集成最先进的计算、通信和自动调整策略以提高应用程序CPMD的性能，用于从头计算分子动力学模拟
Integrating State of the Art Compute, Communication, and Autotuning Strategies to Multiply the Performance of the Application Programm CPMD for Ab Initio Molecular Dynamics Simulations
摘要：
我们提出了我们最近的代码现代化的从头算分子动力学程序CPMD（www.cpmd.org），特别关注超软赝势（USPP）的代码path. Following内部仪器的CPMD，所有的时间关键例程已被修改，以最大限度地提高计算吞吐量和最小化通信开销的最佳性能。在整个程序中，缺少混合MPI+OpenMP并行化已被添加以优化扩展。对于通信密集型例程，由于电子状态的多个分布式3d FFT和与赝势的$β$ -投影仪相关的分布式矩阵-矩阵乘法，该MPI+OpenMP并行化现在重叠计算和通信。工作负载的必要分区通过自动调整算法进行优化。此外，最大的全局MPI_Allreduce操作已被高度调优的节点本地并行化操作所取代，这些操作使用MPI共享内存窗口来避免节点间通信。多个3D FFT的批处理算法提高了MPI_Alltoall通信的吞吐量，因此，实现的可扩展性，无论是USPP和经常使用的范数守恒赝势代码path. The增强的性能和可扩展性上证明了一个中型的基准系统的256个水分子和进一步的水系统从32到2048分子。
英文摘要：
We present our recent code modernizations of the of the ab initio molecular dynamics program CPMD (www.cpmd.org) with a special focus on the ultra-soft pseudopotential (USPP) code path. Following the internal instrumentation of CPMD, all time critical routines have been revised to maximize the computational throughput and to minimize the communication overhead for optimal performance. Throughout the program missing hybrid MPI+OpenMP parallelization has been added to optimize scaling. For communication intensive routines, as the multiple distributed 3d FFTs of the electronic states and distributed matrix-matrix multiplications related to the $β$-projectors of the pseudopotentials, this MPI+OpenMP parallelization now overlaps computation and communication. The necessary partitioning of the workload is optimized by an auto-tuning algorithm. In addition, the largest global MPI_Allreduce operation has been replaced by highly tuned node-local parallelized operations using MPI shared-memory windows to avoid inter-node communication. A batched algorithm for the multiple 3d FFTs improves the throughput of the MPI_Alltoall communication and, thus, the scalability of the implementation, both for USPP and for the frequently used norm-conserving pseudopotential code path. The enhanced performance and scalability is demonstrated on a mid-sized benchmark system of 256 water molecules and further water systems of from 32 up to 2048 molecules.
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