MPI APPLICATIONS

MPI Applications

Message Passing Interface (MPI) is a specification for software developers used to make use of a cluster of computers. A set of libraries exist for using this standard on modern day (High Performance Computing) HPC Clusters. The problem with a computing cluster is that while some of the CPUs share memory (Shared Memory), others have a distributed memory architecture which is only connected by network. Today’s developers are able to make use of these distributed memory, shared memory and a hybrid system of both; all with the power of MPI. Over the years, there have been quite a few MPI libraries available, and today, some of the more common libraries include MPICH, MVAPICH, Open MPI and Intel MPI. We also have quite a few applications that have already been ported to run by using MPI. If you see your application listed and would like some help with testing, Aspen Systems has clusters for testing purposes, Contact Us for a test drive.


BIOINFORMATICS BIOLOGY COMPUTATIONAL FLUID DYNAMICS MATHEMATICS MOLECULAR DYNAMICS PHYSICS WEATHER MODELING

BIOINFORMATICS

mpiBLAST Logo mpiBLAST is a freely available, open-source, parallel implementation of NCBI BLAST. By efficiently utilizing distributed computational resources through database fragmentation, query segmentation, intelligent scheduling, and parallel I/O, mpiBLAST improves NCBI BLAST performance by several orders of magnitude while scaling to hundreds of processors. mpiBLAST is also portable across many different platforms and operating systems.
Industries: Life Sciences Go to the mpiBLAST website for more information.

BIOLOGY

NCBI Logo Basic Local Alignment Search Tool (BLAST) is a sequence comparison algorithm optimized for speed and used to search DNA and protein sequence databases for optimal local alignments to a query.
Industries: Life Sciences Go to the NCBI website for more information.
CLC Assembly Cell Logo CLC Assembly Cell is a high-performance computing solution for read mapping and de novo assembling of next generation sequencing data. With the command-line interface of CLC Assembly Cell, you can easily include these functionalities in scripts and other next generation sequencing workflows. It is easy to install on your desktop computer or a larger compute cluster. CLC Assembly Cell is accelerated through advanced algorithm implementations: they use the SIMD instruction set to parallelize and accelerate compute intensive parts of the algorithms, and make the software one of the fastest and most accurate packages for NGS data analysis on the market.
Industries: Other Go to the Qiagen website for more information.
GERO Logo Gero is a drug discovery company creating first in class small molecule therapeutics using proprietary, industry leading molecular modeling methods and systems biology technologies.
Industries:Life Sciences Go to the GERO website for more information.
Glide Logo Glide offers the full range of speed vs. accuracy options, from the HTVS (high-throughput virtual screening) mode for efficiently enriching million compound libraries, to the SP (standard precision) mode for reliably docking tens to hundreds of thousands of ligand with high accuracy, to the XP (extra precision) mode where further elimination of false positives is accomplished by more extensive sampling and advanced scoring, resulting in even higher enrichment.
Industries: Life Sciences Go to the Glide website for more information.
HMMER Logo HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). HMMER is often used together with a profile database, such as Pfam or many of the databases that participate in Interpro. But HMMER can also work with query sequences, not just profiles, just like BLAST.
Industries: Life Sciences Go to the HMMER website for more information.
MrBayes Logo MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes’s theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees.
Industries: Life Sciences Go to the MrBayes website for more information.

COMPUTATIONAL FLUID DYNAMICS

MPI Applications - AVL Excite Logo The AVL EXCITE product family is a powertrain-oriented rigid and flexible multi-body dynamic analysis solution which provides advanced techniques to calculate the dynamics, strengths, vibration and acoustics of combustion engines, transmissions and conventional or electrified powertrains and drivelines.
Industries: Automotive Go to the AVL website for more information.
BOXERMesh Logo BOXERMesh is an advanced, highly automated, unstructured mesher with robust support for importing both standards-based and popular vendor-specific CAD files. BOXERMesh delivers quality multi-million cell meshes in minutes on geometries of arbitrary complexity and size.
Industries: Aerospace Automotive Go to the Cambridge Flow Solutions website for more information.
Calculix Logo CalculiX is a package designed to solve field problems. The method used is the finite element method. With CalculiX Finite Element Models can be build, calculated and post-processed. The pre- and post-processor is an interactive 3D-tool using the openGL API.
Industries: Aerospace Automotive Go to the Calculix website for more information.
Cart3D Logo Cart3D is a high-fidelity inviscid aerodynamic analysis package for conceptual and preliminary aerodynamic design. It allows users to perform automated CFD analysis on arbitrarily complex geometry. The package includes utilities for geometry import, surface modeling and intersection, mesh generation, flow simulation, and post-processing of results. The main simulation code, flowCart, runs in parallel both in shared memory (OpenMP) and distributed memory (MPI) with excellent scalability.
Industries: Aerospace Go to the Aerion website for more information.
CASE CASE (Cylinder Kit Analysis System for Engines) is a complete software tool for parametric studies of the ring-pack and piston of internal combustion engines. It is used for predicting blowby, cylinder wear, energy losses, and many other dynamic and tribological phenomena.
Industries: Automotive Go to the MMR website for more information.
CFD++ Logo CFD++ can efficiently solve incompressible and compressible flows including both single and multispecies reacting flows, conjugate heat transfer, porous media, rotating machinery, and multiphase flows for both steady and unsteady cases. CFD++ allows for very simple treatment of complex models due to its unification of structured, unstructured, multiblock, and complex overset and patched non-aligned grids.
Industries: Aerospace Automotive Go to the Metacomp website for more information.
Code Aster Logo Code Aster is a software package for civil and structural engineering, finite element analysis, and numerical simulation. It was originally developed by the French company EDF and released as open source software. It is particularly rich in constitutive laws, finite elements, loading types and nonlinear simulations (material, large transformation and contact).
Industries: Other Go to the Code Aster website for more information.
Converge Logo CONVERGE is a commercial computational fluid dynamics (CFD) package that is loaded with physical models for spray, turbulence (including LES), and combustion. CONVERGE is widely used in in the internal combustion engine design community due to its ability to generate high-quality orthogonal and body-fitted meshes automatically at runtime, and also due to its adaptive mesh refinement implementation.
Industries: Aerospace Automotive Go to the Converge website for more information.
Cradle Logo Cradle SC/Tetra is usability-focused software with the specific goal of easily enabling calculation of complex geometries. It provides both automatic mesh generation and a Wizard based interface that guides the user through the set-up process step by step. In addition to simulating standard fluid flow and heat transfer applications, SC/Tetra can calculate various phenomena such as Chemical Reactions, Arbitrary Lagrangian Eulerian for moving and/or rotating boundaries (ALE), Human Body Thermoregulation (JOS), Free Surfaces and Acoustics.
Industries: Aerospace Automotive Go to the Cradle website for more information.
Crunch CFD Logo CRUNCH CFD is an unstructured grid flow solver with multi-physics simulation capabilities. Advanced models for turbulence, cavitation, combustion, and cryogenics are available. CRUNCH CFD also features an extensive list of simulation tools, including non-ideal EOS, mesh motion/adaptation, hybrid LES/RANS and detailed chemical reactions.
Industries: Aerospace Go to the CRAFT Tech website for more information.
EnSight Logo EnSight reads data from many different engineering simulation programs and breathes life into it. Files full of dull numbers are converted by EnSight into airplanes, engines, cars, buses, trucks, ships, factories, and more that you can rotate, pan, and zoom through. EnSight makes that data interactive, plottable, searchable, and exportable.
Industries: Aerospace Automotive Go to the EnSight website for more information.
VR&D GENESIS Logo GENESIS is a fully integrated finite element analysis and design optimization software package. Analysis is based on the finite element method for static, normal modes, direct and modal frequency analysis, random response analysis, heat transfer, and system buckling calculations. Design is based on the advanced approximation concepts approach to find an optimum design efficiently and reliably.
Industries: Aerospace Automotive Go to the VRAND website for more information.
Gerris Logo Gerris is an open-source computational fluid dynamics (CFD) package written in C that solves the incompressible Navier-Stokes equations in 2- or 3- dimensions. Gerris’ implementation and accurate formulation of multiphase flows (including surface tension) is the reason why the software shares the same name as the insect.
Industries: Aerospace Go to the Gerris website for more information.
GT Logo GT-SUITE is a product of Gamma Technologies (GTI), a specialist software company which is solely focused on the Engine and Vehicle Industry. GT-SUITE handles, in a single software tool, a wide variety of vehicle and engine technical applications.
Industries: Automotive Go to the GT-Suite website for more information.
Helyx Logo HELYX is a comprehensive general purpose Computational Fluid Dynamics software solution for engineering analysis and optimization based around ENGYS’ own enhanced version of the OpenFOAM library. ENGYS’ personnel involvement with FOAM and OpenFOAM dates back to 1999, providing unparalleled knowledge and expertise in the development, integration and application of this tool for industry. We take advantage of this experience to offer a unique product that combines the best of both worlds: the proven capabilities, support and reliability of commercial tools with the inherent advantages of cost-effective, scalable open-source solutions.
Industries: Aerospace Automotive Go to the Engys website for more information.
MADYMO Logo MADYMO (MAthematical DYnamic MOdels) is the worldwide standard software for analyzing and optimizing occupant safety designs. It is without rival for its accuracy, efficiency and versatility. Using MADYMO, researchers and engineers can model, thoroughly analyze and optimize safety designs early in the development process. This reduces the expense and time involved in building and testing prototypes. Adopting MADYMO also minimizes the risk of making design changes late in the development phase. For new or improved vehicle models and components, MADYMO cuts cost and reduces the time-to-market substantially.
Industries: Aerospace Automotive Oil and Gas Go to the TASS International website for more information.
Openfoam Logo OpenFOAM (Open-source Field Operation And Manipulation) is a C++ 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).
Industries: Aerospace Automotive Go to the Openfoam website for more information.
ParaView Logo ParaView is an open source multiple-platform application for interactive, scientific visualization. The data exploration can be done interactively in 3D or programmatically using ParaView’s batch processing capabilities.
Industries: Aerospace Automotive Go to the ParaView website for more information.
PTC Creo Simulate Logo PTC Creo Simulate is a structural, thermal, and vibration analysis solution with a comprehensive set of capabilities that allow you to study how your 3D virtual prototypes will perform prior to making the first physical part.
Industries: Aerospace Automotive Go to the PTC website for more information.
PyFR Logo PyFR is an open-source Python based framework for solving advection-diffusion type problems on streaming architectures using the Flux Reconstruction approach of Huynh. The framework is designed to solve a range of governing systems on mixed unstructured grids containing various element types. It is also designed to target a range of hardware platforms via use of an in-built domain specific language derived from the Mako templating engine.
Industries: Aerospace Automotive Go to the PyFR website for more information.
Shipflow Logo SHIPFLOW is optimized for ship hydrodynamics design. The world standard for ship hydrodynamics CFD. Developed by naval architects, physicists and numerical analysts.
Industries: Other Go to the Flowtech website for more information.
GT Logo Star-CD allows for analysis of in-cylinder flow and combustion to be well established. The demands for accuracy, flexibility and turnaround have never been greater as designers face huge challenges to satisfy legislation, deliver performance and lower cost.
Industries: Automotive Go to the Star-CD website for more information.
Ricardo VECTIS Logo VECTIS is a three-dimensional fluid dynamics program that has been developed specifically to address fluid flow simulations in the vehicle and engine industries. VECTIS is developed around a completely automatic mesh generator, providing a rapid turnaround time for CFD analyses. The fully automatic mesh generator, unique to VECTIS, provides a distinct advantage over most other commercial Computational Fluid Dynamics (CFD) tools; in that it ensures CFD is an integral part of modern engineering development programs.
Industries: Automotive Go to the Ricardo Software website for more information.
Ricardo WAVE Logo WAVE is a 1-D engine and gas dynamics simulation package from Ricardo Software. WAVE enables vehicle performance simulations to be carried out based on virtually any intake, combustion, and exhaust system configuration. Also included is a drivetrain model that enables complete vehicle simulations.
Industries: Automotive Go to the Ricardo Software website for more information.
XFlow Logo XFlow is a next generation CFD software system that uses a proprietary state-of-the-art Lattice Boltzmann technology, and is specifically designed for companies who require accurate feedback on flow simulation, transient aerodynamics, water management and fluid-structure interaction.
Industries: Aerospace Automotive Go to the XFlow website for more information.

MATHEMATICS

Atlas Logo Atlas (Automatically Tuned Linear Algebra Software) is a powerful application for performing differential geometry calculations, from formulating and solving 2D and 3D problems to working with an n-dimensional manifold as a whole.
Industries: Life Sciences Go to the WOLFRAM website for more information.
GNU Octave Logo GNU Octave is a high-level interpreted language, primarily intended for numerical computations. It provides capabilities for the numerical solution of linear and nonlinear problems, and for performing other numerical experiments.
Industries: Life Sciences Go to the GNU website for more information.
Maple Logo Maple is the essential technical computing software for today’s engineers and scientists. Whether you need to do quick calculations, develop design sheets, or produce sophisticated high-fidelity simulation models, Maple provides the necessary technology to reduce errors and dramatically increase your analytical productivity at every stage of the design process.
Industries: Life Sciences Go to the Maplesoft website for more information.

MOLECULAR DYNAMICS

ATK Logo Atomistix ToolKit (ATK) offers unique capabilities for simulating electrical transport properties of nanodevices on the atomic scale. Based on an open architecture which integrates a powerful scripting language with a graphical user interface, ATK is a comprehensive platform for studies in nanoelectronics, using both accurate first-principles (DFT) and fast semi-empirical methods and classical potentials. Moreover, ATK includes a very advanced electrostatic model to allow realistic simulations of nanoscale transistor structures.
Industries: Other Go to the Quantum Wise website for more information.
AutoDock Logo AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. AutoDock Vina is an open-source program for doing molecular docking. It was designed and implemented by Dr. Oleg Trott in the Molecular Graphics Lab at The Scripps Research Institute.
Industries: Life Sciences Go to the AutoDock website for more information.
Chimera Logo UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories and conformational ensembles. High-quality images and animations can be generated.
Industries: Life Sciences Go to the UCSF website for more information.
DOCK Logo DOCK addresses the problem of “docking” molecules to each other. In general, “docking” is the identification of the low-energy binding modes of a small molecule, or ligand, within the active site of a macromolecule, or receptor, whose structure is known. A compound that interacts strongly with, or binds, a receptor associated with a disease may inhibit its function and thus act as a drug. Solving the docking problem computationally requires an accurate representation of the molecular energetics as well as an efficient algorithm to search the potential binding modes.
Industries: Life Sciences Go to the UCSF website for more information.

PHYSICS

ATK Logo Automatic Dynamic Incremental Nonlinear Analysis (ADINA) is a finite element analysis (FEA) suite of tools providing a comprehensive FEA solution for modeling structures, fluids, heat transfer, electromagnetics, and multiphysics.
Industries: Aerospace Automotive Go to the ADINA website for more information.
COMSOL Logo The COMSOL Multiphysics software is a simulation software tool used to model and simulate physics-based challenges and build simulation-specific applications. This simulation platform is designed with ease-of-use in mind, featuring a streamlined workflow and the ability to address multiphysics problems. Over 30 available add-on products help expand upon the capabilities of COMSOL Multiphysics.
Industries: Other Go to the COMSOL website for more information.

WEATHER MODELING

AERMOD Logo Aermod (U.S. Environmental Protection Agency) is a steady-state plume model that incorporates air dispersion based on planetary boundary layer turbulence structure and scaling concepts, including treatment of both surface and elevated sources, and both simple and complex terrain.
Industries: Earth Science Go to the Breeze website for more information.
ARPS Logo The Advanced Regional Prediction (ARPS) is a comprehensive regional to stormscale atmospheric modeling/prediction system. It is a complete system that includes a realtime data analysis and assimilation system, a forward prediction model and a post-analysis package. The ARPS was initially developed at the Center for Analysis and Prediction of Storms (CAPS) at the University of Oklahoma, under the support of the National Science Foundation Science and Technology Center (STC) program. CAPS will continue to improve and support the use of ARPS.
Industries: Earth Science Go to the ARPS website for more information.
Calmet Logo CALMET is a diagnostic meteorological model which reconstructs the 3D wind and temperature fields starting from meteorological measurements, orography and land use data. Besides the wind and temperature fields, CALMET determines the 2D fields of micro meteorological variables needed to carry out dispersion simulations (mixing height, Monin Obukhov length, friction velocity, convective velocity and others).
Industries: Earth Science Go to the Enviroware website for more information.
CALPUFF Logo CALPUFF is an advanced non-steady-state meteorological and air quality modeling system developed by Exponent scientists. It is maintained by the model developers and distributed by Exponent. The model has been adopted by the U.S. Environmental Protection Agency (USEPA) in its Guideline on Air Quality Models as the preferred model for assessing long range transport of pollutants and their impacts on Federal Class I areas and on a case-by-case basis for certain near-field applications involving complex meteorological conditions.
Industries: Earth Science Go to the EPA website for more information.
CAMx Logo CAMx is an Eulerian (gridded) regional photochemical dispersion model that allows for integrated “one-atmosphere” assessments of tropospheric air pollution (ozone, particulate matter, air toxics) over spatial scales ranging from neighborhoods to continents.
Industries: Earth Science Go to the CAMx website for more information.
CMAQ Logo CMAQ is an active open-source development project of the U.S. EPA Atmospheric Science Modeling Division that consists of a suite of programs for conducting air quality model simulations. CMAQ is supported and distributed by the CMAS Center. CMAQ combines current knowledge in atmospheric science and air quality modeling with multi-processor computing techniques in an open-source framework to deliver fast, technically sound estimates of ozone, particulates, toxics, and acid deposition.
Industries: Earth Science Go to the CMAS website for more information.
MM5 Logo The PSU/NCAR mesoscale model (known as MM5) is a limited-area, nonhydrostatic, terrain-following sigma-coordinate model designed to simulate or predict mesoscale atmospheric circulation. The model is supported by several pre- and post-processing programs, which are referred to collectively as the MM5 modeling system. The MM5 modeling system software is mostly written in Fortran, and has been developed at Penn State and NCAR as a community mesoscale model with contributions from users worldwide.
Industries: Earth Science Go to the MM5 website for more information.
RAMS Logo RAMS (Regional Atmospheric Modeling System) is a highly versatile numerical code developed by scientists at Colorado State University for simulating and forecasting meteorological phenomena and for depicting the results.
Industries: Earth Science Go to the CSU website for more information.
Smoke Logo SMOKE input data consist of emissions inventories, temporal and chemical speciation profiles, spatial surrogates, gridded meteorology and land use data, and other ancillary files for specifying the timing, location, and chemical nature of emissions.
Industries: Earth Science Go to the CMAS website for more information.