In Proceedings of the 24th IEEE International Conference on Parallel and Distributed Systems (ICPADS), Sentosa, Singapore, December 2018. Best Poster Award
发表信息：
In 2018 IEEE 24th International Conference on Parallel and Distributed Systems (ICPADS), pp. 803-812. IEEE, 2018
Hybrid MPI+threads programming is gaining prominence as an alternative to the traditional "MPI everywhere'" model to better handle the disproportionate increase in the number of cores compared with other on-node resources. Current implementations of these two models represent the two extreme cases of communication resource sharing in modern MPI implementations. In the MPI-everywhere model, each MPI process has a dedicated set of communication resources (also known as endpoints), which is ideal for performance but is resource wasteful. With MPI+threads, current MPI implementations share a single communication endpoint for all threads, which is ideal for resource usage but is hurtful for performance.
In this paper, we explore the tradeoff space between performance and communication resource usage in MPI+threads environments. We first demonstrate the two extreme cases---one where all threads share a single communication endpoint and another where each thread gets its own dedicated communication endpoint (similar to the MPI-everywhere model) and showcase the inefficiencies in both these cases. Next, we perform a thorough analysis of the different levels of resource sharing in the context of Mellanox InfiniBand. Using the lessons learned from this analysis, we design an improved resource-sharing model to produce \emph{scalable communication endpoints} that can achieve the same performance as with dedicated communication resources per thread but using just a third of the resources.
Hybrid MPI+threads programming is gaining prominence, but, in practice, applications perform slower with it compared to the MPI everywhere model. The most critical challenge to the parallel efficiency of MPI+threads applications is slow MPI_THREAD_MULTIPLE performance. MPI libraries have recently made significant strides on this front, but to exploit their capabilities, users must expose the communication parallelism in their MPI+threads applications. Recent studies show that MPI 4.0 provides users with new performance-oriented options to do so, but our evaluation of these new mechanisms shows…
MPI+threads is gaining prominence as an alternative to the traditional MPI everywhere model in order to better handle the disproportionate increase in the number of cores compared with other on-node resources. However, the communication performance of MPI+threads can be 100x slower than that of MPI everywhere. Both MPI users and developers are to blame for this slowdown. Typically, MPI users do not expose logical communication parallelism. Consequently, MPI libraries use conservative approaches, such as a global critical section, to maintain MPI's ordering constraints for MPI+threads, thus ser…
Asynchronous programming models (APM) are gaining more and more traction, allowing applications to expose the available concurrency to a runtime system tasked with coordinating the execution. While MPI has long provided support for multi-threaded communication and non-blocking operations, it falls short of adequately supporting APMs as correctly and efficiently handling MPI communication in different models is still a challenge. Meanwhile, new low-level implementations of light-weight, cooperatively scheduled execution contexts (fibers, aka user-level threads (ULT)) are meant to serve as a bas…
Fault-tolerance has always been an important topic when it comes to running massively parallel programs at scale. Statistically, hardware and software failures are expected to occur more often on systems gathering millions of computing units. Moreover, the larger jobs are, the more computing hours would be wasted by a crash. In this paper, we describe the work done in our MPI runtime to enable both transparent and application-level checkpointing mechanisms. Unlike the MPI 4.0 User-Level Failure Mitigation (ULFM) interface, our work targets solely Checkpoint/Restart and ignores other features s…
The hybrid MPI+X programming paradigm, where X refers to threads or GPUs, has gained prominence in the high-performance computing arena. This corresponds to a trend of system architectures growing more heterogeneous. The current MPI standard only specifies the compatibility levels between MPI and threading runtimes. No MPI concept or interface exists for applications to pass thread context or GPU stream context to MPI implementations explicitly. This lack has made performance optimization complicated in some cases and impossible in other cases. We propose a new concept in MPI, called MPIX stre…
Modern OpenMP threading techniques are used to convert the MPI-only Hartree-Fock code in the GAMESS program to a hybrid MPI/OpenMP algorithm. Two separate implementations that differ by the sharing or replication of key data structures among threads are considered, density and Fock matrices. All implementations are benchmarked on a super-computer of 3,000 Intel Xeon Phi processors. With 64 cores per processor, scaling numbers are reported on up to 192,000 cores. The hybrid MPI/OpenMP implementation reduces the memory footprint by approximately 200 times compared to the legacy code. The MPI/Ope…
The Friends-of-Friends (FoF) algorithm is a standard technique used in cosmological $N$-body simulations to identify structures. Its goal is to find clusters of particles (called groups) that are separated by at most a cut-off radius. $N$-body simulations typically use most of the memory present on a node, leaving very little free for a FoF algorithm to run on-the-fly. We propose a new method that utilises the common Union-Find data structure and a hybrid MPI+threads approach. The algorithm can also be expressed elegantly in a task-based formalism if such a framework is used in the rest of the…
The MPI standard has long included one-sided communication abstractions through the MPI Remote Memory Access (RMA) interface. Unfortunately, the MPI RMA chapter in the 4.0 version of the MPI standard still contains both well-known and lesser known short-comings for both implementations and users, which lead to potentially non-optimal usage patterns. In this paper, we identify a set of issues and propose ways for applications to better express anticipated usage of RMA routines, allowing the MPI implementation to better adapt to the application's needs. In order to increase the flexibility of th…
Asynchronous programming models (APM) are gaining more and more traction, allowing applications to expose the available concurrency to a runtime system tasked with coordinating the execution. While MPI has long provided support for multi-threaded communication and non-blocking operations, it falls short of adequately supporting APMs as correctly and efficiently handling MPI communication in different models is still a challenge. We have previously proposed an extension to the MPI standard providing operation completion notifications using callbacks, so-called MPI Continuations. This interface …
Remote-memory-access models, also known as one-sided communication models, are becoming an interesting alternative to traditional two-sided communication models in the field of High Performance Computing. In this paper we extend previous work on an MPI-based, locality-aware remote-memory-access model with a asynchronous progress-engine for non-blocking communication operations. Most previous related work suggests to drive progression on communication through an additional thread within the application process. In contrast, our scheme uses an arbitrary number of dedicated processes to drive asy…
The FFT of three-dimensional (3D) input data is an important computational kernel of numerical simulations and is widely used in High Performance Computing (HPC) codes running on a large number of processors. Performance of many scientific applications such as Molecular Dynamic simulations depends on the underlying 3D parallel FFT library being used. In this paper, we present C-DACs three-dimensional Fast Fourier Transform (CROFT) library which implements three-dimensional parallel FFT using pencil decomposition. To exploit the hyperthreading capabilities of processor cores without affecting p…
Scientific applications are often complex, irregular, and computationally-intensive. To accommodate the ever-increasing computational demands of scientific applications, high-performance computing (HPC) systems have become larger and more complex, offering parallelism at multiple levels (e.g., nodes, cores per node, threads per core). Scientific applications need to exploit all the available multilevel hardware parallelism to harness the available computational power. The performance of applications executing on such HPC systems may adversely be affected by load imbalance at multiple levels, c…
The University of Edinburgh（爱丁堡大学）；Alan Turing Institute（艾伦·图灵研究所）；Intel（英特尔）；Columbia University（哥伦比亚大学）；Brookhaven National Laboratory（布鲁克海文国家实验室）
We discuss practical methods to ensure near wirespeed performance from clusters with either one or two Intel(R) Omni-Path host fabric interfaces (HFI) per node, and Intel(R) Xeon Phi(TM) 72xx (Knight's Landing) processors, and using the Linux operating system. The study evaluates the performance improvements achievable and the required programming approaches in two distinct example problems: firstly in Cartesian communicator halo exchange problems, appropriate for structured grid PDE solvers that arise in quantum chromodynamics simulations of particle physics, and secondly in gradient reductio…
