High-throughput read alignment with GPU- accelerated exploration of the seed-and- extend search space
Single-end alignment, paired-end alignment Output in SAM or database-ready binary formats Multiple GPU implementation
Yes
Sequence mapping software
Alignment of short sequencing reads, alignment of indels with gap openings and extensions.
Yes
BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. It can make use of highly-parallel processors such as those in graphics cards (GPUs) found in many PCs.
Evaluation of likelihood for sequence evolution on trees and Arbitrary models (e.g. nucleotide, amino acid, codon) Speed-ups (over CPU only version): nucleotide model = up to 25x, codon model = up to 50x.
Yes
An open-source library of GPU-accelerated data clustering algorithms and tools.
K-means (and Kps-means, a K-means variant for GPUs with parallel sorting for improved performance), K-medoids, K-centers (a K-medoids variant in which medoids are placed only once according to a heuristic), Hierarchical clustering and Self-organizing map.
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Open source software for Smith-Waterman protein database searches on GPUs.
Parallel search of Smith-Waterman database.
Yes
Parallelized short read aligner
Parallel, accurate long read aligner for large genomes
Yes
GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST.
Blastn and megablast modes of NCBI-BLAST
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Local search with fast k-tuple heuristic
Protein alignment according to BLASTP
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Ultrafast scalable motif discovery algorithm
Scalable motif discovery algorithm based on MEME.
Yes
High-throughput local sequence alignment
Aligns multiple query sequences against reference sequence in parallel.
TBD
NVBIO is an open source C++ library of reusable components designed to accelerate bioinformatics applications using CUDA.
Data structures, algorithms, and utility routines useful for building complex computational genomics applications on CPU-GPU systems.
Yes
A largely complete implementation of the Bowtie2 aligner on top of NVBIO.
Good coverage of Bowtie2 features and comparable quality results.
Yes
Read mapper for DNA or RNA sequence reads to a known reference genome.
Achieves supreme sensitivity and speed compared to current state of the art read mappers like BWA MEM, Bowtie2 and RazerS3. PEANUT reports both only the best hits or all hits.
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A modified version of GCTA with improved computational performance, support for Graphics Processing Units (GPUs), and additional features. The purpose of REACTA is to quantify the contribution of genetic variation to phenotypic variation for complex traits.
GRM creation, REML analysis, Regional Heritability (including multi-GPU).
Yes
SeqNFind® is a powerful tool suite that addresses the need for complete and accurate alignments of many small sequences against entire genomes utilizing a unique hardware/software cluster system for facilitating bioinformatics research in Next Generation sequencing and genomic comparisons.
Hardware and software for reference assembly, blast, SW, HMM, de novo assembly.
Yes
GPU-based software for aligning short reads with a reference sequence. It can find all alignments with k mismatches, where k is chosen from 0 to 3.
Short read alignment tool that is not heuristic based; reports all answers.
Yes
SOAP3-dp: Ultra-fast GPU-based tool for short read alignment via index-assisted dynamic programming.
Borrows-Wheeler Transformation, Dynamic Programming.
Yes
Open source Smith-Waterman for SSE/ CUDA, Suffix array based repeats finder and dotplot.
Fast short read alignment.
Yes
Fits numerous linear models to a fixed design and response.
Parallel linear regression on multiple similarly-shaped models.
Yes
GPU simulation of molecular mechanics force fields, implicit and explicit solvent
Written for use only on GPUs.
Yes
Suite of programs to simulate molecular dynamics on biomolecule.
PMEMD Explicit Solvent and GB Implicit Solvent
Yes
MD package to simulate molecular dynamics on biomolecule.
Implicit (5x), Explicit (2x) Solvent via OpenMM, now ported natively to GPUs.
Yes
High-speed molecular dynamics simulations of biological systems.
The code uses novel parallel algorithms and numerical techniques to achieve high performance and accuracy.
Yes
Highly versatile software package for performing and analyzing scientific Molecular Dynamics many-particle simulations of coarse-grained atomistic or bead-spring models as they are used in soft-matter research in physics, chemistry and molecular biology.
Hydrodynamic / Electrokinetic forces P3M electrostatics.
Yes
A distributed computing project that studies protein folding, misfolding, aggregation, and related diseases.
Powerful distributed computing molecular dynamics system; implicit solvent and folding.
Yes
A distributed computing project that uses GPUs for molecular simulations.
High-performance all-atom biomolecular simulations; explicit solvent and binding.
Yes
Simulation of biochemical molecules with complicated bond interactions.
Implicit (5x), Explicit (2x) Solvent
Yes
Large-scale simulations of simple and complex liquids.
Simple fluids and binary mixtures (pair potentials, high-precision NVE and NVT, dynamic correlations).
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Particle dynamics package written grounds up for GPUs.
Written for use only on GPUs
Yes
Classical molecular dynamics package
Lennard-Jones, Gay-Berne, Tersoff, and dozens more potentials
Yes
OpenMM plugin written for GPUs
Integrative approach to combine physics and information Orders of magnitude faster protein folding than brute force MD
Yes
Designed for high-performance simulation of large molecular systems.
Full electrostatics with PME and most simulation features; 100M atom capable.
Yes
Library and application for molecular dynamics for HPC with GPUs.
Implicit and explicit solvent, custom forces
Yes
Classical molecular simulation code for studying polymer self-assembly and thermodynamics.
Uses auxiliary fields as the fundamental simulation degrees of freedom, Uses cuFFT extensively (~ 80%), CUDA code is ~20%, Multi CPU or single GPU per job, 1x = Ivy Bridge E5-2690 CPU all 10 cores, 3-8X on K40 or K80 (utilizing 1/2 of the K80).
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SOP-GPU package, where SOP stands for the Self Organized Polymer Model fully implemented on a GPU, is a scientific software package designed to perform Langevin Dynamics Simulations of the mechanical or thermal unfolding, and mechanical indentation of large biomolecular systems in the experimental subsecond (millisecond-to-second) timescale.
Langevin dynamics simulations using the coarse-grained Self Organized Polymer (SOP) model, Multiple simulation trajectories can be performed simultaneously on a single GPU, Calpha and Calpha-Cbeta models are supported, Simulations of protein forced unfolding, Novel simulations of nanoindentation in silico, Support for hydrodynamic interactions, Up to ~100 ms of simulation time per day, Systems of up to 1,000,000 amino-acids (on GPUs with 6GB or great memory).
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Allows to find total energy, charge density and electronic structure of systems made of electrons and nuclei within DFT.
Local Hamiltonian, non-local Hamiltonian, LOBPCG algorithm, diagonalization/ orthogonalization.
Yes
Takes best features of parallel implementations of quantum chemistry methods for electronic structure.
Integrating scheduling GPU into SIAL programming language and SIP runtime environment.
Yes
Density Functional Theory (DFT) software package that enables first-principles electronic structure calculations.
Geometry optimizations and frequency calculations with GGA functionals.
Yes
Implements density functional theory by solving the Kohn-Sham equations describing the electrons in a material.
DFT; Daubechies wavelets, part of Abinit
Yes
CASTEP is a leading code for calculating the properties of materials from first principles. Using density functional theory, it can simulate a wide range of properties of materials proprieties including energetics, structure at the atomic level, vibrational properties, electronic response properties etc.
TBD
Yes
Program to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems.
DBCSR (space matrix multiply library)
Yes
The general purpose ab initio molecular electronic structure program for performing SCF-, DFT- and MCSCF-gradient calculations.
(ss|ss) type integrals within calculations using Hartree-Fock ab initio methods and density functional theory. Supports organics and inorganics.
Yes
Computational chemistry suite used to simulate atomic and molecular electronic structure.
Libqc with Rys Quadrature Algorithm, Hartree-Fock, MP2 and CCSD.
Yes
Predicts energies, molecular structures, and vibrational frequencies of molecular systems.
Joint NVIDIA, PGI and Gaussian collaboration.
Yes
Real-space grid DFT code written in C and Python
Electrostatic poisson equation, orthonormalizing of vectors, residual minimization method (rmm-diis).
Yes
Materials code for investigating the effects of temperature on magnetism.
Generalized Wang-Landau method
Yes
Density matrix computations
CU_BLAS, SP2 Algorithm
Yes
Linear-scaling HF and DFT code suitable for large molecular systems, now also with some CCSD capabilities
(T) correction to the CCSD energy. • RI-MP2 energy/gradient (in development). • CCSD energy (in development). • GPU-based ERI generator (in development).
Yes
Methods for calculating general electronic structures in molecular systems in both ground and excited states.
CU_BLAS
Single only Additional GPU support coming in Version 8
Semiempirical Quantum Chemistry
Pseudodiagonalization, full diagonalization, and density matrix assembling via Magma libraries.
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Calculations
Triples part of Reg-CCSD(T), CCSD and EOMCCSD task schedulers.
Yes
Used for ab initio virtual experimentation and quantum chemistry calculations.
Full GPU support for ground-state, real-time calculations; Kohn-Sham Hamiltonian, orthogonalization, subspace diagonalization, poisson solver, time propagation.
TBD
ONETEP (Order-N Electronic Total Energy Package) is a linear-scaling code for quantum-mechanical calculations based on density-functional theory.
TBD
Yes
First principles materials code that computes the behavior of the electron structures of materials.
Density functional theory (DFT) plane wave pseudopotential calculations.
Yes
The fastest plane wave pseudopotential code for density functional theory simulations based on GPU.
It can perform extremely fast plane wave DFT calculations based on GPU machines and single precision and double precision mixed algorithm. It deploys the state-of- the-art electronic structure calculation methods with many new features and algorithm innovations. It performs ab initio material science simulations, designed for both theoretical and experimental groups.
Yes
Computational chemistry package designed for HPC clusters.
Various features including RI-MP2
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Solves the many-body Schrodinger equation for electronic structures using a quantum Monte Carlo method.
Main features
Yes
An integrated suite of computer codes for electronic structure calculations and materials modeling at the nanoscale.
PWscf package: linear algebra (matix multiply), explicit computational kernels, 3D FFTs.
Yes
QUICK is a GPU-enabled ab intio quantum chemistry software package.
Running Hartree-Fock and DFT energy on GPU, Supports s, p, d, f orbitals on energy calculation, HF gradient with s,p,d orbital support, GPU-based ERI generator.
Yes
Quantum chemistry software designed to run on NVIDIA GPU.
Full GPU-based solution; Performance compared to GAMESS CPU version.
Yes
Complex package for performing ab-initio quantum-mechanical molecular dynamics (MD) simulations using pseudopotentials or the projector-augmented wave method and a plane wave basis set.
Blocked Davidson (ALGO = NORMAL & FAST), RMM-DIIS (ALGO = VERYFAST & FAST), K-Points and optimization for critical step in exact exchange calculations.
Yes
A multifaceted software platform for visualizing, manipulating, and understanding Life Science and bio-medical data.
3D visualization of volumetric data and surfaces
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A virtual screening methodology that uses GPUs to determine protein binding sites.
Allows fast processing of large ligand databases
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Molecular docking program
Empirical Free Energy Force field
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Molecule shape comparison application
Real-time shape similarity searching/ comparison
Yes
Experimental interactive molecule visualizer based on a ray-tracing engine.
Targeting high quality images and ease of interaction, IMV uses the latest GPUcomputing acceleration techniques, combined with natural user interfaces such as Kinect and Wiimotes.
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Method for performing high accuracy flexible molecular docking.
Energy grid computation, pose evaluation and guided differential evolution.
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A Vectorized Algorithm for Probabilistic Phylogeny-Aware Alignment Extension.
Up to 15-fold run time improvements by deploying SIMD vector intrinsics to accelerate the alignment kernel.
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Protein-protein docking program
Molecule docking
TBD
User-sponsored molecular visualization system on an open-source foundation
Lines: 460% increase Cartoons: 1246% increase Surface: 1746% increase Spheres: 753% increase Ribbon: 426% increase
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Molecular Modeling Toolkit
Virtual logP, molecular surface values
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Visualization and analyzing large bio- molecular systems in 3-D graphics
High quality rendering, large structures (100M atoms), analysis and visualization tasks, multiple GPU support for display of molecular orbitals
Yes
Comprehensive GPU function library
Hundreds of functions for math, signal/ image processing, statistics, and more.
Yes
3High Performance Linear Algebra in R
Supports GPU and multi-core platforms, compatible with legacy R code, no new data types or operators, auto-tuning, support for R Matrix package.
Yes (for algebra functions via Magma 1.5 or later)
A symbolic technical computing language and development environment.
Development environment for CUDA and OpenCL. GPU acceleration for Wolfram Finance Platform.
Yes
GPU acceleration for MATLAB (high-level technical computing language).
Support for 200+ of most used MATLAB functions (incl. Signal Processing, Image Processing, Communications Systems, etc).
Yes
GPU-accelerated math and statistics for .NET, automatically detects the presence of a CUDA-enabled GPU at runtime and seamlessly redirects appropriate computations to it.
Automatically offloads computations to the GPU.
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The Anelastic Wave Propagation, AWP- ODC, independently simulates the dynamic rupture and wave propagation that occurs during an earthquake. Dynamic rupture produces friction, traction, slip, and slip rate information on the fault. The moment function is constructed from this fault data and used to initialize wave propagation.
3D Finite Difference Computation
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Lattice quantum chromodynamics application, used for nuclear ad high energy physics calculations.
Wilson-clover fermion linear solver
Yes
A multicomponent compressible hydrodynamic code for astrophysical flows including self-gravity, nuclear reactions and radiation. CASTRO uses an Eulerian grid and incorporates adaptive mesh refinement (AMR). The approach uses a nested hierarchy of logically-rectangular grids with simultaneous refinement in both space and time.
Gravitational Field Solver
Yes
Astrophysics code performs collisionless N-body simulations. It can perform cosmological simulations with periodic boundary conditions in comoving coordinates or simulations of isolated stellar systems.
Gravitational Model has been accelerated using CUDA
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Chemora is a system for performing simulations of systems described by differential equations running on accelerated computational clusters.
Chemora embeds the equations’ computational kernels into dynamically compiled loop nests shaped for input size and GPU structure.
Yes
Lattice Quantum Chromodynamics (LQCD)
Wilson-clover fermions, Krylov solvers, Domain-decomposition
Yes
Lattice quantum chromodynamics application, used for nuclear ad high energy physics calculations.
Wilson, domain-wall and Möbius fermion linear solvers
Yes
3D block-structured AMR code for cosmological structure formation.
Accelerated magneto hydrodynamics solvers
Yes
Simulates microturbulence and transport in magnetically confined fusion plasma.
Electron push and shift (accounting for >80% of run time)
Yes
A development code for optimization of plasma physics. Full science and data sets are included, but in a simplified form to allow performance testing and tuning.
Optimized with CUDA. OpenACC development underway
Yes
Simulates microturbulence and the motion of charged particles and interactions in fusion plasma.
Push and shift for both electron and ion dynamics
Yes
Simulates N-Body Astrophysics
This code has been optimized with CUDA runs in full production mode.
Yes
A low Mach number stellar hydrodynamics code that can be used to simulate long- time, low-speed flows that would be prohibitively expensive to model using traditional compressible code.
Gravitational Field Solver
Yes
Lattice Quantum Chromodynamics (LQCD) codes simulate how elemental particles are formed and bound by the “strong force” to create larger particles like protons and neutrons.
Staggered fermions, Krylov solvers, Gauge- link fattening.
Yes
Simulates Plasma Physics including Laser interaction
2 dimensions of the particle push have been optimized with CUDA. Additional optimization is being planned with OpenACC.
Yes
A relativistic Particle-in-Cell code that describes the dynamics of a plasma by computing the motion of electrons and ions subject to the Maxwell-Vlasov equation.
Simulation of laser-wakefield acceleration of electrons.
Yes
Piecewise parabolic method, a higher- order extension of Godunov’s method which uses spatial interpolation and allows for a steeper representation of discontinuities, particularly contact discontinuities.
Turbulent, compressible mixing of gases in the context of stars near the ends of their lives and also in inertial confinement fusion.
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Library for Lattice QCD calculations using GPUs.
CUDA supports the following fermion formulations: Wilson,Wilson-clover,Twisted mass,Improved staggered (asqtad or HISQ) and Domain wall.
Yes
Simulates astrophysical problems on different scales (e.g. star formation, galaxy dynamics, cosmological structure formation).
CUDA acceleration is applied for radiative transfer for reionization, and the hydrodynamic solver using AMR.
Yes
Simulates edge effects for MHD plasma physics
The particle push portion has been optimized with CUDA and is being fully optimized with OpenACC and CUDA.
Yes
Medical visualization & segmentation
Rendering, image processing
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Visualization and analysis application for CAE
Rendering
Yes
Interactive rendering tool for confocal microscopy data visualization.
Multi-channel volume rendering
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Data analysis application
Analysis tasks
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Interactive volume rendering application
Volume rendering
Yes
Simple, scalable, and interactive volume rendering application.
Out-of-core volume rendering
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Visualization application for CFD
Rendering
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Data analysis and visualization application
Rendering and analysis tasks
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Scalable data anlysis and visualization application
Rendering and analysis tasks
Yes
Segmentation application for medical data
Rendering, image processing
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Data anlysis and visualization toolkit
Rendering
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Scalable data anlysis and visualization application
Rendering and analysis tasks
Yes
Large dataset visualization in cosmology, astrophysics, and biosciences fields.
Volume rendering of particles
Yes
Visualization and analysis of large bio- molecular systems in 3-D graphics.
High-qulity rendering, large structures (100M atoms), analysis and visualization tasks, multiple GPU support for display of molecular orbitals.
Yes