Search Results for "parallel computing" - Page 5
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Showing 220 open source projects for "parallel computing"
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GXP is a parallel/distributed shell, plus a parallel task execution engine that runs your Makefile in parallel on distributed machines. Very easy to install (no need to compile. install it on YOUR machine and use it on ALL machines).
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Fast Matrix for Java
General purpose matrix utilities for Java in Parallel Computing
Fast Matrix for Java (fm4j) is a general-purpose matrix utility library for computing with dense matrices. fm4j encapsulated different underlying implementations and select the optimal one in run-time depending on the size of the input matrix. Moreover, fm4j employs Java (Tm) Concurrency to take advantage of the computation power of multi-cor processors. -
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The sequence alignment task in MAGI (magi.ucsd.edu) is based on the miRanda algorithm, but we redesign the miRanda algorithm on GPU by taking its advantages of massively parallel computing and extra high memory bandwidth using using NVIDIA’s Compute Unified Device Architecture (CUDA). The CUDA-miRanda implementation is a fast microRNA target identification algorithm that aligns short nucleotide sequences (i.e., < 32 nucleotides) against longer reference sequences (e.g., 20k nucleotides). It has the ability to report multiple alignments and the corresponding traceback sequences for any given query-reference pair with up to 166x speedup on 4 GPUs compared to regular CPUs.
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PPSeq: Parallel NGS Analysis
Parallel Processing for Next-Generation Sequencing (NGS) Analysis
High-throughput next generation sequencing (NGS) technology has quickly emerged as a powerful tool in many aspects of biomedical research. However, along with its rapid development, the data magnitude and analysis complexity for NGS far exceed the capacity and capability of traditional small-scale computing facilities, such as multithreading algorithms on standalone workstations. To address this issue, here we present a solution using the ever-increasing supply of processing power by massive parallel processing (MPP) systems. -
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GENIE (GEne-geNe IntEraction)
GPU based Parallel Gene-Gene Interaction Analysis
Gene-gene interaction in genetic association studies is computationally intensive when a large number of SNPs are involved. Most of the latest Central Processing Units (CPUs) have multiple cores, whereas Graphics Processing Units (GPUs) also have hundreds of cores and have been recently used to implement faster scientific software. However, currently there are no genetic analysis software packages that allow users to fully utilize the computing power of these multi-core devices for genetic... -
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corunner
A utility to transport files and execute at remote in prarallel
Are you maitaining many machines and bored with the tedious operation of logging to those machines one by one just for checking the machine's status? Or are you losing patient for your simple script that have to run command in those machines in sequence? The corunner is just for those senarios. It's designed to speed up execution in your machines. It can executes command in handreds of or thousands of machines concurrently. Provide it with your files and command and the machines' location,... -
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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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PASHA: Parallelized Short Read Assembly
One of the fastest parallel short read assemblers for large genomes.
PASHA is a parallel short read assembler for large genomes using de Bruijn graphs. Taking advantage of both shared-memory multi-core CPUs and distributed-memory compute clusters, PASHA has demonstrated its potential to perform high-quality de-novo assembly of large genomes in reasonable time with modest computing resources. Our evaluation using three small real paired-end datasets shows that PASHA is able to produce better assemblies with comparable genome coverage and mis-assembly rates compared to three leading assemblers: Velvet, ABySS and SOAPdenovo. ... -
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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. ... -
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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 project based on NS-3 for modeling and real-time emulation of Coherent Heterogeneous Integrated Cellular networks on parallel computing systems.
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FastDMA
Infinium HumanMethylation450 BeadChip analysis tool
FastDMA is a software analyzing Illumina Infinium HumanMethylation450 BeadChip data, which is featured as multiple core parallel computing. -
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MapPSO is a tool for Ontology Alignment, which uses Discrete Particle Swarm Optimisation. A particle swarm is used to search for the optimal alignment. The algorithm is massively parallel and adapts naturally on parallel architectures.
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ViennaX
A flexible plugin execution framework for scientific computing in C++
Welcome to the project homepage of ViennaX, a high-performance scientific computing C++ framework for executing plugins. A plugin system allows to wrap already available functionality into reusable components, which can have data input and output dependencies via a socket system. Different scheduler kernels are available, supporting serial and MPI-based distributed executions, supporting task and data parallelism. -
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AWK~plus is the next generation script practice environment. The AWK Language specifications and a main extension of GNU GAWK. Combination of Dynamic and Static typing. Parallel computing that a lock is free, and is thread safe at a language level.
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a fast dynamic traffic assignment engine Please visit the github website for latest release: https://github.com/xzhou99/dtalite_software_release
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SPJS is a simple skeleton for creating job programs which can be executed on different CPU cores or can be submitted to a batch system or any other parallel computer farm.
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Tuple Spaces
Tuple space with time outs and transactions.
Java implementation of a Tuplespace. Moved to https://github.com/mike-k-houghton/tuplespace A Tuple is an ordered list of items. A Tuple Space is a form of associative memory where entries, tuples, are stored in the space and are retrieved using search criteria that are based on the intrinsic properties of the tuples. The two key operations are put get And that is it! There are refinements on these operations including, for example, timeouts where the tuple will only exist... -
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Simuquant
A quantum circuit simulator written in Scala
Simuquant is made to construct and simulate universal quantum circuits. It's GUI enables intuitive access and direct graphical feedback, making it useful in a classroom situation and the like. Simulation processing is done in parallel, utilizing parallel collections introduced in scala 2.9. This application has been created as part a bachelor-thesis at the Hamburg University of Applied Sciences. The thesis is available... -
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PyDSH is a remote administration tool, consisting of pydsh and pydcp. Pydsh allows you to run a command on multiple hosts in parallel over RSH, SSH or Telnet, OR manage your SSH public keys. The pydcp command allows copying files to/from multiple hosts.
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SECTOR: A Distributed Data Storage and Processing Platform
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Project provides a set of concurrent building blocks (Java & C/C++) that can be used to develop parallel/multi-threaded applications. Components are grouped into 4 categories: 1.Data Structures 2. Parallel Patterns 3.Parallel functions 4.Atomics and STM
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Platform for parallel computation in the Amazon cloud, including machine learning ensembles written in R for computational biology and other areas of scientific research. Home to MR-Tandem, a hadoop-enabled fork of X!Tandem peptide search engine.
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