Search Results for "mpi" - Page 2
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Showing 102 open source projects for "mpi"
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NOMAD is a C++ code that implements the MADS algorithm (Mesh Adaptive Direct Search) for difficult blackbox optimization problems. Such problems occur when the functions to optimize are costly computer simulations with no derivatives.
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CUDA-MEME
Ultrafast scalable motif discovery algorithm using GPU computing
mCUDA-MEME is a well-established ultrafast scalable motif discovery algorithm based on MEME (version 4.4.0) algorithm for multiple GPUs using a hybrid combination of CUDA, MPI and OpenMP parallel programming models. This algorithm is a further extension of CUDA-MEME (based on MEME version 3.5.4) with respect to accuracy and speed and has been tested on a GPU cluster with eight compute nodes and two Fermi-based Tesla S2050 (and Tesla-based Tesla S1070) quad-GPU computing systems, running the Linux OS with the MPICH2 library. ... -
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Grid-based Coupled Electron and Electromagnetic field Dynamics (GCEED) is an open-source software package for massively parallel first-principles calculations of electron dynamics in real time and real space. The program codes are written in the Fortran 90/95 language with MPI and OpenMP. Time dependent density functional theory (TD-DFT) calculations can be performed on 100,000 CPU cores of K Computer with high parallel efficiency.
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SW#
smith waterman, gpu, cuda, alignment
...It utilizes Hirschbergs and Ukkonens algorithm for memory efficiency and additional speed up. The library is scalable for use with multiple GPUs. Some parts of the library utilize MPI for CUDA enabled clusters. This work has been supported in part by Croatian Science Foundation under the project UIP-11-2013-7353. Database search now available! Publications: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0145857 http://bioinformatics.oxfordjournals.org/content/29/19/2494 http://nar.oxfordjournals.org/content/early/2013/11/23/nar.gkt1164.abstract#! ... -
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Schnek
A C++ library for developing parallel simulations on Cartesian grids
...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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2d Heat advection Parallelized
MPI based Parallelized C Program code to solve for 2D heat advection.
Type - 2D Grid - Structured Cartesian Case - Heat advection Method - Finite Volume Method Approach - Flux based Accuracy - First order Scheme - Explicit, QUICK Temporal - Unsteady Parallelized - MPI (for cluster environment) Inputs: [ Length of domain (LX,LY) Time step - DT Material properties - Conductivity (k or kk) Density - (rho) Heat capacity - (cp) Boundary condition and Initial condition. ] Setup: The left and top edges are heated to 100 C and the right and bottom boundaries are heated to 0 C. The flow is along the main diagonal. -
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GMES
GMES is a free Python package for FDTD electromagnetic simulations.
GMES is a free finite-difference time-domain (FDTD) simulation Python package developed at GIST to model photonic devices. Its features include simulation in 1D, 2D, and 3D Cartesian coordinates, distributed memory parallelism on any system supporting the MPI standard, portable to any Unix-like system, variuos dispersive ε(ω) models, CPML absorbing boundaries and/or Bloch-periodic boundary conditions, and arbitrary material and source distributions. GMES officially stands for GIST Maxwell’s Equations Solver. -
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Parallel Quicksort with MPI
Parallel Quicksort with MPI
...It was invented by C.A.R Hoare in 1961and is using the divide-and-conquer strategy for solving problems [3]. Its partitioning aspects make QuickSort amenable to parallelization using task parallelism. MPI is a message passing interface library allowing parallel computing by sending codes to multiple processors, and can therefore be easily used on most multi-core computers available today. The main aim of this study is to implement the QuickSort algorithm using the Open MPI library and therefore compare the sequential with the parallel execution. -
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3d heat conduction parallelized
MPI based Parallelized C Program code to solve for 3D heat conduction.
Type - 3D Grid - Structured Cartesian Case - Heat conduction Method - Finite Volume Method Approach - Flux based Accuracy - First order Scheme - Explicit Temporal - Unsteady Parallelized - Yes Inputs: [ Length of domain (LX,LY,LZ) Time step - DT Material properties - Conductivity (k or kk) Density - (rho) Heat capacity - (cp) Boundary condition and Initial condition. ] Setup : The six boundaries are heated to 100 C, 200 C, 300 C, 400 C, 500 C, 600 C respectively. -
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memP is a parallel heap profiling library based on the mpiP MPI profiling tool. The intent of memP is to identify the heap allocation that causes a task to reach its memory in use high water mark for each task in a parallel job.
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AMBER10_Brownian_Dynamics
Designed for coarse-grained protein association simulations
...The code includes additional Hamiltonian terms for the coarse-grained model (as described in http://www.pnas.org/content/110/51/20545.abstract) and uses the algorithm developed by Northup-Allison-Mccammon. The code is parallelized with MPI and allows association in a large timescale of ms. Users need to have a complete set of amber10 code for application of this modification. -
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Morpheus
MORPHEUS is a 3D MPI-OPENMP hydrodynamic simulation code
Manchester Omni-geometRical Program for Hydrodynamical EUlerian Simulations Copyright © N. Vaytet & T. O'Brien (2008-2014) The University of Manchester Current version 1.33 - 07/2014 MORPHEUS is a 3D MPI-OPENMP Eulerian second-order Godunov hydrodynamic simulation code in cartesian, spherical and cylindrical coordinates which includes radiative cooling and gravity. -
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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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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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MPI/C++ code to generate initial conditions for cosmological simulations using multiscale gaussian random fields, based on Edmund Bertschinger's GRAFIC-2 package. Provides a replacement for both grafic1 and grafic2.
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Spherical Harmonics Manipulator
Software to make fast synthesis of spherical harmonics global models
This software computes synthesis of spherical harmonics models on sparse coordinates or grids (provided in a geodetic or geocentric reference system). It exploits basic parallelism using openmp directives. A solution with MPI has not be taken into account since it cannot be so easily manageble by final users. -
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cloud-mpi
cloud-mpi is a simple means for using Open MPI on EC2 instances.
WORK IN PROGRESS. Please note that although the software is available, cloud-mpi CANNOT be used until Amazon lists our AMIs. Thanks for your patience. cloud-mpi is a simple means for using Open MPI on a network of Amazon EC2 instances. It provides (i) a graphical UI for launching and managing a network of EC2 instances running Open MPI, (ii) Amazon Machine images (AMIs) with Open MPI and network management software installed. -
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ParisSimulator
PArallel Robust Interface Simulator combines VOF and Front-Tracking
Paris, or ParisSimulator, is a PArallel Robust Interface Simulator. It combines VOF and Front-Tracking to create simulations of interfacial fluid flow, such as droplet bubbles or waves. It computes complex flows such as fast atomizing jets and has a Lagrangian particle option. -
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MasQu
Finite-differencing on the sphere
MasQU is a code for calculating derivatives on grids with regular or irregular pixel distributions, using finite differences. Particularly, it is constructed to perform tensor-mode separation on the HEALPix spherical grid, but can be generalized. -
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Distributed Multithread Apriori (DMTA)
A parallel implementation using MPI and OpenMP to Apriori algorithm
DMTA (Distributed Multithreaded Apriori) is a parallel implementation of Apriori algorithm, which exploits the parallelism at the level of threads and processes, seeking to perform load balancing among the cores. Was implemented in C++ language, using the parallelization libraries OpenMP and MPI. The algorithm was generated as a result of a project developed by André Camilo Bolina, under the guidance of teachers Marluce Rodrigues Pereira, Ahmed Ali Abdalla Esmin and Denilson Alves Pereira, in Department of Computer Science at Federal University of Lavras. The results of this project were published in the Revista de Sistemas de Informação da FSMA and is available in http://www.fsma.edu.br/si/edicao11/FSMA_SI_2013_1_Principal_1.html -
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Computational Fluid Dynamics (CFD) solver aimed to solve multi-physics problems on unstructured grids (inviscid Euler, Navier-Stokes flows, Heat transfer). F90 based. MPI, cgns, Metis libraries used.
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Ray: scalable assembly
Ray -- Parallel genome assemblies for parallel DNA sequencing
de novo genome assembly is now a challenge because of the overwhelming amount of data produced by sequencers. Ray assembles reads obtained with new sequencing technologies (Illumina, 454, SOLiD) using MPI 2.2 -- a message passing inferface standard. -
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MPI Baccarat Game
MPI Baccarat Game
This is a baccarat game application developed in java 1.7 version with swing interface. It is developed by the gaming lab (MPI-GERDC). This game is aimed for students in MPI Bachelor of Science in Computing programme to study the gaming specialist. This simulation will help students to learn the baccarat game rules, logic, and test the betting systems of their own.
