high performance computing on graphics processing units: hgpu.org

Ruibang Luo, Thomas Wong, Jianqiao Zhu, Chi-Man Liu, Edward Wu, Lap-Kei Lee, Haoxiang Lin, Wenjuan Zhu, David W. Cheung, Hing-Fung Ting, Siu-Ming Yiu, Chang Yu, Yingrui Li, Ruiqiang Li, Tak-Wah Lam

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Next-Generation sequencing, nVidia, Package, Tesla C2070, Tesla M2050

February 25, 2013 by hgpu

G-SNPM – A GPU-based SNP mapping tool

Alessandro Orro, Andrea Manconi, Emanuele Manca, Giuliano Armano, Luciano Milanesi

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Next-Generation sequencing, nVidia, nVidia GeForce GTX 480, Package, Python, Smith-Waterman algorithm

November 14, 2012 by hgpu

GHOSTM: A GPU-Accelerated Homology Search Tool for Metagenomics

Shuji Suzuki, Takashi Ishida, Ken Kurokawa, Yutaka Akiyama

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Tags: Algorithms, Biology, CUDA, Databases, Next-Generation sequencing, nVidia, Package, Tesla S1070

May 10, 2012 by hgpu

Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming

Jochen Blom, Tobias Jakobi, Daniel Doppmeier, Sebastian Jaenicke, Jorn Kalinowski, Jens Stoye, Alexander Goesmann

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Next-Generation sequencing, nVidia, Package

May 10, 2011 by hgpu

Exact and complete short read alignment to microbial genomes using GPU programming

Jochen Blom, Tobias Jakobi, Daniel Doppmeier, Sebastian Jaenicke, Jorn Kalinowski, Jens Stoye, Alexander Goesmann

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Tags: Bioinformatics, Biology, CUDA, Next-Generation sequencing, nVidia, nVidia GeForce GTX 280, Package

April 11, 2011 by hgpu

DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI

Yongchao Liu, Bertil Schmidt, Douglas Maskell

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Tags: Bioinformatics, Biology, CUDA, MPI, Next-Generation sequencing, nVidia, OpenMP, Package, Tesla S1070

April 11, 2011 by hgpu

KernelZero: Co-Evolving Proposer and Coder for Continuously Improved GPU Kernel Generation

Introduction to Computer Vision

ACT: Accelerator Compiler Toolkit

Automatically Generating ML Compiler Backends from Tensor Accelerator ISA Descriptions

pytest-gpu-proof: A Simple Pytest Extension for Local GPU Code Testing

pytest-gpu-proof: Enabling Cloud-CPU Continuous Integration for GPU Code with Local GPU Attestation

Accelerating the Mitigation of LLM Inference Nondeterminism Across GPU Architectures

AutoTuneBench: Trustworthy Measurement for Agent Auto-Tuning of LLM Serving Engines

nvsass-disassembler

Automated Instruction Encoding Synthesis for Modern GPU ISA Compression

PrefixBench-H100: Characterizing Prefix Reuse and Time-to-First-Token in H100 LLM Serving

FP4 FlashAttention forward, backward, and TorchTitan reproduction code

Hardware-Aware FP4 FlashAttention-4

EinsummableV3 - graph-based computation with tensor operations support

Every Kernel Is a Join: Automatic Multi-GPU Parallelism for AI Computations in Einsummable

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high performance computing on graphics processing units: hgpu.org

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

eccCL: parallelized GPU implementation of Ensemble Classifier Chains

Parallelization, Scalability, and Reproducibility in Next-Generation Sequencing Analysis

SW#db: GPU-accelerated exact sequence similarity database search

GPU-accelerated Computation for Statistical Analysis of the Next-Generation Sequencing Data

cuBLASTP: Fine-Grained Parallelization of Protein Sequence Search on a GPU

SOAP3-dp: Fast, Accurate and Sensitive GPU-based Short Read Aligner

G-SNPM – A GPU-based SNP mapping tool

GHOSTM: A GPU-Accelerated Homology Search Tool for Metagenomics

Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming

Exact and complete short read alignment to microbial genomes using GPU programming

DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI

Recent source codes

KernelZero: Co-Evolving Proposer and Coder for Continuously Improved GPU Kernel Generation

Introduction to Computer Vision

ACT: Accelerator Compiler Toolkit

pytest-gpu-proof: A Simple Pytest Extension for Local GPU Code Testing

Accelerating the Mitigation of LLM Inference Nondeterminism Across GPU Architectures

AutoTuneBench: Trustworthy Measurement for Agent Auto-Tuning of LLM Serving Engines

nvsass-disassembler

PrefixBench-H100: Characterizing Prefix Reuse and Time-to-First-Token in H100 LLM Serving

FP4 FlashAttention forward, backward, and TorchTitan reproduction code

EinsummableV3 - graph-based computation with tensor operations support

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