Search Results for "parallel computing" - Page 4
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Showing 188 open source projects for "parallel computing"
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MPJ Express is an implementation of an MPI-like API—standardized by the Java Grande forum—used to write parallel Java applications, which can execute on a variety of parallel platforms ranging from multicore processors to compute clusters/clouds.
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Ichnaea
Performance Timing Tools
Ichnaea is a set of tools that aid in collecting and tracking parameters and timings for parallel applications. The Performance Modelling Timing Module, PMTM, is a library that wraps system timing calls to abstract these from code developers and aid portability. It also has functionality to store parameters and print those, along with the timing information to a comma separated variable file. The Performance Modelling Analysis Tool, PMAT, is coming soon. This is able to read in and... -
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parSRA
Portable Framework for the Parallel Execution of Short Read Aligners
...It uses the following techniques in order to improve scalability: 1) a fast splitting of the input reads using the FUSE kernel module available in most of current Linux distributions; 2) a balanced on-demand distribution of the reads based on the shared locks of UPC++, an extension of C++ for parallel computing that follows the Partitioned Global Address Space (PGAS) paradigm. parSRA is portable as its configuration file allows the users to parallelize the execution of existing SRA tools without the need to modify the source code of parSRA or the aligner. -
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Distributed Video Transcoding
Distributed Video Transcoding
Simple Scalable, Parallel, Multi-bitrate Video Transcoding On Centos / Ubuntu / Suse / RedHat (Bash Scripts) Multi-bitrate Video processing requires lots of computing power and time to process full movie. There are different open source video transcoding and processing tools freely available in Linux, like libav-tools, ffmpeg, mencoder, and handbrake. -
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COMRAD-MPI
Compression of Large Genomic Datasets using Parallel Computing
COMRAD-MPI is a parallel computing algorithm for reducing the computational time for compressing the large genomic data sets based on COMRAD algorithm. It captures the long range repeat redundancies in large genomes there by providing a way to compress the large DNA data set. Three stages- Substitution, Clean up and Huffman encoding have been parallelized using message passing library. -
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HpcTemplateLib
HPC Template Library to supplement the STL
This package is intended to provide the user with threadsafe containers and classes for applications in High Performance Computing (HPC) where parallel programming is commonplace. Today’s multi-core computers bring that parallelism into the realm of everyday use. It is important to provide thread safe containers and classes in this environment. The HPC Template Library (HTL) aims to replace certain portions of the STL. It is a merger and rewrite of classes from the STL, QT, Boost, and SigSlots libraries. ... -
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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. Microthreads are general processing elements that can also represent non-neural elements, such as cell populations, extracellular space, emulating... -
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mapgraph
Massively Parallel Graph processing on GPUs -- now part of Blazegraph
Mapgraph is SYSTAP’s disruptive new technology to exploit the main memory bandwidth advantages of GPUs. The early work was co-developed with the University of Utah SCI Institute and has its pedigree in the UINTAH software running on over 750M cores on the TITAN Super Computer. Today, SYSTAP has commercialized this technology into it’s Blazegraph Accelerator and Blazegraph HPC products. Checkout our options for GPU acceleration of graphs or contact us to learn more: ... -
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myopentrader
Open-source complex-event based trading engine
...We have started MOT in 2012 and we have been using MOT ever since successfully. The best way of describing MOT is a flexible open-source trading framework. It is built from ground up as a parallel computing engine, which allows to do large scale parallel backtesting. MOT is distributed under the GPL v3 License and is free to use for everyone without warranty. MyOpenTrader.org is not responsible for any of your trading losses and can not be held accountable. Use the framework at your OWN risk. MOT is written purely in Java (1.6++) and has dependencies on a DB as well as a MQ Broker (such as ActiveMQ). -
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Genetic Programming in OpenCL is a parallel implementation of genetic programming targeted at heterogeneous devices, such as CPU and GPU. It is written in OpenCL, an open standard for portable parallel programming across many computing platforms.
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Ezys
Ezys 3D medical image registration program
Ezys is a non-linear 3D medical image registration program. Ezys fully exploits the parallel computing power of inexpensive commercial graphics processing units (GPU), resulting in a very fast and accurate program capable of running on desktop PCs and even some laptops. On these systems, non-linear image registrations take less than a minute to complete. Ezys implements a diffeomorphic inverse consistent image registration algorithm with a demons-style regularization based on a non-parametric free form deformation model. ... -
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PuSSH is Pythonic, Ubiquitous SSH, a Python wrapper/script that runs commands in parallel on clusters/ranges of linux/unix machines via SSH, ideally where SSH is configured to use Kerberos, RSA/DSA keys, or ssh-agent as to avoid password authentication.
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Fast Gauss-Legendre Quadrature Rules
Computes Gauss-Legendre quadrature nodes and weights
This software computes Gauss-Legendre quadrature nodes and weights using the formulas developed in "Iteration-Free Computation of Gauss-Legendre Quadrature Nodes and Weights", I. Bogaert, published in the SIAM Journal of Scientific Computing (Permalink: http://dx.doi.org/10.1137/140954969). The key features are: - Speed: due to the simplified formulas and the O(1) complexity computation of individual Gauss-Legendre quadrature nodes and weights. The latter also makes this software perfectly compatible with parallel computing paradigms. - Accuracy: the error on the nodes and weights is smaller than a few ulps (see the paper for details). -
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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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FastDMA
Infinium HumanMethylation450 BeadChip analysis tool
FastDMA is a software analyzing Illumina Infinium HumanMethylation450 BeadChip data, which is featured as multiple core parallel computing.
