Search Results for "mpi" - Page 3
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Showing 186 open source projects for "mpi"
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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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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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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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LSDMap
Locally-Scaled Diffusion Maps from molecular dynamics trajectories
LSDMap is a set of Fortran90 codes parallelised with MPI for the calculation of Locally Scaled Diffusion Maps. The eigenvectors of the diffusion matrix can be used to form a small set of reaction coordinates describing the behaviour of a high-dimensional data set such as an equilibrium MD trajectory. -
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ParDRR-MPI
Parallel Duplicate Read Remover with MPI
ParDRR-MPI is a parallel tool to remove duplicate reads. Duplicate reads can be seen as identical or nearly identical sequences with some mismatches. This tool will let the users to avoid the analysis of not necessary reads, reducing the time of subsequent procedures with the dataset (e.g., assemblies, mappings, etc.). The tool is implemented with MPI in order to exploit the parallel capabilities of multicore clusters. -
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This software searches the potential energy surface of small to medium size atomic systems for global minima using quantum ab initio techniques. It performs bond rotations and molecule translations and rotations on a Linux cluster with MPI.
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ParaStation is a robust and efficient cluster middleware, consisting of a high-performance communication layer (MPI) and a sophisticated management layer. Please notice, the public development has moved to github: https://github.com/ParaStation
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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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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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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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SWAPHI-LS: Alignment on Xeon Phi Cluster
Smith-Waterman long DNA sequence alignment on Xeon Phi clusters
The first parallel Smith-Waterman algorithm exploiting Intel Xeon Phi clusters to accelerate the alignment of long DNA sequences. This algorithm is written in C++ (with a set of SIMD intrinsic extensions), OpenMP and MPI. The performance evaluation revealed that our algorithm achieves very stable performance, and yields a performance of up to 30.1 GCUPS on a single Xeon Phi and up to 111.4 GCUPS on four Xeon Phis sharing a host. -
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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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SIMBUCA (before called Simonion) is a simulation package that simulates the motion of charged particles under the influence of Electric and/or Magnetic fields. What makes Simbuca unique is that you can choose to calculate the Coulomb interaction between ions on a Graphics cards which is much faster than calculating this on the conventional CPU (reducing the simulation time from years to days). Therefore Simbuca has been applied in various projects which required to understand the...
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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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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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Hrothgar Parallel LM/MCMC Minimizer
A versatile MCMC and downhill optimization engine
Hrothgar is a parallel minimizer and Markov Chain Monte Carlo generator by Andisheh Mahdavi of San Francisco State University. It has been used to solve optimization problems in astrophysics (galaxy cluster mass profiles) as well as in experimental particle physics (hadronic tau decays). It is probably adaptable enough to be applied to your merit function if you can write it in C. -
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PARUS
Dataflow parallel programming language for clusters
PARUS is a data-flow parallel programming language that allows to build parallel programs for clusters and MPP multiprocessors. The data-flow graph is automatically converted to the C++/MPI source and linked with the libparus runtime library. Also there are available tools for benchmarking cluster interconnect and visualize it. -
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pmutualinformation
Computes pairwise genes mutual information using GEPs
pmutualinformation (parallel mutual information) computes the pairwise Mutual Information for all pairs of genes from a potentially massive and heterogeneous dataset containing GEPs. GEPs can be part of different experiments collected from public repositories. pmutualinformation runs on MIMD systems and has been implemented in C using the MPI standard.
