GPU-optimized AI, Machine Learning, & HPC Software

NVIDIA

The NVIDIA HPC-Benchmarks collection provides four accelerated HPC benchmarks: HPL-NVIDIA, HPL-MxP-NVIDIA, HPCG-NVIDIA, and STREAM.

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Mathworks

MATLAB

MATLAB is a programming platform designed for engineers and scientists. The MATLAB Deep Learning Container provides algorithms, pretrained models, and apps to create, train, visualize, and optimize deep neural networks.

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SISSA

Quantum ESPRESSO

Quantum ESPRESSO is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale based on density-functional theory, plane waves, and pseudopotentials.

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Gordon Group

GAMESS

GAMESS is used for computational chemistry calculations including DFT which is used to understand the potential of a drug molecule binding with proteins for drug discovery.

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Open Source

Relion

RELION implements an empirical Bayesian approach for analysis of electron cryo-microscopy.

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Jefferson Lab

CHROMA

CHROMA is a Physics application designed for solving the theory of quarks and gluons.

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Folding@home

Folding@home is a distributed computing project for simulating protein dynamics, including the process of protein folding and the movements of proteins implicated in a variety of diseases. It brings together citizen scientists who volunteer to run simulations of protein dynamics on their computers. Insights from this data are helping scientists to better understand biology, and providing new opportunities for developing therapeutics.

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Julia

julia

The Julia programming language is a flexible dynamic language, appropriate for scientific and numerical computing, with performance comparable to traditional statically-typed languages.

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UIUC

vmd

VMD is designed for modeling, visualization, and analysis of biomolecular systems such as proteins, nucleic acids, lipid membranes, carbohydrate structures, etc. VMD provides a wide variety of graphical representations for visualizing and coloring molecular structures: molecular surfaces, space-filling CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, secondary structure cartoons, and others.

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NVIDIA

ParaView

ParaView is one of the most popular visualization software for analyzing HPC datasets.

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Tinker Tools

Tinker-HP

Tinker-HP is a CPUs and GPUs based, multi-precision, MPI massively parallel package dedicated to long polarizable molecular dynamics simulations and to polarizable QM/MM.

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NVIDIA, OpenACC.org, UDEL

OpenACC Training Materials

These training materials have been developed as a collaboration between the University of Delaware and NVIDIA Corporation and are provided free of charge by OpenACC.org.

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Open Porous Media Initiative

LBPM

LBPM is an open source software framework designed to model flow processes based on digital rock physics

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CEA INAC

BigDFT

BigDFT is a DFT massively parallel electronic structure code using a wavelet basis set with the capability to use a linear scaling method.

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The Glotzer Group

HOOMD-blue

HOOMD-blue is a highly flexible and scalable particle simulation toolkit. It makes use of high-level Python scripts to set initial conditions, control simulation parameters, and extract data for in situ analysis.

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Roitberg group

TorchANI

TorchANI is a PyTorch implementation of ANI and contains classes like AEVComputer, ANIModel, and EnergyShifter that can be pipelined to compute molecular energies from the 3D coordinates of molecules

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HZDR

PIConGPU

PIConGPU is a plasma physics application to solve the dynamics of a plasma by computing the motion of electrons and ions in the plasma field.

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Kipoi

kipoi

Kipoi (pronounce: kípi; from the Greek κήποι: gardens) is an API and a repository of ready-to-use trained models for genomics. It currently contains 2131 different models, covering canonical predictive tasks in transcriptional and post-transcriptional gene regulation. Kipoi's API is implemented as a python package (github.com/kipoi/kipoi) and it is also accessible from the command line or R.

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UIUC

Lattice Microbes

Lattice Microbes is a QC software package for efficiently sampling trajectories from the chemical reaction in bacteria.

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Microvolution

Microvolution is a high-performance 3D deconvolution application, designed to deconvolve images from widefield, confocal, two photon, light sheet, and HCA microscopes, as well as perform blind deconvolution to ameliorate noise in other data types such as deep-tissue images.

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Open Source

CANDLE

The CANDLE project is focused on facilitating cancer research with deep learning. The CANDLE software allows deep learning workflows to be deployed at large scale supercomputers.

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