mpi
MPI Ruby 0.4
Wrapper for the Message Passing Interface originally written in C more>> Wrapper for the Message Passing Interface originally written in C
MPI Ruby is a high performance computing library written for parallel programming.
MPI Ruby also aims to be a complete binding to MPI in that it offers access to nearly all functionality of MPI. While there is not a one-to-one correspondence to functions and constants in the Ruby and C/C++/Fortran bindings, all of the communication and topology features are available.
There are fewer methods in the Ruby binding than there are functions in the C/C++/Fortran bindings, but this is mainly due to the fact that the developer no longer needs to deal with datatypes and buffers.
FreeMat 3.3
FreeMat is a free environment for rapid engineering and scientific prototyping and data processing more>>
FreeMat includes several novel features such as a codeless interface to external C/C++/FORTRAN code, parallel/distributed algorithm development (via MPI), and plotting and visualization capabilities. FreeMat is available under an MIT-type license. Supported platforms include Linux, Windows and Mac OS X.
Its been nearly a year (!) since the last release of FreeMat. A new version is now ready for testing. I have elected to release it as a Release Candidate instead of a full release because of the significant changes that have been made since version 1.1.
Main features:
- Handle-based Graphics including 3D surface plots, multiple plots per figure, and full customization of axes properties. Preliminary support for OpenGL rendering.
- Support for MATLAB-style classes and object oriented programming, including operator overloading.
- New GUI interface based on Qt4. FreeMat now sports a new terminal interface, a highlighting editor, and some new tools.
- Speed improvements and optimizations (some loops are 10-100 times faster).
- Preliminary support for reading and writing MATLAB .MAT files.
- PDF output on all platforms.
- New build system based on qmake.
- Many new MATLAB-compatibility functions and scripts.
- Native Aqua application on Mac OS X.
- Linux distribution now includes a binary release that should run on several distributions.
- Over 200 new pages of documentation, and an improved built in help browser.
OsiriX 3.0a1
OsiriX is a DICOM viewer application for Mac OS X computers more>>
OsiriX is a DICOM viewer application for Mac OS X computers
OsiriX has been specifically designed for image fusion, cardiac CT, multi-series MRI exams and 3D reconstructions. It supports 5D viewers for PET-CT series and Cardiac-CT exams.
Please read the Quick Manual to learn how to do image fusion, use the 4D viewer and do 3D reconstructions. This alpha version is incomplete and doesnt include many features, but it will allow you to discover what is OsiriX. This first version has been developed in less than 4 months... Many, many new features will come! Please, send any comments, bug reports and ideas to improve OsiriX!
Main features:
- DICOM Listener to receive images from your PACS.
- Support multiple buttons mouse, including scroll wheel.
- Massively optimized for Altivec (a.k.a Velocity Engine) for G4 and G5 computers.
- Multi-threaded for full support of multi-processors Macs
- Code and memory alignment optimized for G5 computers
- Optimized for OpenGL, fully and really use your graphic board!
- Realtime convolution filters 3x3 and 5x5
- Support custom Color Look Up Tables (CLUT)
- Realtime and multi-threading files loading and conversion
- Realtime zoom & rotation with linear interpolation
- WYSIWYG Quicktime export (size, zoom, rotation, frame rate)
- All series are loaded as volumetric data (no processing/memory required for 3D views)
- All pixels are converted as float for best performance & quality
- 3D MPR
- 2D MPR
- 3D Surface Rendering
- 3D Maximum Intensity Projection
- 3D Volume Rendering
- DICOM Files support: mono 8 & 16bits, RGB, YBR, Palettes, JPEG lossless & lossy
- Image Fusion: PET-CT, MRI-MRI, CT-CT, MRI-CT, ...
- PDF Files support with multi-pages
- Multimedia file formats support: JPEG, TIFF, Photoshop, PNG, ...
- 4D Viewer
- 2D thick slab: altivec optimized
- X-Grid/MPI support for MIP, Volume Rendering and Surface Rendering
the slice interval with thick slab in MPR-2D
petsc4py 1.0.2
Free and open source Python bindings for the PETSc scientific libraries more>>
petsc4py 1.0.2 is yet another excellent tool for programmers. it is actually a free and open source Python bindings for PETSc, the Portable, Extensible Toolkit for Scientific Computation.
PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. PETSc employs the MPI standard for all message-passing communication.
NOTE: petsc4py is developed, distributed and licensed under the terms of the New BSD License.
Requirements:
- Mac OS X
TotalView 8.7.0
TotalView is a program useful for applications written for simulation and modeling, special effects, finance, telecommunications, scientific analysis, animation, biotechnology and many other fields. more>>
TotalView 8.7.0 is a program useful for applications written for simulation and modeling, special effects, finance, telecommunications, scientific analysis, animation, biotechnology and many other fields. Etnus TotalView leverages more than 19 years of continuous product development to maintain its clear leadership position.
Available on Linux, UNIX and Mac OS X, TotalView supports threads, MPI, OpenMP, C/C++, and Fortran, plus mixed-language codes. Advanced features like on-demand memory leak detection, other heap allocation debugging features, and Standard Template Library Viewer (STLView) are not found in average debuggers, and make debugging a breeze. Unique features like dive, a wide variety of breakpoints, the Message Queue Graph/Visualizer, powerful data analysis, and control at the thread level give you the power you need to solve tough problems.
Available on Linux, UNIX and Mac OS X, TotalView supports threads, MPI, OpenMP, C/C++, and Fortran, plus mixed-language codes. Major Features: On-demand memory leak detection, other heapFFTW 3.2 Alpha 3
C library that will help you compute the Discrete Fourier Transform more>> C library that will help you compute the Discrete Fourier Transform
FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size. FFTW will compute the DFT in both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST).
Main features:>
- Speed. (Supports SSE/SSE2/3dNow!/Altivec, since version 3.0.)
- Both one-dimensional and multi-dimensional transforms.
- Arbitrary-size transforms. (Sizes with small prime factors are best, but FFTW uses O(N log N) algorithms even for prime sizes.)
- Fast transforms of purely real input or output data.
- Transforms of real even/odd data: the discrete cosine transform (DCT) and the discrete sine transform (DST), types I-IV. (Version 3.0 or later.)
- Efficient handling of multiple, strided transforms. (This lets you do things like transform multiple arrays at once, transform one dimension of a multi-dimensional array, or transform one field of a multi-component array.)
- Parallel transforms: parallelized code for platforms with Cilk or for SMP machines with some flavor of threads (e.g. POSIX). An MPI version for distributed-memory transforms is also available, currently only as part of FFTW 2.1.5.
- Portable to any platform with a C compiler. Documentation in HTML and other formats.
- Both C and Fortran interfaces.
Enhancements:
- Performance improvements for sizes with factors of 5 and 10.
- Documented FFTW_WISDOM_ONLY flag, at the suggestion of Mario Emmenlauer and Phil Dumont.
- Port Cell code to SDK2.1 (libspe2), as opposed to the old libspe1 code.
- Performance improvements in Cell code for N < 32k, thanks to Jan Wagner for the suggestions.
- Cycle counter for Sun x86_64 compiler, and compilation fix in cycle counter for AIX/xlc (thanks to Jeff Haferman for the bug report).
- Fixed incorrect type prefix in MPI code that prevented wisdom routines from working in single precision (thanks to Eric A. Borisch for the report).
- Added make check for MPI code (which still fails in a couple corner cases, but should be much better than in alpha2).
- Many other small fixes.
An MPI version for distributed-memory transforms is also available, currently only as part of FFTW 2.1.5. - Portable to any platform with a C compiler. Documentation in HTML and other formatsLicense:GPL
Power Fractal 1.4
Power Fractal - A numerically-intensive parallel graphics application more>>
Power Fractal will also compute correctly on single processor machines and non-G4/G5s.
Enhancements:
- Universal Application release for mixed clusters of PowerPC G3s, G4s, G5s and Intel Cores simultaneously.
- Reoptimized vector algorithms to use SSE on Intel.
- Endian conversions implemented for communication using MacMPI_XUB.
RtBTool 2.0
RtBTool - Modding tool for *.mpi, *.gdg, *.azp, *.pix and *.tex files of the games CC4/CC5/CCM/RtB more>>
This tool is not supported or endorsed by the original authors/publishers of these games.
The tool is still in beta stage, you use it at your own risk. Functionality not guarenteed. Loss of data may occur when using this program. Make backups of your work often!
Enhancements:
- editing screen layouts in the *.exe/*.icd implemented.
Tachyon 0.93.4
Tachyon is designed to be a smart system of multiprocessor ray tracing which can work as a standalone program, or as a library within other programs. more>>
Tachyon 0.93.4 is designed to be a smart system of multiprocessor ray tracing which can work as a standalone program, or as a library within other programs. It supports almost any Unix-like system, Windows, MacOS-X, BeOS, and VMS, as well as several embedded systems and high end supercomputers.
Tachyon is written in C, uses POSIX threads and/or MPI for utilization of multiple processors, and can also run on uniprocessor machines. Tachyon is easy to port to new machines, and is fast, using ray tracing acceleration schemes to achieve good performance on very complex scenes. (It will handle scenes containing more than 1,000,000 objects on a fairly average computer)
Boost 1.36.0
Open source and widely useful library package usable across a broad spectrum of applications more>> Open source and widely useful library package usable across a broad spectrum of applications
The Boost libraries are intended to be usable and widely useful across a broad spectrum of applications. The Boost license encourages both commercial and non-commercial use.
Boost aims to establish "existing practice" and provide reference implementations so that Boost libraries are suitable for eventual standardization. Ten Boost libraries are already included in the C++ Standards Committees Library Technical Report (TR1) as a step toward becoming part of a future C++ Standard.
Boost works on almost any modern operating system, including UNIX and Windows variants. Boost may also already be available on your organizations internal web server.
Enhancements:
- New Libraries: Accumulators, Exception, Units, Unordered. Updated Libraries: Asio, Assign, Circular Buffer, Foreach, Function, Hash, Interprocess, Intrusive, Math, Multi-index Containers, MPI, PtrContainer, Spirit, Thread, Wave, Xpressive.
Crux 1.0.0
A free software toolkit for molecular phylogenetic inference that runs on (at least) Mac OS X, Linux, FreeBSD more>> A free software toolkit for molecular phylogenetic inference that runs on (at least) Mac OS X, Linux, FreeBSD
Crux is structured as a set of Python modules, which makes it possible to quickly develop Python scripts that perform unique, non-canned analyses.
The Python language is elegant and powerful, but it does not have any high performance implementations, which does make it a challenge to use for scientific computing.
Crux is actually implemented as a combination of Python, Cython and C code. Cython is a superset of Python, with various features that allow compiled results to substantially out-perform pure Python code.
The result is that Crux supports a wide variety of users:
- End users can use canned scripts, either those included with Crux, or scripts developed for them by computer-savvy collaborators.
- Computer-savvy users can develop custom scripts that utilize the components of Crux in unforseen ways.
- Power users can use Crux as a component of a custom software package, or extend Crux itself. The source code is available under a very permissive license, with the intent that it be used.
Main features:
- Multifurcating trees can be manipulated at a low level. Various standard operations are implemented, such as canonization (ordering the tree according to a ranking of the taxa), collapsing of zero-length branches, Robinson-Foulds distance computation, and so on.
- Parsers are included for various file formats, including Newick trees, FASTA sequences, and PHYLIP distance matrices.
- Pairwise distances between sequences can be computed based on percent identity, or using methods that correct for multiple hits (Jukes-Cantor, Kimura, and logDet).
- The neighbor joining (NJ) and relaxed neighbor joining (RNJ) implementations are among the fastest in existence, along with Clearcut.
- Tree log-likelihoods can be computed under a variety of models, including all specializations of GTR+I+? and mixture models. Tree likelihoods can be computed in parallel via pthreads. Additionally, Crux is capable of simulating character data under any model its likelihood engine is capable of. The huge range of simulation options makes a canned command line interface like that of Seq-Gen rather unweildy, so simulation is perhaps the most obvious compelling reason to develop Crux scripts.
- Bayesian Markov chain Monte Carlo (MCMC) methods (with Metropolis coupling and optional MPI support for parallel computation) can sample among non-nested models using reversible model jumps. Polytomous trees can be sampled, also via reversible jumps. In fact, every model parameter that Cruxs MCMC implementation estimates can be expunged via reversible jumps.
System requirements:
- Xcode (to build Crux from source)
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