HOOMD-blue performs general-purpose particle dynamics simulations on a single workstation, taking advantage of NVIDIA GPUs to attain a level of performance equivalent to many cores on a fast cluster. Flexible and configurable, HOOMD-blue is currently being used for coarse-grained molecular dynamics simulations of nano-materials, glasses, and surfactants, dissipative particle dynamics simulations (DPD) of polymers, and crystallization of metals.

HOOMD-blue 0.9.2 adds many new features. Highlights include:

• Long-ranged electrostatics via PPPM
• Support for CUDA 3.2 and 4.0
• New neighbor list option to exclude by particle diameter (for pair.slj)
• New syntax to specify multiple pair coefficients at once
• Improved documentation
• Significant performance boosts for small simulations
• RPM and .deb packaging for CentOS, Fedora, and Ubuntu
• and more

HOOMD-blue 0.9.2 is available for download under an open source license. Check out the quick start tutorial to get started, or check out the full documentation to see everything it can do.

The North Carolina Renaissance Computing Institute (RENCI) is running Amber PMEMD on the Open Science Grid, the high throughput computing (HTC) fabric used by the Large Hadron Collider (LHC). This approach is likely to be helpful to researchers with any of these challenges:

1. Constrained by limited computing resources including access to GPGPUs
2. Manually executing the same simulation repeatedly with different parameters
3. Making simulations easier to understand, share, scale and re-use across compute resources

For more information see these two blog posts: High Throughput Parallel Molecular Dynamics and CUDA/Tesla Accelerated PMEMD on OSG. Contact Steve Cox (scox@renci.org) if you’d like to discuss further and determine if your application is a fit. If it is, RENCI can provide access to the grid as well as tools for executing and managing simulations.

Tina’s Random Number Generator Library (TRNG) version 4.11 has been released. TRNG is a state of the art open-source C++ pseudo-random number generator library for sequential and parallel Monte Carlo simulations. Its design principles are based on a proposal for an extensible random number generator facility that will be part of the forthcoming revision of the ISO C++ standard. The TRNG library features an object oriented design, is easy to use and has been speed optimized. Its implementation does not depend on any communication library or hardware architecture. TRNG is suited for shared memory as well as for distributed memory computers and may be used in various parallel programming environments, e.g. Message Passing Interface Standard or OpenMP. As an outstanding new feature of the latest TRNG release 4.11 it also supports CUDA. All generators that are implemented by TRNG have been subjected to thorough statistical tests in sequential and parallel setups. Download and further information: http://trng.berlios.de/

HOOMD-blue performs general-purpose particle dynamics simulations on a single workstation, taking advantage of NVIDIA GPUs to attain a level of performance equivalent to many cores on a fast cluster. Flexible and configurable, HOOMD-blue is currently being used for coarse-grained molecular mynamics simulations of nano-maertials, glasses, and surfactants, dissipative particle dynamics simulations (DPD) of polymers, and crystallization of metals.

HOOMD-blue 0.9.1 adds many new features. Highlights include:

• 10 to 50 percent faster performance over 0.9.0
• DPD (Dissipative Particle Dynamics) capability
• EAM (Embedded Atom Method) capability
• Removed limitation on number of exclusions
• Support for compute 2.1 devices (such as the GTX 460)
• Support for CUDA 3.1
• and more

HOOMD-blue 0.9.1 is available for download under an open source license. Check out the quick start tutorial to get started, or check out the full documentation to see everything it can do.

Thrust v1.3, an open-source template library for CUDA applications, has been released. Modeled after the C++ Standard Template Library (STL), Thrust brings a familiar abstraction layer to the realm of GPU computing.

Version 1.3 adds several new features, including:

• a state-of-the-art sorting implementation, recently featured on Slashdot.
• performance improvements to stream compaction and reduction
• robust error reporting and failure detection
• support for CUDA 3.2 and gf104-based GPUs
• search algorithms
• and more!

Get started with Thrust today! First download Thrust v1.3 and then follow the online quick-start guide. Refer to the online documentation for a complete list of features. Many concrete examples and a set of introductory slides are also available. Read the rest of this entry »

OpenNL (Open Numerical Library) is a library for solving sparse linear systems on CPUs and GPUs. Features include various preconditioned Krylov subspace solvers for several data structures. The library is explicitly designed for easy interfacing with existing codes and their storage schemes.

Highlights of version 3.2.1 include:

• Support for double precision on the GPU
• Support for the Fermi architecture

The Swarm-NG package helps scientists and engineers harness the power of GPUs. In the early releases, Swarm-NG will focus on the integration of an ensemble of N-body systems evolving under Newtonian gravity. Swarm-NG does not replicate existing libraries that calculate forces for large-N systems on GPUs, but rather focuses on integrating an ensemble of many systems where N is small. This is of particular interest for astronomers who study the chaotic evolution of planetary systems. In the long term, we hope Swarm-NG will allow for the efficient parallel integration of user-defined systems of ordinary differential equations.

HOOMD-blue stands for Highly Optimized Object-oriented Many-particle Dynamics — Blue Edition. It performs general-purpose particle dynamics simulations on a single workstation, taking advantage of  NVIDIA GPUs to attain a level of performance equivalent to dozens of processor cores on a fast cluster.

HOOMD-blue 0.9.0 is a major new release. Highlights include:

• Support for Fermi generation GPUs
• Performance enhancements
• New pair potentials
• Particle data is now accessible from hoomd scripts
• Binary format dump files for simulation restarts
• Numerous small enhancements to enable easily restartable jobs
• 2D simulations are now possible
• Integration methods can now be applied to specified groups of particles
• All IMD commands issued by VMD are now understood
• … and more

HOOMD-blue 0.9.0 is available for download under an open source license.

GeoSpin has released the first version of CLyther for beta testing. Please visit the CLyther SourceForge website for more information.  CLyther enables developers to seamlessly write GPGPU code completely in python with no additional syntax. CLyther’s core driver contains a python compiler to convert Python functions and types to OpenCL during runtime.

CLyther currently only supports a subset of the Python language definition but adds many new features to OpenCL such as:

• OpenCL interface similar to PyOpenCL
• Dynamic compilation of OpenCL code at runtime
• Fast prototyping of OpenCL code
• Create OpenCL code using the Python language definition
• Passing functions as arguments to OpenCL kernels
• Pure Python emulation mode of kernel functions

Read the rest of this entry »

Version 1.2 of Thrust, an open-source template library for developing CUDA applications, has been released. Modeled after the C++ Standard Template Library (STL), Thrust brings a familiar abstraction layer to the realm of GPU computing. This version adds several new features, including:

• support for multicore CPUs via OpenMP
• support for CUDA 3.0 and new GPUs based on the Fermi architecture
• support for the Ocelot virtual machine
• pseudo random number generation
• key-value reduction
• set intersection
• and many more

The Thrust web page provides a quick-start guide, online documentation, many examples and introductory slides. Thrust is open-source software distributed under the OSI-approved Apache License v2.0.