VMD is a popular molecular visualization and analysis program used by thousands of researchers worldwide. VMD accelerates many of the most computationally demanding visualization and analysis features using GPU computing techqniques, resulting in improved performance and new capabilities beyond what is possible using only conventional multi-core CPUs. VMD 1.9.1 advances these capabilities further with a CUDA implementation of the new QuickSurf molecular surface representation, enabling smooth interactive animation of moderate sized biomolecular complexes consisting of a few hundred thousand to one million atoms, and allowing interactive display of molecular surfaces for static structures of very large complexes containing tens of millions of atoms, e.g. large virus capsids.
CLOGS is a library for higher-level operations on top of the OpenCL C++ API. It is designed to integrate with other OpenCL code, including synchronization using OpenCL events. Currently only two operations are supported: radix sorting and exclusive scan. Radix sort supports all the unsigned integral types as keys, and all the built-in scalar and vector types suitable for storage in buffers as values. Scan supports all the integral types. It also supports vector types, which allows for limited multi-scan capabilities.
CLCC, the light-weight and flexible utility for integrating OpenCL source builds into your project has just been updated to version 0.3.0. This version allows developers to save compiled binaries as object files for distribution with their programs and adds a series of options to select specific target platform/device combinations. Documentation and further information is available at http://clcc.sourceforge.net.
Version 1.2.0 of the OpenCL-based C++ linear algebra library ViennaCL is now available for download! It features a high-level interface compatible with Boost.ublas, which allows for compact code and high productivity. Highlights of the new release are the following features (all experimental):
Proxies for manipulating subvectors and submatrices
The features are expected to reach maturity in the 1.2.x branch. More information about the library including download links is available at http://viennacl.sourceforge.net.
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.
A major new release of the Intel SPMD Program Compiler (ispc) was posted on December 5, 2011. ispc is an extended version of the C programming language with support for “single program, multiple data” (SPMD) programming on the CPU; the SPMD model makes it easy to harness the full power of both the SIMD vector units and multiple cores on modern CPUs. The major features added in the 1.1 release include:
Full support for pointers, including pointer arithmetic, function pointers, and all other features of pointers in C.
A new parallel “foreach” statement, for more easily mapping computation to data.
Substantially revised documentation, including a new Performance Guide.
Many other small bug fixes and improvements.
ispc is open-source and is licensed under the BSD license. Source and binaries are available from http://ispc.github.com.
Exposure Render is a Direct Volume Rendering Application that applies progressive Monte Carlo raytracing, coupled with physically based light transport to heterogeneous volumetric data. Exposure Render enables the configuration of any number of arbitrarily shaped area lights, models a real-world camera, including its lens and aperture, and incorporates complex materials, whilst still maintaining interactive display updates. It features both surface and volumetric scattering, and applies noise reduction to remove the unwanted startup noise associated with progressive Monte Carlo rendering. The complete implementation is available in source and binary forms under a permissive free software license.
The new version 3.1 of rCUDA (Remote CUDA), the Open Source package that allows performing CUDA calls to remote GPUs, is now available. Release highlights:
Fully updated API to CUDA 4.0 (added support for modules “Peer Device Memory Access” and “Unified Addressing”).
OCLTools is a powerful, yet compact, suite of Open Source tools that provide OpenCL developers with more alternatives to kernel compilation. OCLTools enables developers to eliminate costly kernel compilation time from the runtime of your application. With OCLTools developers can embed the source code of their kernels (clear text or encrypted) directly into their program binaries, eliminating the need to distribute kernel source code in the open while still maintaining the flexibility of runtime compilation. Both source code and precompiled binaries can be embedded into OpenCL binaries, effectively eliminating the additional kernel compilation overhead from the run time of your application.
The latest release of Symscape’s ofgpu (v0.2) for OpenFOAM® 2.0.x is now available. ofgpu is an open source experimental linear solver library that targets NVIDIA CUDA GPU devices on Windows, Linux, and (untested) Mac OS X. ofgpu now has support for the Cusp preconditioners:
smoothed_aggregation – equivalent to Algebraic Multi-Grid (AMG)
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