MOIL-opt: Energy-Conserving Molecular Dynamics on a GPU/CPU system.
MOIL-opt: Energy-Conserving Molecular Dynamics on a GPU/CPU system.
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DOI：
10.1021/ct200360f
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发表时间：
2011-08-26
影响因子：
5.5
通讯作者：
Elber, Ron
中科院分区：
文献类型：
--
作者：
Ruymgaart, A. Peter;Cardenas, Alfredo E.;Elber, Ron
我们报告了一个优化版本的分子动力学程序MOIL，它运行在一个共享的内存系统与OpenMP和利用图形处理单元（GPU）的力量。该模型是在一个单一的节点上的异构计算系统与多个核心共享相同的内存和一个GPU。这是一个典型的实验室工具，以最低的成本提供卓越的性能。除了性能，重点是明确的溶剂原子详细模型的能量守恒探索算法的准确性和稳定性。特别是对于长时间的模拟，由于被称为“能量漂移”的现象，其中能量误差作为模拟时间的函数线性累积，能量守恒是至关重要的。为了实现具有可接受精度的长时间动态，漂移必须特别小。我们确定了几种方法来控制长时间的数值精度，同时保持良好的加速比。为了保持高水平的能量守恒，SHAKE和Ewald倒数求和以双精度运行。实空间非键相互作用的双精度求和提高了能量守恒。在我们的最佳选择中，在限制所有键的距离的同时使用1fs的时间步长的能量漂移在溶剂化DHFR（二氢叶酸还原酶）的10 ns模拟中是不可检测的。更快的选择，只震动与氢原子的键，也表现得非常好，并且在同一系统中每纳秒的漂移小于1千卡/摩尔。CPU/GPU实现需要改变编程模型。我们考虑在不同大小的查找表中使用邻居列表和二次与线性插值。具有较少网格点的二次插值比线性查找表（具有更精细的表示）更快，而不会损失精度。原子邻居列表被认为是最有效的。与单核单精度代码相比，典型的加速比约为10倍。
We report an optimized version of the molecular dynamics program MOIL that runs on a shared memory system with OpenMP and exploits the power of a Graphics Processing Unit (GPU). The model is of heterogeneous computing system on a single node with several cores sharing the same memory and a GPU. This is a typical laboratory tool, which provides excellent performance at minimal cost. Besides performance, emphasis is made on accuracy and stability of the algorithm probed by energy conservation for explicit-solvent atomically-detailed-models. Especially for long simulations energy conservation is critical due to the phenomenon known as “energy drift” in which energy errors accumulate linearly as a function of simulation time. To achieve long time dynamics with acceptable accuracy the drift must be particularly small. We identify several means of controlling long-time numerical accuracy while maintaining excellent speedup. To maintain a high level of energy conservation SHAKE and the Ewald reciprocal summation are run in double precision. Double precision summation of real-space non-bonded interactions improves energy conservation. In our best option, the energy drift using 1fs for a time step while constraining the distances of all bonds, is undetectable in 10ns simulation of solvated DHFR (Dihydrofolate reductase). Faster options, shaking only bonds with hydrogen atoms, are also very well behaved and have drifts of less than 1kcal/mol per nanosecond of the same system. CPU/GPU implementations require changes in programming models. We consider the use of a list of neighbors and quadratic versus linear interpolation in lookup tables of different sizes. Quadratic interpolation with a smaller number of grid points is faster than linear lookup tables (with finer representation) without loss of accuracy. Atomic neighbor lists were found most efficient. Typical speedups are about a factor of 10 compared to a single-core single-precision code.
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