high performance computing on graphics processing units: hgpu.org

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Molecular Simulation of ab Initio Protein Folding for a Millisecond Folder NTL9(1-39)

Vincent A. Voelz, Gregory R. Bowman, Kyle Beauchamp, Vijay S. Pande

Tags: Bioinformatics, Biology, Chemistry, Molecular dynamics

November 4, 2010 by hgpu

Fast and accurate protein substructure searching with simulated annealing and GPUs

Alex D. Stivala, Peter J. Stuckey, Anthony I. Wirth

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Tags: Bioinformatics, Biological Physics, Biology, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 285, Package, Tesla C1060

November 2, 2010 by hgpu

GPU-ClustalW: Using Graphics Hardware to Accelerate Multiple Sequence Alignment

Weiguo Liu, Bertil Schmidt, Gerrit Voss, Wolfgang Müller-Wittig

Tags: Bioinformatics, Biology, Computational biology, Computer science, Sequence alignment

November 1, 2010 by hgpu

GPU Accelerated Smith-Waterman

Yang Liu, Wayne Huang, John Johnson, Sheila Vaidya

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Tags: Bioinformatics, Biology, Computational biology, Computer science, GLSL, nVidia, nVidia GeForce 7800 GTX, OpenGL, Smith-Waterman algorithm

November 1, 2010 by hgpu

High-throughput sequence alignment using Graphics Processing Units

Michael Schatz, Cole Trapnell, Arthur Delcher, Amitabh Varshney

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Tags: Bioinformatics, Biology, Computational biology, CUDA, nVidia, nVidia GeForce 8800 GTX, Package, Sequence alignment

November 1, 2010 by hgpu

Optimizing data intensive GPGPU computations for DNA sequence alignment

Cole Trapnell, Michael C. Schatz

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Tags: Bioinformatics, Biology, Computational biology, CUDA, nVidia, nVidia GeForce 8800 GTX, Package, Sequence alignment, Short read mapping, Suffix trees

October 30, 2010 by hgpu

Exploiting graphics processing units for computational biology and bioinformatics

Joshua L. Payne, Nicholas A. Sinnott-Armstrong, Jason H. Moore

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Tags: All-Pairs Distance, Bioinformatics, Biology, Computational biology, CUDA, nVidia, nVidia GeForce 9600 M, Package

October 30, 2010 by hgpu

CUSA and CUDE: GPU-accelerated methods for estimating solvent accessible surface area and desolvation

David Dynerman, Erick Butzlaff, Julie C. Mitchell

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Tags: Bioinformatics, Biology, Biophysics, Chemistry, Computational biology, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 280, Solvent effects

October 29, 2010 by hgpu

An efficient implementation of Smith Waterman algorithm on GPU using CUDA, for massively parallel scanning of sequence databases

Lukasz Ligowski, Witold Rudnicki

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Tags: Bioinformatics, Biology, Computational biology, Computer science, CUDA, nVidia, nVidia GeForce 9800 GX2, Sequence alignment, Smith-Waterman algorithm

October 28, 2010 by hgpu

CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment

Svetlin Manavski, Giorgio Valle

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Tags: Bioinformatics, Biology, Computational biology, Computer science, CUDA, nVidia, nVidia GeForce 8800 GTX, Package, Sequence alignment, Smith-Waterman algorithm

October 28, 2010 by hgpu

High performance cellular level agent-based simulation with FLAME for the GPU

Paul Richmond, Dawn Walker, Simon Coakley, Daniela Romano

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Tags: Bioinformatics, Cellular modelling, Computational modelling, Computer science, CUDA, nVidia, Package

October 28, 2010 by hgpu

Sequence alignment with GPU: Performance and design challenges

Gregory M. Striemer, Ali Akoglu

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Tags: Bioinformatics, Biology, Computational biology, Computer science, CUDA, nVidia, Package, Sequence alignment, Smith-Waterman algorithm, Tesla C870

October 27, 2010 by hgpu

Code generated HPC Kernels Using Llama-2-70b

Comparing Llama-2 and GPT-3 LLMs for HPC kernels generation

Scope is all you need: Transforming LLMs for HPC Code

pocl - Portable Computing Language

PoCL-R: An Open Standard Based Offloading Layer for Heterogeneous Multi-Access Edge Computing with Server Side Scalability

HPAC-Offload: Accelerating HPC Applications with Portable Approximate Computing on the GPU

openCLDispatcher

Novel insights on atomic synchronization for sort-based group-by on GPUs

CEED Benchmarks

Performant low-order matrix-free finite element kernels on GPU architectures

Sieve: Stratified GPU-Compute Workload Sampling

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high performance computing on graphics processing units: hgpu.org

Molecular Simulation of ab Initio Protein Folding for a Millisecond Folder NTL9(1-39)

Fast and accurate protein substructure searching with simulated annealing and GPUs

GPU-ClustalW: Using Graphics Hardware to Accelerate Multiple Sequence Alignment

GPU Accelerated Smith-Waterman

High-throughput sequence alignment using Graphics Processing Units

Optimizing data intensive GPGPU computations for DNA sequence alignment

Exploiting graphics processing units for computational biology and bioinformatics

CUSA and CUDE: GPU-accelerated methods for estimating solvent accessible surface area and desolvation

An efficient implementation of Smith Waterman algorithm on GPU using CUDA, for massively parallel scanning of sequence databases

CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment

High performance cellular level agent-based simulation with FLAME for the GPU

Sequence alignment with GPU: Performance and design challenges

Recent source codes

Code generated HPC Kernels Using Llama-2-70b

Scope is all you need: Transforming LLMs for HPC Code

pocl - Portable Computing Language

HPAC-Offload: Accelerating HPC Applications with Portable Approximate Computing on the GPU

openCLDispatcher

CEED Benchmarks

Sieve: Stratified GPU-Compute Workload Sampling

EngineCL: Usability and Performance in Heterogeneous Computing

Ginkgo: high-performance linear algebra library for manycore systems

AlphaFold2

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