high performance computing on graphics processing units: hgpu.org

Tommaso Biagini, Giovanni Chillemi, Gianluigi Mazzoccoli, Alessandro Grottesi, Caterina Fusilli, Daniele Capocefalo, Stefano Castellana, Angelo Luigi Vescovi, Tommaso Mazza

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Tags: Benchmarking, Bioinformatics, Biology, Chemistry, CUDA, Genomics, Molecular dynamics, nVidia, OpenCL, Physics, Tesla C2070

December 19, 2017 by hgpu

Real-Time Rendering of Molecular Dynamics Simulation Data: A Tutorial

N.Alharbi, M. Chavent, RS. Laramee

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Tags: Computer science, Image generation, Intel HD 6100, Molecular dynamics, OpenCL, OpenGL, Package, Rendering, Tutorial

September 3, 2017 by hgpu

Over-synchronization in GPU Programs

profile_util: simple C++ library to report memory, timing, thread affinity

Profile Util library: A quick and easy way to get MPI, OpenMP and GPU runtime information

MaC: Mamba CPU performance predictor

MambaCPU: Enhanced Correlation Mining with State Space Models for CPU Performance Prediction

Mixed-precision finite element kernels

Mixed-precision finite element kernels and assembly: Rounding error analysis and hardware acceleration

SHMT: The Simultaneous and Heterogenous Multithreading project

General-Purpose Computing on Tensor Processors

Superpipeline: A Universal Approach for Reducing GPU Memory Usage in Large Models

EnergyUCB-Bandit

Online Energy Optimization in GPUs: A Multi-Armed Bandit Approach

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high performance computing on graphics processing units: hgpu.org

Pushing the limit of molecular dynamics with ab initio accuracy to 100 million atoms with machine learning

86 PFLOPS Deep Potential Molecular Dynamics simulation of 100 million atoms with ab initio accuracy

JAX, M.D.: End-to-End Differentiable, Hardware Accelerated, Molecular Dynamics in Pure Python

PANNA: Properties from Artificial Neural Network Architectures

Raising the Performance of the Tinker-HP Molecular Modeling Package on Intel’s HPC Architectures: a Living Review [Article v1.0]

FPGA-based acceleration of a particle simulation High Performance Computing application

Using Compiler Directives for Performance Portability in Scientific Computing: Kernels from Molecular Simulation

A Case Study in Using OpenCL on FPGAs: Creating an Open-Source Accelerator of the AutoDock Molecular Docking Software

FPGA in HPC: High Level Synthesys of OpenCL kernels for Molecular Dynamics

Fast and Flexible GPU Accelerated Binding Free Energy Calculations within the AMBER Molecular Dynamics Package

Molecular dynamics recipes for genome research

Real-Time Rendering of Molecular Dynamics Simulation Data: A Tutorial

Recent source codes

Kokkidio: Kokkos+Eigen - write fast, readable multi-platform code

LLaMA-Inference-Bench

MATAR