Search Results for "parallel" - Page 28
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Showing 1671 open source projects for "parallel"
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Explicit/Impicit Finite Element Program with linear/nonlinear, elastic/hyperelastic/hypoelastic/plastic/visco, contact,thermal, fluid capabilities. h/p refinements. Parallel/Distributed solvers available. No shell elements but has 2D beams, trusses.
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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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Schnek
A C++ library for developing parallel simulations on Cartesian grids
NOTICE: The current version of Schnek is hosted on GitHub https://github.com/holgerschmitz/Schnek This repository on Sourceforge is no longer maintained! Schnek is a library for the fast development of parallel simulation codes using multidimensional arrays. It is designed to work both on single processor and massively parallel architectures. The library is intended mainly for use in physics simulations on regular grids but some of its features might be useful for other types of simulation codes. Features include - setup file reader with C style syntax - extendable for formulas in setup files - hierarchical structure of simulation components - mutli-dimensional grids - initialisation of grid from formulas in setup file - boundary cells and ghost cells - MPI support for parallelisation - MPI update of ghost cells to neighbouring processes - easy to use parallel and serial HDF5 output of grids -
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HPC Challenge
HPC Challenge is an HPC benchmark for memory access patterns
HPC Challenge benchmark consists of 7 tests: (1) HPL - the Linpack TPP benchmark which measures the floating point rate of execution for solving a linear system of equations. (2) DGEMM - measures the floating point rate of execution of double precision real matrix-matrix multiplication. (3) STREAM - a simple synthetic benchmark program that measures sustainable memory bandwidth (in GB/s) and the corresponding computation rate for simple vector kernel. (4) PTRANS (parallel matrix transpose) - exercises the communications where pairs of processors communicate with each other simultaneously - a useful test of the total communication capacity of the network. (5) RandomAccess - measures the rate of integer random updates of memory (GUPS). (6) FFT - measures the floating point rate of execution of double precision complex one-dimensional Discrete Fourier Transform (DFT). (7) Communication bandwidth and latency test for simultaneous communication patterns. http://icl.cs.utk.edu/hpcc -
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PhyloPart
automated partition of phylogenetic trees
Understanding the determinants of virus transmission is a fundamental step for effective design of screening and intervention strategies to control viral epidemics. Phylogenetic analysis can be a valid approach for the identification of transmission chains, and very-large data sets can be analysed through parallel computation. Here we propose and validate a new methodology for the partition of large-scale phylogenies and the inference of transmission clusters. This approach, on the basis of a depth-first search algorithm, conjugates the evaluation of node reliability, tree topology and patristic distance analysis. -
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P3BSseq
Parallel processing pipeline for analysis of bisulfite sequencing data
...Though some BSseq processing tools are available, they are scattered, require puzzling parameters and are running-time and memory-usage demanding. We have developed P3BSseq, a parallel processing pipeline for fast, accurate and automatic analysis of BSseq reads that trims, aligns, annotates, records the intermediate results, performs bisulfite conversion quality assessment, generates BED methylome and report files following the NIH standards. P3BSseq outperforms the known BSseq mappers regarding running time, computer hardware requirements. ... -
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Ship Lock Scheduling
Scheduling lockages at ship locks with several parallel lock chambers
This Java software includes algorithms of combinatorical optimization for the NP-hard offline ship lock scheduling problem. Solutions and performed computations can be displayed graphically. Besides, there is a framework for generating test instances and running these in parallel, as well as R/JGR code for statistical evaluation. Some tools for estimating the quality of calculated solutions will be further improved. Initially the software was developed within a project of TU Berlin regarding the Kiel Canal. See project wiki for conditions that should be met by applications. -
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Pop Framework
Use Java bean as model of web page, reference beans in hyperlinks
...Views and Models are therefore loosely coupled in Pop. A model can have multiple views for different devices and different locales. Each view and each model can be maintained and optimized independently and in parallel. -
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ThéMA libs
Commons and utils Java classes used in ThéMA projects
This project contains 7 Java libraries developped in ThéMA laboratory : - common - data - parallel - drawshape - graph - network - msca -
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The English-Vietnamese Bilingual Corpus (EVBCorpus) is a collection of English and Vietnamese parallel translations and bitexts.
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...Program is crushing and repairing over 500 per second (don't depend on file size) and makes your files & folders unoppenable and undetectable by search engines and other progam in windows etc. Demo vid (older version): http://www.youtube.com/watch?v=nFH2FB7OOHc v1.3 - Fixed problem with files attributes v1.4 - App Speed improvement v1.5 - Parallel task processing - can't get much better then this one (THIS VERSION IS ONLY ONLY AN EXPERIMENT, AND MIGHT NOT WORK CORRECTLY, TO BE SAVE DOWNLOAD ONLY v1.4) You nead .NET 2.0 or .NET 4.0 liblaries to run this program.
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AutoGen is designed to generate text files containing repetitive text with varied substitutions. Its goal is to simplify the maintenance of programs that contain large amounts of repetitious text, especially when needed in parallel tables.
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5.Kernelized qtl-haplotype mapping (HPC)
Fortran/R program for kernelized qtl-haplotype mapping by mixed model
Kernelized qtl-haplotype mapping (named KHAMMIX) is a Fortran/R program which performs parallel haplotype based scans of chromosomes, by mixed model analyses, for diploid organisms. Two kernels; the Gaussian and Van Raden kernels, are allowed for the mixed model analyses. The haplotypes are defined by a sliding window of L SNP markers (L is an integer greater or equal to 1). Hence, 2^L haplotypes can be (not necessarily) observed for a sliding window (e.g. 2^6=64 for L=6). -
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The Rope Java Virtual Machine implements the Rope model which is a novel thread level speculative execution model called Rushing Object Parallel Environment. This is a research project aimed at exploiting parallelism in traditional object oriented programs.
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GMaVis: A DSL for Geo-Visualization
It is a domain-specific language for large data geo-visualizations
...GMaVis' compiler. It is used to recognize GMaVis' code and transform it in a geospatial data visualizations. Usage: bin/gmavis [-i/--input] <arg> [-o/--output] <arg> [-p/--parallel] <arg> Example: bin/gmavis -i my_gmavis_code.vis -o out.html -
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Hound
Elixir library for writing integration tests and browser automation
...It wraps the WebDriver protocol, allowing developers to write ExUnit tests that control browsers like Firefox, Chrome, or PhantomJS via Selenium or ChromeDriver. Hound supports parallel sessions, asynchronous test execution, JavaScript-heavy interactions, screenshots, and more—all directly in Elixir test suites. -
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VITAMINS
Visual and Insitu Analytics for Molecular Interactive Simulation
A framework to support the high performance analysis and visualisation of molecular dynamics trajectories directly acquired in-situ while the simulation is running, or read from files. Vitamins relies on the FlowVR software and comes with binding with Gromacs. Vitamins (Visual and In Situ Analytics for Molecular Interactive Simulation) is an open source framework for the analysis and visualisation of large molecular dynamics trajectories directly acquired in-situ while the simulation... -
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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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SPRITE
Parallel SNP detection pipeline
SPRITE is an open-source software package providing a parallel implementation of the Single Nucleotide Polymorphisms (SNP) detection genomic data analysis workflow. It consists of three tools: PRUNE for read alignment, SAMPA for intermediate file processing, and PARSNIP for parallel SNP calling. -
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MSRE-HTPrimer
A high-throughput primer design tool for MSRE-assay in epigenetics
...MSRE-HTPrimer provides significant improvements over existing solutions with following unique features: 1) visualization of primer pairs in UCSC genome browser, 2) search each resulting primer pair in UCSC In-Silico PCR database, 3) flexible primer selection and filtering based on custom quality matrix and 4) parallel primer design for several target sequences. The pipeline is equipped with multiprocessing capability and uses custom inputs and parameters to design specific primers. -
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...Installation instructions are provided in the INSTALL file of the project and in https://sourceforge.net/p/trjcavity/wiki/Home/#ffad If you need support using this tool (or report bugs), please post it in the discussion forum. Remarks: v2 runs in parallel and supports GROMACS v5.1+ series. If you want to continue on using GROMACS v4.x, please use trj_cavity_v1.1.
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4. Bagging Nadaraya Watson Estim. (HPC)
Shell/R program to perform Bagging of the Nadaraya Watson Estimator
Shell/R program which performs bagging of the Nadaraya Watson Kernel estimator by parallel computing -
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...We employed an existing algorithm to analyze the modularity of directed graphs and a Boolean network model for robustness calculation. In particular, to ensure the robustness algorithm’s applicability to large-scale networks, we implemented it as a parallel algorithm by using the OpenCL library. A batch-mode simulation function was also developed to verify whether an observed relationship between modularity and robustness is conserved in a large set of randomly structured networks. The app provides various visualization modes to better elucidate topological relations between modules, and tabular results of centrality and gene ontology enrichment analyses of modules.
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PPMScope
Microcontroller based PC Oscilloscope
...This is a version based on the PIC16F877A microcontroller running with a 20MHz clock. The maximum sampling rate is 1 MHz with a 5 Mhz equivalent sampling mode. Currently, the computer interface supports USB, serial, and parallel ports. Good luck on the construction and I hope you enjoy your oscilloscope. I am happy to answer any questions or provide technical support for this design.
