The distributed-computing project Folding@home uses scientific computer programs, referred to as "cores" or "fahcores", to perform calculations. [1] [2] Folding@home's cores are based on modified and optimized versions of molecular simulation programs for calculation, including TINKER, GROMACS, AMBER, CPMD, SHARPEN, ProtoMol and Desmond. [1] [3] [4] These variants are each given an arbitrary identifier (Core xx). While the same core can be used by various versions of the client, separating the core from the client enables the scientific methods to be updated automatically as needed without a client update. [1]
These cores listed below are currently used by the project. [1]
Cores for the Graphics Processing Unit use the graphics chip of modern video cards to do molecular dynamics. The GPU Gromacs core is not a true port of Gromacs, but rather key elements from Gromacs were taken and enhanced for GPU capabilities. [7]
These are the third generation GPU cores, and are based on OpenMM, Pande Group's own open library for molecular simulation. Although based on the GPU2 code, this adds stability and new capabilities. [8]
These cores are not currently used by the project, as they are either retired due to becoming obsolete, or are not yet ready for general release. [1]
TINKER is a computer software application for molecular dynamics simulation with a complete and general package for molecular mechanics and molecular dynamics, with some special features for biopolymers. [12]
Short for Car–Parrinello Molecular Dynamics, this core performs ab-initio quantum mechanical molecular dynamics. Unlike classical molecular dynamics calculations which use a force field approach, CPMD includes the motion of electrons in the calculations of energy, forces and motion. [40] [41] Quantum chemical calculations have the possibility to yield a very reliable potential energy surface, and can naturally incorporate multi-body interactions. [41]
The software for this core was developed at D. E. Shaw Research. Desmond performs high-speed molecular dynamics simulations of biological systems on conventional computer clusters. [47] [48] [49] [50] The code uses novel parallel algorithms [51] and numerical techniques [52] to achieve high performance on platforms containing a large number of processors, [53] but may also be executed on a single computer. Desmond and its source code are available without cost for non-commercial use by universities and other not-for-profit research institutions.
Short for Assisted Model Building with Energy Refinement, AMBER is a family of force fields for molecular dynamics, as well as the name for the software package that simulates these force fields. [55] AMBER was originally developed by Peter Kollman at the University of California, San Francisco, and is currently maintained by professors at various universities. [56] The double-precision AMBER core is not currently optimized with SSE nor SSE2, [57] [58] but AMBER is significantly faster than Tinker cores and adds some functionality which cannot be performed using Gromacs cores. [58]
ProtoMol is an object-oriented, component based, framework for molecular dynamics (MD) simulations. ProtoMol offers high flexibility, easy extendibility and maintenance, and high performance demands, including parallelization. [59] In 2009, the Pande Group was working on a complementary new technique called Normal Mode Langevin Dynamics which had the possibility to greatly speed simulations while maintaining the same accuracy. [8] [60]
These are the second generation GPU cores. Unlike the retired GPU1 cores, these variants are for ATI CAL-enabled 2xxx/3xxx or later series and NVIDIA CUDA-enabled NVIDIA 8xxx or later series GPUs. [62]
These are the third generation GPU cores, and are based on OpenMM, Pande Group's own open library for molecular simulation. Although based on the GPU2 code, this adds stability and new capabilities. [8]
GROMACS is a molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids. It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers worldwide. GROMACS is one of the fastest and most popular software packages available, and can run on central processing units (CPUs) and graphics processing units (GPUs). It is free, open-source software released under the GNU Lesser General Public License (LGPL).
A graphics processing unit (GPU) is a specialized electronic circuit initially designed to accelerate computer graphics and image processing. After their initial design, GPUs were found to be useful for non-graphic calculations involving embarrassingly parallel problems due to their parallel structure. Other non-graphical uses include the training of neural networks and cryptocurrency mining.
Folding@home is a distributed computing project aimed to help scientists develop new therapeutics for a variety of diseases by the means of simulating protein dynamics. This includes the process of protein folding and the movements of proteins, and is reliant on simulations run on volunteers' personal computers. Folding@home is currently based at the University of Pennsylvania and led by Greg Bowman, a former student of Vijay Pande.
Mesa, also called Mesa3D and The Mesa 3D Graphics Library, is an open source implementation of OpenGL, Vulkan, and other graphics API specifications. Mesa translates these specifications to vendor-specific graphics hardware drivers.
A physics processing unit (PPU) is a dedicated microprocessor designed to handle the calculations of physics, especially in the physics engine of video games. It is an example of hardware acceleration.
PhysX is an open-source realtime physics engine middleware SDK developed by Nvidia as a part of Nvidia GameWorks software suite.
A free and open-source graphics device driver is a software stack which controls computer-graphics hardware and supports graphics-rendering application programming interfaces (APIs) and is released under a free and open-source software license. Graphics device drivers are written for specific hardware to work within a specific operating system kernel and to support a range of APIs used by applications to access the graphics hardware. They may also control output to the display if the display driver is part of the graphics hardware. Most free and open-source graphics device drivers are developed by the Mesa project. The driver is made up of a compiler, a rendering API, and software which manages access to the graphics hardware.
CoreAVC was a proprietary codec for decoding the H.264/MPEG-4 AVC video format.
Compute Unified Device Architecture (CUDA) is a proprietary parallel computing platform and application programming interface (API) that allows software to use certain types of graphics processing units (GPUs) for accelerated general-purpose processing, an approach called general-purpose computing on GPUs (GPGPU). CUDA API and its runtime: The CUDA API is an extension of the C programming language that adds the ability to specify thread-level parallelism in C and also to specify GPU device specific operations (like moving data between the CPU and the GPU). CUDA is a software layer that gives direct access to the GPU's virtual instruction set and parallel computational elements for the execution of compute kernels. In addition to drivers and runtime kernels, the CUDA platform includes compilers, libraries and developer tools to help programmers accelerate their applications.
PGI was a company that produced a set of commercially available Fortran, C and C++ compilers for high-performance computing systems. On July 29, 2013, Nvidia acquired The Portland Group, Inc. As of August 5, 2020, the "PGI Compilers and Tools" technology is a part of the Nvidia HPC SDK product available as a free download from Nvidia.
AMD FireStream was AMD's brand name for their Radeon-based product line targeting stream processing and/or GPGPU in supercomputers. Originally developed by ATI Technologies around the Radeon X1900 XTX in 2006, the product line was previously branded as both ATI FireSTREAM and AMD Stream Processor. The AMD FireStream can also be used as a floating-point co-processor for offloading CPU calculations, which is part of the Torrenza initiative. The FireStream line has been discontinued since 2012, when GPGPU workloads were entirely folded into the AMD FirePro line.
AMD Software is a device driver and utility software package for AMD's Radeon graphics cards and APUs. Its graphical user interface is built with Qt and is compatible with 64-bit Windows and Linux distributions.
A mini PC is a small-sized, inexpensive, low-power, legacy-free desktop computer designed for basic tasks such as web browsing, accessing web-based applications, document processing, and audio/video playback.
Molecular modeling on GPU is the technique of using a graphics processing unit (GPU) for molecular simulations.
Desmond is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems on conventional computer clusters. The code uses novel parallel algorithms and numerical methods to achieve high performance on platforms containing multiple processors, but may also be executed on a single computer.
OpenMM is a library for performing molecular dynamics simulations on a wide variety of hardware architectures. First released in January 2010, it was written by Peter Eastman at the Vijay S. Pande lab at Stanford University. It is notable for its implementation in the Folding@home project's core22 kernel. Core22, also developed at the Pande lab, uses OpenMM to perform protein dynamics simulations on GPUs via CUDA and OpenCL. During the COVID-19 pandemic, a peak of 280,000 GPUs were estimated to be running OpenMM via core22.
Nvidia Optimus is a computer GPU switching technology created by Nvidia which, depending on the resource load generated by client software applications, will seamlessly switch between two graphics adapters within a computer system in order to provide either maximum performance or minimum power draw from the system's graphics rendering hardware.
The Radeon HD 7000 series, codenamed "Southern Islands", is a family of GPUs developed by AMD, and manufactured on TSMC's 28 nm process.
AMD PowerTune is a series of dynamic frequency scaling technologies built into some AMD GPUs and APUs that allow the clock speed of the processor to be dynamically changed by software. This allows the processor to meet the instantaneous performance needs of the operation being performed, while minimizing power draw, heat generation and noise avoidance. AMD PowerTune aims to solve thermal design power and performance constraints.
Nvidia NVDEC is a feature in its graphics cards that performs video decoding, offloading this compute-intensive task from the CPU. NVDEC is a successor of PureVideo and is available in Kepler and later NVIDIA GPUs.
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