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Application packages

Chemistry & Materials Sciences

NameVersionDescriptionParallel programming technologiesLicensePresentation
ABINIT8.8.4ABINIT 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 many-body Green's functions (GW and DMFT).MPI,
OpenMP,
CUDA
GNU GPLPDF
BigDFT1.8.2BigDFT is a DFT massively parallel electronic structure code using a wavelet basis set.MPI,
OpenMP,
CUDA
GNU GPLPDF
CP2K6.1CP2K 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 GPLPDF1
PDF2
PDF3
CPMD4.1The CPMD code is a parallelized plane wave / pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics.MPI,
OpenMP
LinkPDF
Dalton & LSDalton2016This 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
Elk5.2.14An all-electron full-potential linearised augmented-plane wave (LAPW) code with many advanced features.MPI, 
OpenMP
GNU GPL / LGPL
ESPResSo4.0ESPResSo is a 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.MPI,
CUDA (in part)
GNU GPL
Firefly8.2.0Firefly (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 2-e integral evaluation for direct calculation methods, very efficient MP2 energy and energy gradient modules, very fast RHF MP3/MP4 energy code, and state-of-the-art DFT, TDDFT, MCSCF, MRMP2, MCQDPT, and XMCQDPT implementation.MPI,
CUDA (in part)
Link
GAMESS-USSept 30th, 2017The General Atomic and Molecular Electronic Structure System is a general ab initio quantum chemistry package.MPI,
OpenMP,
CUDA
Link
GROMACS2018.3GROMACS 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 LGPLPDF1
PDF2
PDF3
LAMMPS22 Aug 2018LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics code with a focus on materials modeling. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained 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 GPLPDF1
PDF2
PDF3
Molcas & openMolcas8.2Molcas 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
MPB1.6.1MPB (MIT Photonic Bands) is a free and open-source 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 definite-frequency eigenstates, or harmonic modes, of Maxwell's equations in periodic dielectric structures for arbitrary wavevectors, using fully-vectorial and three-dimensional methods. MPI,
OpenMP
GNU GPL
NAMD2.13NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.MPI,
OpenMP,
CUDA
Link PDF1
PDF2
NWChem6.8NWChem is open source high-performance computational chemistry software package.MPI,
CUDA
ECL 2.0PDF
Octopus8.2Octopus is a scientific program aimed at the ab initio virtual experimentation on a hopefully ever-increasing range of system types. Electrons are described quantum-mechanically within density-functional theory (DFT), in its time-dependent form (TDDFT) when doing simulations in time. Nuclei are described classically as point particles. Electron-nucleus interaction is described within the pseudopotential approximation.MPI,
OpenMP,
CUDA
GNU GPLPDF
OpenMX3.8.5OpenMX (Open source package for Material eXplorer) is a software package for nano-scale material simulations based on density functional theories (DFT), norm-conserving pseudopotentials, and pseudo-atomic localized basis functions.MPI,
OpenMP
GNU GPLPDF
ORCA4.0.1The program ORCA is a modern electronic structure program package. ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell 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.MPILink
Quantum ESPRESSO6.3Quantum ESPRESSO is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.MPI,
OpenMP,
CUDA
GNU GPLPDF
SIESTA4.0.2SIESTA 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
WIEN2K18.2The program package WIEN2k allows to perform electronic structure calculations of solids using density functional theory (DFT). It is based on the full-potential (linearized) augmented plane-wave ((L)APW) + local orbitals (lo) method, one among the most accurate schemes for band structure calculations.MPILink
VASP5.4.4The VASP (Vienna Ab initio Simulation Package) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles.MPI,
OpenMP,
CUDA
LinkPDF

Biology & Life Sciences

NameVersionDescriptionParallel programming technologiesLicensePresentation
ABySS2.1.1ABySS (Assembly By Short Sequences) is a de novo, parallel, paired-end sequence assembler that is designed for short reads.MPI, 
OpenMP,
CUDA
GNU GPLPDF
BEAST1.10.1BEAST is a program for Bayesian analysis of molecular sequences using MCMC. It is entirely orientated towards rooted, time-measured 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 (high-performance 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, ScalaBlastGPU-Blast. See also Blast2GOMPI,
OpenMP,
CUDA
Public Domain
HMMER3.2.1HMMER 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 3-Clause
MAKER2.31.10MAKER 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 ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values.MPI GNU GPL
Migrate3.6Migrate 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.MPIMIT License
mothur1.41.0mothur is a software package for processing bioinformatics data (incl. for the analysis of microbial communities) generated by Sanger, PacBio, IonTorrent, 454, Illumina (MiSeq/HiSeq).MPIGNU GPL
MPI-PHYLIP3.697MPI-PHYLIP is a software for computationally intensive phylogenetic analysis; parallel implementation of a popular package PHYLIP (PHYLogeny Inference Package).MPI
MrBayes 3.2.6MrBayes 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 GPLPDF
pBWA0.5.9pBWA (Parallel Burrows-Wheeler Aligner) is a parallel implementation of the popular software BWA for mapping low-divergent sequences against a large reference genome, such as the human genome.MPI,
OpenMP
GNU GPL, MIT License
RAxML8.0.0RAxML (Randomized Axelerated Maximum Likelihood) is a tool for phylogenetic analysis and post-analysis of large phylogenies.MPI,
OpenMP
GNU GPL
Ray2.3.1Ray is a parallel genome assemblies for parallel DNA sequencing.MPI GNU GPL
VinaLC1.1.2VinaLC is a parallel implementation of the very popular molecular docking program AutoDock Vina. See also: VinaMPI.MPIApache License 2.0

Mathematics & Computer Science

NameVersionDescriptionParallel programming technologiesLicensePresentation
CPLEX12.8.0CPLEX is an optimization software package.MPILinkPDF
HordeSAT & HordeQBFMassively parallel portfolio-based SAT/QBF solvers (include modified source codes of MiniSAT and DepQBF).MPIPDF1
PDF2
MPIDepQBFMPIDepQBF is a parallel QBF solver based on a search-space splitting approach. It uses DepQBF as the base solver.MPIBSD License (Toss)PDF
PaMiraXTPaMiraXT is a powerful parallel SAT solver that implements a master/client model based on message passing. For the clients, a thread-based solver MiraXT is used.MPI
PaQuBEPaQuBE is a parallel QBF solver implementing a master/client model and using QBF solver QuBE as a client.MPI
PDSAT0.9PDSAT (Parallel and Distributed SAT solver) - an MPI-based divide-and-conquer SAT solver based on the Monte Carlo method and local search heuristics.MPI
PMSatPMSat is a parallel SAT-solver that uses MiniSAT as engine.MPIMIT License

Engineering & Mechanics

NameVersionDescriptionParallel programming technologiesLicensePresentation
OpenFOAM1806OpenFOAM (Open source Field Operation And Manipulation) is a toolbox for the development of customized numerical solvers, and pre-/post-processing 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.MPIGNU GPLPDF1
PDF2
SALOME8.5.0SALOME is an open-source software that provides a generic Pre- and Post-Processing platform for numerical simulation.MPIGNU LGPL

Physics & Space Sciences

NameVersionDescriptionParallel programming technologiesLicensePresentation
Corsika7.6400COsmic 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. MPILink
LCODE2.6.8LCODE is a freely-distributed code for simulations of particle beam-driven plasma wakefield acceleration.MPI
ROOT MPI6.14ROOT 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.MPIGNU LGPL