Scalability Enhancements to FMM for Molecular Dynamics Simulations

Research topic and goals

This joint-lab cooperation covers the topic of parallel programming and numerical algorithms. We are especially interested in increasing the scalability (strong scaling) of the Fast Multipole Method (FMM) for very large numbers of ranks. Therefore, we will examine and extend the JSC-developed, high-performance FMM library called FMSolvr. This will allow us to improve the usability of the FMM Coulomb solver in molecular dynamics simulations with only a few particles per rank. Initial research already discovered, that the current intrinsic parallel scaling limitations stem from thread synchronization (intranode) and process synchronization (internode) on large-scale systems. We will investigate weak and delayed synchronization models, as well as node-level tasking approaches and other techniques with MPI-3 and upcoming MPI-4 extensions to alleviate some of these performance bottlenecks.

Results for 2015/2016

The project was initiated at the JLESC meeting in November 2014 between ANL and JSC. To provide a consistent interface for measuring and tuning parallel code performance some profound changes had to be made to the code. We started implementing an abstract parallelization layer for the FMSolvr library. This especially includes a flexible parallelization approach for inter-node communication via MPI. The adopted abstraction layer allows easier replacement/improvement of different synchronization strategies within the code. Besides the structural changes, a latency-avoiding communication scheme was implemented to improve the strong scaling. Together with the automatic testing framework, scaling bottlenecks of the method can be investigated much easier.

Results for 2016/2017

During the visit of David Haensel at ANL we implemented a data-driven version of the FMM on top of Argobots. With the experience from this implementation we implemented a tasking framework with C++ standard library features. This tasking library is specialized for communication bound problems like they arose in MD simulations. For the fine grained resolution of dependencies we implemented a dependency resolver which is configurable at compile time via template meta programming.

Visits and meetings

David Haensel (JSC) joined the group of Pavan Balaji (ANL) in Mai/June 2016 to develop a tasking scheme for FMSolvr on top of Argobots. This visit was vital to the success of this project, since we require a very flexible and fine-grained tasking scheme with only minimal overhead from the tasking runtime (e.g. Argobots).

Impact and publications

None yet.

    Future plans

    Currently we are integrating the tasking framework with the communication layers. This enables us to control the algorithmic flow and parallelization in detail. With this MPI-enabled tasking framework we will elaborate alternative communication strategies using MPI-3 and MPI-4.

    References