
Application packages
Chemistry & Materials Sciences
Name  Version  Description  Parallel programming technologies  License  Presentation 
ABINIT  8.8.4  ABINIT is a software suite to calculate the optical, mechanical, vibrational, and other observable properties of materials. Starting from the quantum equations of density functional theory, you can build up to advanced applications with perturbation theories based on DFT, and manybody Green's functions (GW and DMFT).  MPI,
OpenMP,
CUDA  GNU GPL  PDF 
BigDFT  1.8.2  BigDFT is a DFT massively parallel electronic structure code using a wavelet basis set.  MPI,
OpenMP,
CUDA  GNU GPL  PDF 
CP2K  6.1  CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. CP2K provides a general framework for different modeling methods such as DFT using the mixed Gaussian and plane waves approaches GPW and GAPW.  MPI,
OpenMP,
CUDA  GNU GPL  PDF1
PDF2
PDF3 
CPMD  4.1  The CPMD code is a parallelized plane wave / pseudopotential implementation of Density Functional Theory, particularly designed for abinitio molecular dynamics.  MPI,
OpenMP  Link  PDF 
Dalton & LSDalton  2016  This programs provide an extensive functionality for the calculations of molecular properties at the HF, DFT, MCSCF, and CC levels of theory.  MPI,
OpenMP (LSDalton only),
CUDA (LSDalton only)  GNU LGPL  
Elk  5.2.14  An allelectron fullpotential linearised augmentedplane wave (LAPW) code with many advanced features.  MPI,
OpenMP  GNU GPL / LGPL  
ESPResSo  4.0  ESPResSo is a highly versatile software package for performing and analyzing scientific Molecular Dynamics manyparticle simulations of coarsegrained atomistic or beadspring models as they are used in soft matter research in physics, chemistry and molecular biology.  MPI,
CUDA (in part)  GNU GPL  
Firefly  8.2.0  Firefly (previously known as the PC GAMESS) is a freely available ab initio and DFT computational chemistry program. Firefly has been constantly being developed to incorporate new functionality, improve performance, and extend existing features. For example, Firefly uses real time data compression/decompression, efficient modern algorithms of 2e integral evaluation for direct calculation methods, very efficient MP2 energy and energy gradient modules, very fast RHF MP3/MP4 energy code, and stateoftheart DFT, TDDFT, MCSCF, MRMP2, MCQDPT, and XMCQDPT implementation.  MPI,
CUDA (in part)  Link  
GAMESSUS  Sept 30th, 2017  The General Atomic and Molecular Electronic Structure System is a general ab initio quantum chemistry package.  MPI,
OpenMP,
CUDA  Link  
GROMACS  2018.3  GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.  MPI,
CUDA  GNU LGPL  PDF1
PDF2
PDF3 
LAMMPS  22 Aug 2018  LAMMPS (Largescale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics code with a focus on materials modeling. LAMMPS has potentials for solidstate materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarsegrained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.  MPI,
OpenMP,
CUDA  GNU GPL  PDF1
PDF2
PDF3 
Molcas & openMolcas  8.2  Molcas is an ab initio quantum chemistry software package. The basic philosophy is to be able to treat general electronic structures for molecules consisting of atoms from most of the periodic table. As such, the primary focus of the package is on multiconfigurational methods with applications typically connected to the treatment of highly degenerate states.  MPI,
OpenMP,
CUDA  Link  
MPB  1.6.1  MPB (MIT Photonic Bands) is a free and opensource software package for computing the band structures, or dispersion relations, and electromagnetic modes of periodic dielectric structures, on both serial and parallel computers. MPB computes definitefrequency eigenstates, or harmonic modes, of Maxwell's equations in periodic dielectric structures for arbitrary wavevectors, using fullyvectorial and threedimensional methods.  MPI,
OpenMP  GNU GPL  
NAMD  2.13  NAMD is a parallel molecular dynamics code designed for highperformance simulation of large biomolecular systems.  MPI,
OpenMP,
CUDA  Link  PDF1
PDF2 
NWChem  6.8  NWChem is open source highperformance computational chemistry software package.  MPI,
CUDA  ECL 2.0  PDF 
Octopus  8.2  Octopus is a scientific program aimed at the ab initio virtual experimentation on a hopefully everincreasing range of system types. Electrons are described quantummechanically within densityfunctional theory (DFT), in its timedependent form (TDDFT) when doing simulations in time. Nuclei are described classically as point particles. Electronnucleus interaction is described within the pseudopotential approximation.  MPI,
OpenMP,
CUDA  GNU GPL  PDF 
OpenMX  3.8.5  OpenMX (Open source package for Material eXplorer) is a software package for nanoscale material simulations based on density functional theories (DFT), normconserving pseudopotentials, and pseudoatomic localized basis functions.  MPI,
OpenMP  GNU GPL  PDF 
ORCA  4.0.1  The program ORCA is a modern electronic structure program package. ORCA is a flexible, efficient and easytouse general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of openshell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single and multireference correlated ab initio methods.  MPI  Link  
Quantum ESPRESSO  6.3  Quantum ESPRESSO is an integrated suite of OpenSource computer codes for electronicstructure calculations and materials modeling at the nanoscale. It is based on densityfunctional theory, plane waves, and pseudopotentials.  MPI,
OpenMP,
CUDA  GNU GPL  PDF 
SIESTA  4.0.2  SIESTA is both a method and its computer program implementation to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.  MPI,
OpenMP  GNU GPL  
WIEN2K  18.2  The program package WIEN2k allows to perform electronic structure calculations of solids using density functional theory (DFT). It is based on the fullpotential (linearized) augmented planewave ((L)APW) + local orbitals (lo) method, one among the most accurate schemes for band structure calculations.  MPI  Link  
VASP  5.4.4  The VASP (Vienna Ab initio Simulation Package) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantummechanical molecular dynamics, from first principles.  MPI,
OpenMP,
CUDA  Link  PDF 
Biology & Life Sciences
Name  Version  Description  Parallel programming technologies  License  Presentation 
ABySS  2.1.1  ABySS (Assembly By Short Sequences) is a de novo, parallel, pairedend sequence assembler that is designed for short reads.  MPI,
OpenMP,
CUDA  GNU GPL  PDF 
BEAST  1.10.1  BEAST is a program for Bayesian analysis of molecular sequences using MCMC. It is entirely orientated towards rooted, timemeasured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST is used in conjunction with BEAGLE (highperformance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages).  MPI,
CUDA  GNU LGPL  
BLAST  2.8.0  The BLAST (Basic Local Alignment Search Tool) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. Various parallel implementations of the BLAST are known, for ex.: mpiBLAST, ScalaBlast, GPUBlast. See also Blast2GO  MPI,
OpenMP,
CUDA  Public Domain  
HMMER  3.2.1  HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).  MPI  BSD 3Clause  
MAKER  2.31.10  MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces abinitio gene predictions and automatically synthesizes these data into gene annotations having evidencebased quality values.  MPI  GNU GPL  
Migrate  3.6  Migrate estimates effective population sizes and past migration rates between n population assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes. Migrate uses maximum likelihood or Bayesian inference to jointly estimate all parameters.  MPI  MIT License  
mothur  1.41.0  mothur is a software package for processing bioinformatics data (incl. for the analysis of microbial communities) generated by Sanger, PacBio, IonTorrent, 454, Illumina (MiSeq/HiSeq).  MPI  GNU GPL  
MPIPHYLIP  3.697  MPIPHYLIP is a software for computationally intensive phylogenetic analysis; parallel implementation of a popular package PHYLIP (PHYLogeny Inference Package).  MPI   
MrBayes  3.2.6  MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters. MrBayes is compatible with the library BEAGLE. See also: GPU MrBayes project.  MPI,
CUDA  GNU GPL  PDF 
pBWA  0.5.9  pBWA (Parallel BurrowsWheeler Aligner) is a parallel implementation of the popular software BWA for mapping lowdivergent sequences against a large reference genome, such as the human genome.  MPI,
OpenMP  GNU GPL, MIT License  
RAxML  8.0.0  RAxML (Randomized Axelerated Maximum Likelihood) is a tool for phylogenetic analysis and postanalysis of large phylogenies.  MPI,
OpenMP  GNU GPL  
Ray  2.3.1  Ray is a parallel genome assemblies for parallel DNA sequencing.  MPI  GNU GPL  
VinaLC  1.1.2  VinaLC is a parallel implementation of the very popular molecular docking program AutoDock Vina. See also: VinaMPI.  MPI  Apache License 2.0  
Mathematics & Computer Science
Name  Version  Description  Parallel programming technologies  License  Presentation 
CPLEX  12.8.0  CPLEX is an optimization software package.  MPI  Link  PDF 
HordeSAT & HordeQBF   Massively parallel portfoliobased SAT/QBF solvers (include modified source codes of MiniSAT and DepQBF).  MPI   PDF1
PDF2 
MPIDepQBF   MPIDepQBF is a parallel QBF solver based on a searchspace splitting approach. It uses DepQBF as the base solver.  MPI  BSD License (Toss)  PDF 
PaMiraXT   PaMiraXT is a powerful parallel SAT solver that implements a master/client model based on message passing. For the clients, a threadbased solver MiraXT is used.  MPI   
PaQuBE   PaQuBE is a parallel QBF solver implementing a master/client model and using QBF solver QuBE as a client.  MPI   
PDSAT  0.9  PDSAT (Parallel and Distributed SAT solver)  an MPIbased divideandconquer SAT solver based on the Monte Carlo method and local search heuristics.  MPI   
PMSat   PMSat is a parallel SATsolver that uses MiniSAT as engine.  MPI  MIT License  
Engineering & Mechanics
Name  Version  Description  Parallel programming technologies  License  Presentation 
OpenFOAM  1806  OpenFOAM (Open source Field Operation And Manipulation) is a toolbox for the development of customized numerical solvers, and pre/postprocessing utilities for the solution of continuum mechanics problems, including computational fluid dynamics (CFD). OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to acoustics, solid mechanics and electromagnetics.  MPI  GNU GPL  PDF1
PDF2 
SALOME  8.5.0  SALOME is an opensource software that provides a generic Pre and PostProcessing platform for numerical simulation.  MPI  GNU LGPL  
Physics & Space Sciences
Name  Version  Description  Parallel programming technologies  License  Presentation 
Corsika  7.6400  COsmic Ray SImulations for KAscade – CORSIKA (COsmic Ray SImulations for KAscade) is a program for detailed simulation of extensive air showers initiated by high energy cosmic ray particles (protons, light nuclei up to iron, photons, and many other particles may be treated as primaries). Corsika includes the CoREAS module  Monte Carlo code for the simulation of radio emission from extensive air showers.  MPI  Link  
LCODE  2.6.8  LCODE is a freelydistributed code for simulations of particle beamdriven plasma wakefield acceleration.  MPI   
ROOT MPI  6.14  ROOT is a modular scientific software toolkit that provides all the functionalities needed to deal with big data processing, statistical analysis, visualization and storage. ROOT MPI is the integration of ROOT and MPI technologies in a framework for parallel computing.  MPI  GNU LGPL  
