Search Results for "parallel" - Page 2
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Showing 84 open source projects for "parallel"
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diauxic growth model ensemble
An ensemble of models showing diauxic growth behavior
...Carbon catabolite repression (CCR) is the main mechanism controlling carbohydrate uptake in bacteria, and therefore also controlling whether or not different carbon sources are metabolized in parallel or sequentially. Although described as a paradigm of the regulation of bacterial metabolism, the underlying mechanisms remain controversial. The models in the ensemble can be categorized according to regulatory, stoichiometric, and physiological constraints and differ from each other on only a single aspect. We distinguish four groups of models: (1) flux balance models that only define reaction kinetics for substrate uptake and by-product excretion, (2) kinetic models without and (3) kinetic models with regulation on the metabolic and/or genetic level, and (4) resource allocation models. -
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AcouSTO (Acoustic Simulation TOol) is a low-order BEM code to solve the Kirchhoff Integral Equation. An arbitrary number of scattering/radiating bodies, monopoles, and plane waves is allowed. Runs in parallel on MPI2-equipped clusters.
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optpack
FE simulation based automatic global optimisation in modern Fortran
...The initial application is for FE simulation of elasto-plastic buckling of steel rods aimed at tuning the hardening model. Unix shell scripts are used extensively. High concurrency is achieved with parallel multi-start global search and with parallel MPI FE. Powell's BOBYQA or LINCOA are used (not included in this package). Automatic mesh generation of 3D cylinders is provided + automatic boundary conditions, all via Fortran and shell scripting. -
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Advanced Simulation Library
Free multiphysics simulation software package
...Its computational engine is based, among others, on the Lattice Boltzmann Methods (http://en.wikipedia.org/wiki/Lattice_Boltzmann_methods) and is written in OpenCL (http://en.wikipedia.org/wiki/OpenCL) which enable extraordinarily efficient deployment (http://asl.org.il/benchmarks) on a variety of massively parallel architectures, ranging from inexpensive FPGAs, DSPs and GPUs up to heterogeneous clusters and supercomputers. The engine is hidden entirely behind C++ classes, so that no OpenCL knowledge is required from application programmers. ASL can be utilized to model various coupled physical and chemical phenomena and employed in a multitude of fields: computational fluid dynamics, virtual sensing, industrial process data validation and reconciliation, image-guided surgery, computer-aided engineering, high-performance scientific computing, etc.. -
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cupSODA
Deterministic simulator of mass-action based models
cupSODA is a simulator of biological systems that exploits the remarkable memory bandwidth and computational capability of GPUs. cupSODA allows to efficiently execute in parallel large numbers of simulations, which are usually required to investigate the emergent dynamics of a given biological system under different conditions. cupSODA works by automatically deriving the system of ordinary differential equations from a reaction-based mechanistic model, defined according to the mass-action kinetics, and then exploiting the numerical integration algorithm, LSODA -
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...This tool performs Virtual Nodes Parallelization on a given MicroModelica model for being simulated in QSS Solver. The objective is to reduce the error introduced by simulating large-scaled models in parallel on QSS Solver simulating tool. This is done through redundant computations on certain state variables of the model. These redundant computations are called Virtual Nodes.
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runjags
The 'runjags' R package and standalone JAGS extension module
This package provides high-level interface utilities for MCMC models via Just Another Gibbs Sampler (JAGS), facilitating the use of parallel (or distributed) processors for multiple chains, automated control of convergence and sample length diagnostics, and evaluation of the performance of a model using drop-k validation or against simulated data. Template model specifications can be generated using a standard lme4-style formula interface to assist users less familiar with the BUGS syntax. ... -
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OPar
OPen ARchitecture PARallel PARticle code
NOTICE: The current version of OPar is hosted on GitHub https://github.com/holgerschmitz/Opar This repository on Sourceforge is no longer maintained! OPar is an open architecture Particle-In-Cell (PIC) code for plasma simulations. The code is based on the Schnek framework. -
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SWIFT
SPH With Inter-dependent Fine-grained Tasking
Shared-Memory Parallel Smoothed Particle Hydrodynamics (SPH) code for large-scale cosmological simulations. -
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Folder
Toolbox for modelling deformation in layered media in 2D
Folder is a tool to simulate and analyse the development of structures in mechanically layered media during layer parallel shortening or extension. It includes a graphical user interface that allows for easy designing of complex geometrical models, defining material parameters (including linear and non-linear rheology), and specifying type and amount of deformation. It also includes a range of features that facilitate the visualization and examination of various relevant quantities e.g. velocities, stress, rate of deformation, pressure, and finite strain. ... -
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ViennaWD
Classical and quantum semiconductor device simulation
The ViennaWD package provides a selection of simulation tools supporting classical and quantum approaches for semiconductor device simulation. -
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neuranep
Neural Network Engineering Platform
A parallel-programming framework for concurrently running large numbers of small autonomous jobs, or microthreads, across multiple cores in a CPU or CPUs in a cluster. NeuraNEP emulates a distributed processing environment capable of handling millions of microthreads in parallel, for example running neural networks with millions of spiking cells. -
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fPotencia
Power flow library in C++
...After observing the lack of ready-to-implement libraries for power system analisys, and that the existing ones focus on command line workflow, I decided myself to start a project to fill the gap. Since Power system simulations have started needing to be executed in parallel, the old C-like designs are outdated; modular design is now needed to launch many simulations at the same time based on a base circuit. fPotencia is programmed in C++, but my intention is to bring JAVA, C#, Python and perhaps MATLAB versions of it. All of them in native code and whenever possible with the same modular structure. -
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MDcore is an Open-Source library implementing the core functionality of a Molecular Dynamics engine. The engine is inherently multi-threaded and runs efficiently on multi-processor/multi-core shared-memory architectures.
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piv_clustering
structural clustering of atomic trajectories based on PIV
This program allows to perform a structural cluster analysis of atomic trajectories obtained, e.g., from molecular dynamics simulations. At variance with other approaches, it is possible to analyse also processes in solution, e.g., chemical reactions in liquid water, since the distance metric is based on a Permutation Invariant Vector (PIV) that is symmetric under exchange of identical atoms or molecules, including on the same footing both solute and solvent degrees of freedom. The... -
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BriCS
SaaS for running simulation models in the cloud
The Bristol Cloud Service simulation runner is a cloud computing Software as a Service designed to enable users to quickly launch simulation code on Amazon AWS' Elastic Compute Cloud (EC2). BRiCS is written in Python using the Django framework and interacts with EC2 using the boto API. BriCS enables multiple simulation runs to be launched in parallel from a web browser. Model configuration (parameters) files are uploaded via the browser and results files are downloadable on completion. BriCS enables researchers with software simulation models to access the rapid scale out opportunities of the cloud. Why wait days or weeks for a series of trials to complete when you can run them in parallel in the time it takes to complete one? -
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FlowVR is an open source middleware tailored for high performance in situ data processing and analytics running on large parallel machines
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LARA
Lightweight Architecture for boundedly Rational Agents
For the purpose of policy simulation in coupled social-ecological systems (e.g. energy supply), a credible modelling of actors – especially citizens – and their decision processes is needed. This requires a framework capable of handling high numbers of heterogeneous agents (several hundreds of thousands). LARA (Lightweight Architecture for boundedly Rational Agents) meets these requirements and fills the gap between frameworks without built-in psychological foundations and full-fledged... -
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A parallel-programming framework for concurrently running large numbers of small autonomous jobs, or microthreads, across multiple cores in a CPU or CPUs in a cluster. Each microthread is conceptually similar to a task in Ada and it is much lighter weight than an operating system thread. SpikeOS was designed to handle millions of microthreads, for example in a neural network hosting millions of spiking model neurons.
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ParallelSim
ParallelSim is a parallel processor simulator written in java.
ParallelSim is a parallel processor simulator written in Java which shows the effect of increasing the workload keeping the number of processing elements constant in one simulation. The number of processors is scalable and can be increased in subsequent iterations of simulation. The parameters like initial load, load offset, number of processors are declared as constants and can be changed directly in the source code to emulate different scenarios. -
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Parallel SCVT generator, using a new method for the parallel computation of Spherical Delaunay Triangulations. Uses Jonathan Shewchuk's Triangle http://www.cs.cmu.edu/~quake/triangle.html
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parFE is fully-parallel high-performance finite element code targeted to the modeling of trabecular bones in humans. It employs scalable multigrid solvers for efficient solutions on massively parallel computers.
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SPSens
Stochastic parameter sensitivity analysis for chemical networks
...Additionally the package includes basic stochastic simulation algorithms. The package includes several example networks which can be easily modified for other networks. Serial and parallel MPI implementations can be built and called from the command line. The serial implementation of the package can also be called from Matlab via the MEX interface with limited functionality. It supports many user specified options, including the use of antithetic sampling that can be used in some cases to increase efficiency. -
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caseGen
... [BATCH], [ANALYZE] and [OPTIMIZE] cases in OpenFOAM and others
'caseGen' allows you to simplify your numerical simulation problem! Actual its not fairly tested so please contact me if you see any refinements or found bugs.
