鴻鵠國際為台灣地區官方合作廠商，並且可提供技術支援與收費的教育訓練
Modern graphics processing units (GPUs) contain hundreds of arithmetic units and can be harnessed to provide tremendous acceleration for numerically intensive scientific applications such as molecular modeling. The increased capabilities and flexibility of recent GPU hardware combined with high level GPU programming languages such as CUDA and OpenCL has unlocked this computational power and made it accessible to computational scientists. The key to effective GPU computing is the design and implementation of data-parallel algorithms that scale to hundreds of tightly coupled processing units. Many molecular modeling applications are well suited to GPUs, due to their extensive computational requirements, and because they lend themselves to data-parallel implementations. Several exemplary results from our GPU computing work are presented in Klaus Schulten's Keynote Lecture from the 2010 GPU Technology Conference.Molecular DynamicsContinuing increases in high performance computing technology have rapidly expanded the domain of biomolecular simulation from isolated proteins in solvent to complex aggregates, often in a lipid environment. Such systems routinely comprise 100,000 atoms, and several published NAMD simulations have exceeded 1,000,000 atoms. Studying the function of even the simplest biomolecular machines requires simulations of 100 ns or longer, even when employing simulation techniques for accelerating processes of interest. One of the most time consuming calculations in a typical molecular dynamics simulation is the evaluation of forces between atoms that do not share bonds. The high degree of parallelism and floating point arithmetic capability of GPUs can attain performance levels twenty times that of a single CPU core. The twenty-fold acceleration provided by the GPU decreases the runtime for the non-bonded force evaluations such that it can be overlapped with bonded forces and PME long-range force calculations on the CPU. These and other CPU-bound operations must be ported to the GPU before further acceleration of the entire NAMD application can be realized.Multi-Resolution Molecular Surface VisualizationMolecular surface visualization allows researchers to see where structures are exposed to solvent, where structures come into contact, and to view the overall architecture of large biomolecular complexes such as trans-membrane channels and virus capsids. Recently, we have developed a new GPU-accelerated multi-resolution molecular surface representation, enabling smooth interactive animation of moderate sized biomolecular complexes consisting of a few hundred thousand to one million atoms, and interactive display of molecular surfaces for multi-million atom complexes, e.g. large virus capsids. The GPU-accelerated QuickSurf representation in VMD achieves performance orders of magnitude faster than the conventional Surf and MSMS representations, and makes VMD the first molecular visualization tool capable of achieving smooth animations of surface representations for systems of up to one million atoms.Molecular Orbital DisplayVisualization of molecular orbitals (MOs) is important for analyzing the results of quantum chemistry simulations. The functions describing the MOs are computed on a three-dimensional lattice, and the resulting data can then be used for plotting isocontours or isosurfaces for visualization as well as for other types of analyses. Existing software packages that render MOs perform calculations on the CPU and require runtimes of tens to hundreds of seconds depending on the complexity of the molecular system. We have developed present novel data-parallel algorithms for computing MOs on modern graphics processing units (GPUs) using CUDA. As recently reported, the fastest GPU algorithm achieves up to a 125-fold speedup over an optimized CPU implementation running on one CPU core. We have implemented these algorithms within the popular molecular visualization program VMD, which can now produce high quality MO renderings for large systems in less than a second, and achieves the first-ever interactive animations of quantum chemistry simulation trajectories using only on-the-fly calculation.Ion PlacementTo best reproduce physiological conditions, molecular dynamics simulations must be run in the presence of appropriate ions. Generally such simulations are performed in the presence of sodium chloride, although in some cases (such as simulations including nucleic acid) other ions such as magnesium are necessary. Although many tools such as the VMD Autoionize plugin can place a random distribution of ions, molecules requiring counterions for their stability are better treated using ion placement methods which take the electrostatics of the solute into account. One method for doing this is to place important counterions at minima in the electrostatic potential field generated by the biomolecule of interest, iteratively updating the potential field after each ion is placed.  While this method of ion placement is simple and computes ion positions matched to the specific target molecule, it can be very computationally demanding for large structures because it requires calculation of the electrostatic potential at all points on a high-resolution 3-D lattice in the neighborhood of the solute. Coulomb-based ionization of very large structures such as viruses could require several days even using moderately sized clusters of computers. However, the calculation of a function on a lattice where all points are independent is an ideal application for GPU acceleration, and as recently reported in the Journal of Computational Chemistry, the use of GPUs to accelerate Coulomb-based ion placement leads to speedups of 100 times or more, allowing large structures to be properly ionized in less than an hour on a single desktop computer.   | | GPU accelerated ion placement for large bacterial ribosome and STMV virus structures |
The direct summation of the Coulomb potential from all atoms to every lattice point requires computational work that grows quadratically, proportional to the product of the number of atoms and the number of lattice points. An algorithmic enhancement known as multilevel summation uses hierarchical interpolation of softened pairwise potentials from lattices of increasing coarseness to compute an approximation to the Coulomb potential. The amount of computational work for multilevel summation grows linearly, proportional to the sum of the number of atoms and the number of lattice points. Ourreported GPU-assisted implementation of this method further reduces the time of obtaining large ionized structures to just a few minutes on a single desktop computer. The accuracy of the implementation is sufficient (with an average difference from the direct approach demonstrated to be in the range of 0.025% to 0.037%) to permit identical ion placement as the direct summation approach for small test molecules and nearly identical results for the ribosome. The GPU-accelerated Coulomb potential calculation can be directly applied to calculate time-averaged electrostatic potentials from molecular dynamics simulations. As we reported, a VMD calculation of the electrostatic potential for one frame of a molecular dynamics simulation of the ribosome takes 529 seconds on a single GPU, as opposed to 5.24 hours on a single CPU core. A multilevel summation calculation for a single frame requires 67 seconds on one GPU. Multi-GPU Coulomb Summation The direct Coulomb summation algorithm implemented in VMD is an exemplary case for multi-GPU acceleration. The scaling efficiency for direct summation across multiple GPUs is nearly perfect -- the use of 4 GPUs delivers almost exactly 4X performance increase. A single GPU evaluates up to 39 billion atom potentials per second, performing 290 GFLOPS of floating point arithmetic. With the use of four GPUs, total performance increases to 157 billion atom potentials per second and 1.156 TFLOPS of floating point arithmetic, for a multi-GPU speedup of 3.99 and a scaling efficiency of 99.7%, as recently reported. To match this level of performance using CPUs, hundreds of state-of-the-art CPU cores would be required, along with their attendant cabling, power, and cooling requirements. While only one of the first steps in our exploration of the use of multiple GPUs, this result clearly demonstrates that it is possible to harness multiple GPUs in a single system with high efficiency.  |
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