Manuel Prieto-Matías

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Tags: AMD Radeon RX 6700 XT, AMD Radeon RX Vega 6, ATI, Bioinformatics, Biology, Computational biology, CUDA, Heterogeneous systems, Intel Arc A770, Intel UHD 630, nVidia, nVidia GeForce GTX 1080, nVidia GeForce GTX 980, nVidia GeForce RTX 2070, nVidia GeForce RTX 3090, nVidia V100, oneAPI, Package, Sequence alignment, SYCL

February 25, 2024 by hgpu

Accelerating bioinformatics applications on CUDA-enabled multi-GPU systems

Robin Kobus

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Tags: Bioinformatics, Biology, CUDA, Databases, Hashing, nVidia, nVidia Quadro GV100, Package, Sequence alignment, Tesla P100, Tesla V100, Thesis

November 27, 2023 by hgpu

APACE: AlphaFold2 and advanced computing as a service for accelerated discovery in biophysics

Hyun Park, Parth Patel, Roland Haas, E. A. Huerta

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Tags: AI, Algorithms, Biology, Biomolecules, Biophysics, nVidia, nVidia A100, nVidia A40, Package

August 20, 2023 by hgpu

EfficientBioAI: Making Bioimaging AI Models Efficient in Energy, Latency and Representation

Yu Zhou, Justin Sonneck, Sweta Banerjee, Stefanie Dörr, Anika Grüneboom, Kristina Lorenz, Jianxu Chen

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Tags: Artificial intelligence, Biology, Computer science, CUDA, nVidia, nVidia Quadro RTX 4000, Package

June 18, 2023 by hgpu

minimap2-fpga: Integrating hardware-accelerated chaining for efficient end-to-end long-read sequence mapping

Kisaru Liyanage, Hiruna Samarakoon, Sri Parameswaran, Hasindu Gamaarachchi

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Tags: Bioinformatics, Biology, Cloud, FPGA, OpenCL, Package, Sequence alignment

June 11, 2023 by hgpu

Genomics-GPU: A Benchmark Suite for GPU-accelerated Genome Analysis

Zhuren Liu, Shouzhe Zhang, Justin Garrigus, Hui Zhao

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Tags: Benchmarking, Bioinformatics, Biology, Computer science, CUDA, Genomics, nVidia, nVidia GeForce RTX 3070, Package

May 28, 2023 by hgpu

Improving Performance of Hardware Accelerators by Optimizing Data Movement: A Bioinformatics Case Study

Peter Knoben, Nikolaos Alachiotis

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Tags: Bioinformatics, Biology, Computer science, FPGA, OpenCL, Package

February 12, 2023 by hgpu

PySAGES: flexible, advanced sampling methods accelerated with GPUs

Pablo F. Zubieta Rico, Ludwig Schneider, Gustavo Perez-Lemus, Riccardo Alessandri, Siva Dasetty, Cintia A. Menéndez, Yiheng Wu, Yezhi Jin, Trung Nguyen, John Parker, Andrew L. Ferguson, Juan J. de Pablo

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Tags: Biology, Chemistry, Computational Physics, CUDA, Molecular dynamics, nVidia, Package, Physics, Python, Tesla V100

January 22, 2023 by hgpu

Understanding the Power of Evolutionary Computation for GPU Code Optimization

Jhe-Yu Liou, Muaaz Awan, Steven Hofmeyr, Stephanie Forrest, Carole-Jean Wu

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Tags: Bioinformatics, Biology, Computer science, CUDA, Evolutionary Computations, Neural and Evolutionary Computing, nVidia, nVidia GeForce GTX 1080 Ti, Package, performance portability, Sequence alignment, Tesla P100, Tesla V100

September 4, 2022 by hgpu

AnySeq/GPU: A Novel Approach for Faster Sequence Alignment on GPUs

André Müller, Bertil Schmidt, Richard Membarth, Roland Leißa, Sebastian Hack

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Tags: AMD Radeon Instinct MI100, ATI, Bioinformatics, Biology, CUDA, Next-Generation sequencing, nVidia, nVidia GeForce RTX 3090, OpenCL, Package, Sequence alignment, Tesla A100

May 22, 2022 by hgpu

Coccinelle: a C code transformation engine using SmPL for matches, refactorings, and bug fixing

Advances in Semantic Patching for HPC-oriented Refactorings with Coccinelle

DuoReduce: MLIR's benchmark

Hardware-Assisted Software Testing and Debugging for Heterogeneous Computing

Shamrock: Multi-GPU hydrodynamics for astrophysics

The Shamrock code: I- Smoothed Particle Hydrodynamics on GPUs

LLMPerf: GPU Performance Modeling meets Large Language Models

Hercules: A Compiler for Productive Programming of Heterogeneous Systems

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high performance computing on graphics processing units: hgpu.org

Packages

Analyzing the Performance Portability of SYCL across CPUs, GPUs, and Hybrid Systems with Protein Database Search

gpuPairHMM: High-speed Pair-HMM Forward Algorithm for DNA Variant Calling on GPUs

Assessing opportunities of SYCL for biological sequence alignment on GPU-based systems

Accelerating bioinformatics applications on CUDA-enabled multi-GPU systems

APACE: AlphaFold2 and advanced computing as a service for accelerated discovery in biophysics

EfficientBioAI: Making Bioimaging AI Models Efficient in Energy, Latency and Representation

Genomics-GPU: A Benchmark Suite for GPU-accelerated Genome Analysis

Improving Performance of Hardware Accelerators by Optimizing Data Movement: A Bioinformatics Case Study

PySAGES: flexible, advanced sampling methods accelerated with GPUs

Understanding the Power of Evolutionary Computation for GPU Code Optimization

AnySeq/GPU: A Novel Approach for Faster Sequence Alignment on GPUs

Recent source codes

Coccinelle: a C code transformation engine using SmPL for matches, refactorings, and bug fixing

DuoReduce: MLIR's benchmark

Shamrock: Multi-GPU hydrodynamics for astrophysics

LLMPerf: GPU Performance Modeling meets Large Language Models

Hercules: A Compiler for Productive Programming of Heterogeneous Systems

Celerity Runtime: High-level C++ for Accelerator Clusters

wgpy: WebGL accelerated numpy-compatible array library for web browser

Microbenchmarking OpenMP target offload with Catch2

SUperman: Highly Efficient Permanent Computation Library

TransCL: An Automatic CUDA-to-OpenCL Programs Transformation Framework

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