Large-scale parallelization of molecular dynamics simulations is facing challenges which seriously affect the simula- tion efficiency, among which the load imbalance problem is the most critical. In this paper, we propose, a new molecular dynamics static load balancing method （MDSLB）. By analyzing the characteristics of the short-range force of molecular dynamics programs running in parallel, we divide the short-range force into three kinds of force models, and then pack- age the computations of each force model into many tiny computational units called ＂cell loads＂, which provide the basic data structures for our load balancing method. In MDSLB, the spatial region is separated into sub-regions called ＂local domains＂, and the cell loads of each local domain are allocated to every processor in turn. Compared with the dynamic load balancing method, MDSLB can guarantee load balance by executing the algorithm only once at program startup without migrating the loads dynamically. We implement MDSLB in OpenFOAM software and test it on TianHe-lA supercomputer with 16 to 512 processors. Experimental results show that MDSLB can save 34%-64% time for the load imbalanced cases.
As the scale of supercomputers rapidly grows, the reliability problem dominates the system availability. Existing fault tolerance mechanisms, such as periodic checkpointing and process redundancy, cannot effectively fix this problem. To address this issue, we present a new fault tolerance framework using process replication and prefetching （FTRP）, combining the benefits of proactive and reactive mechanisms. FTRP incorporates a novel cost model and a new proactive fault tolerance mechanism to improve the application execution efficiency. The novel cost model, called the ＇work-most＇ （WM） model, makes runtime decisions to adaptively choose an action from a set of fault tolerance mechanisms based on failure prediction results and application status. Similar to program locality, we observe the failure locality phenomenon in supercomputers for the first time. In the new proactive fault tolerance mechanism, process replication with process prefetching is proposed based on the failure locality, significantly avoiding losses caused by the failures regardless of whether they have been predicted. Simulations with real failure traces demonstrate that the FTRP framework outperforms existing fault tolerance mechanisms with up to 10% improvement in application efficiency for common failure prediction accuracy, and is effective for petascale systems and beyond.
The mismatch between compute performance and I/O performance has long been a stumbling block as supercomputers evolve from petaflops to exaflops. Currently, many parallel applications are I/O intensive,and their overall running times are typically limited by I/O performance. To quantify the I/O performance bottleneck and highlight the significance of achieving scalable performance in peta/exascale supercomputing, in this paper, we introduce for the first time a formal definition of the ‘storage wall' from the perspective of parallel application scalability. We quantify the effects of the storage bottleneck by providing a storage-bounded speedup,defining the storage wall quantitatively, presenting existence theorems for the storage wall, and classifying the system architectures depending on I/O performance variation. We analyze and extrapolate the existence of the storage wall by experiments on Tianhe-1A and case studies on Jaguar. These results provide insights on how to alleviate the storage wall bottleneck in system design and achieve hardware/software optimizations in peta/exascale supercomputing.
Wei HUGuang-ming LIUQiong LIYan-huang JIANGGui-lin CAI
