RMA-MT: A Benchmark Suite for Assessing MPI Multi-threaded RMA Performance.
Abstract not provided.
Dosanjh, Matthew↗
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RMACXX: An Efficient High-Level C++ Interface over MPI-3 RMA
Parallel scientific applications can benefit from de- coupling communication and synchronization. One-sided pro- gramming abstractions, which separate communication from syn- chronization, have in fact served as a motivation for partitioned global address space (PGAS) models. However, the use of PGAS models in application codes in a manner that fully exploits the benefit of these programming models requires significant development effort. Meanwhile, a vast majority of scientific codes already use the Message Passing Interface (MPI) and need convenient features to support application-specific one-sided communication scenarios. MPI Remote Memory Access (RMA) can be employed for this purpose. MPI is a low-level API, however, and developing applications with MPI RMA requires programmers to be well versed in its nuances. We present RMACXX, a compact set of C++ bindings to MPI-3 RMA, to ease the use of MPI RMA. Unlike other PGAS models, which may have interoperability issues with MPI, RMACXX is written on top of MPI and uses the same runtime as MPI. The basic functionality of RMACXX adds only a relatively small number of extra instructions (about 20) to the critical communication path. Moreover, RMACXX provides an intuitive API for building a wide variety of scientific applications while enjoying performance matching handwritten MPI-3 RMA codes.
MPI-3 RMA, one-sided communication, PGAS, C++, exp↗
RMA-MT Benchmarks
The RMA-MT benchmarks are a suite of performance tests for multi-threaded Message Passing Interface (MPI) Remote Memory Access (RMA) implementations. The suite includes tests for bandwidth and latency with any number of threads. This suite was originally developed and release by Sandia National Laboratory. LANL modifications to the suite include a complete re-write of much of the source code, bi-directional bandwidth, and message rate tests.
Hjelm, Nathan↗
GASNet-EX RMA Communication Performance on Recent Supercomputing Systems
Partitioned Global Address Space (PGAS) programming models, typified by systems such as Unified Parallel C (UPC) and Fortran coarrays, expose one-sided Remote Memory Access (RMA) communication as a key building block for High Performance Computing (HPC) applications. Architectural trends in supercomputing make such programming models increasingly attractive, and newer, more sophisticated models such as UPC++, Legion and Chapel that rely upon similar communication paradigms are gaining popularity. GASNet-EX is a portable, open-source, high-performance communication library designed to efficiently support the networking requirements of PGAS runtime systems and other alternative models in emerging exascale machines. The library is an evolution of the popular GASNet communication system, building upon 20 years of lessons learned. We present microbenchmark results which demonstrate the RMA performance of GASNet-EX is competitive with MPI implementations on four recent, high-impact, production HPC systems. These results are an update relative to previously published results on older systems. The networks measured here are representative of hardware currently used in six of the top ten fastest supercomputers in the world, and all of the exascale systems on the U.S. DOE road map.
Hargrove, Paul H↗
Dynamic Adaptable Asynchronous Progress Model for MPI RMA Multiphase Applications
Casper is a process-based asynchronous progress model for MPI one-sided communication on multi-and many-core architectures. The one-sided communication is not truly one-sided in most MPI implementations: the target process still relies on software progress to complete incoming operations. Casper allows the user to specify an arbitrary number of cores dedicated to background ghost processes and transparently redirects the RMA operations to ghost processes by utilizing the PMPI redirection and MPI-3 shared-memory technologies. Although Casper benefits applications that suffer from lack of asynchronous progress, the operation redirection design might not support complex multiphase applications effectively, which often involve dynamically changing communication density and computing workloads. In this paper, we present an adaptive mechanism in Casper to address the limitation of static asynchronous progress in multiphase applications. For this we exploit two adaptive strategies, a user-guided strategy and a fully transparent and automatic strategy based on self-profiling and prediction, to dynamically reconfigure the asynchronous progress in Casper according to real-time performance characteristics during multiphase execution. We evaluate the adaptive approaches in both microbenchmarks and a real quantum chemistry application suite, NWChem, on the Cray XC30 supercomputer and an Intel Omni-Path cluster.
97 MATHEMATICS AND COMPUTING↗
Scaling NWChem with Efficient and Portable Asychronous Communication in MPI RMA
NWChem is one of the most widely used computational chemistry application suites for chemical and biological systems. Despite its vast success, the computational efficiency of NWChem is still low. This is especially true in higher accuracy methods such as the CCSD(T) coupled cluster method, where it currently achieves a mere 50% computational efficiency when run at large scales. In this paper, we demonstrate the most computationally efficient scaling of NWChem CCSD(T) to date, and use it to solve large water clusters. We use our recently proposed process-based asynchronous progress framework for MPI RMA, called Casper, to scale the computation on water clusters at near-100% computational efficiency on up to 12288 cores.
Si, Min↗
Efficient Active Message RMA in GASNet Using a Target-Side Reassembly Protocol (Extended Abstract)
GASNet is a portable, open-source, high-performance communication library designed to efficiently support the networking requirements of PGAS runtime systems and other alternative models on future exascale machines. This paper investigates strategies for efficient implementation of GASNet’s “AM Long” API that couples an RMA (Remote Memory Access) transfer with an Active Message (AM) delivery. We discuss several network-level protocols for AM Long and propose a new target-side reassembly protocol. We present a microbenchmark evaluation on the Cray XC Aries network hardware. The target-side reassembly protocol on this network improves AM Long end-to-end latency by up to 33%, and the effective bandwidth by up to 49%, while also enabling asynchronous source completion that drastically reduces injection overheads. The improved AM Long implementation for Aries is available in GASNet-EX release v2019.9.0 and later.
Hargrove, P↗
Multi-Doppler radar analysis from CSAPR, CHIVO, COW, and RMA-1 radars during the CACTI/RELAMPAGO experiments in Argentina in 2018
This data set contains multi-Doppler radar analysis from CSAPR-2, CSU-CHIVO, COW, and RMA-1 radars. These radars were collecting dual-polarization data during the CACTI/RELAMPAGO experiments in Argentina in 2018. Doppler analysis is systematically conducted for 31 days with convection. Three-dimensional wind fields are retrieved using the PyDDA algorithm. Dual-polarization information is also included in the data set.
3D cartesian gridded corrected mean Doppler veloci↗
MPI-RMA: State of the Art in Open MPI
Explore the source record for details and available documents.
Computer Science↗
Evaluating OpenSHMEM Explicit Remote Memory Access Operations and Merged Requests
The OpenSHMEM Library Specification has evolved consid- erably since version 1.0. Recently, non-blocking implicit Remote Memory Access (RMA) operations were introduced in OpenSHMEM 1.3. These provide a way to achieve better overlap between communication and computation. However, the implicit non-blocking operations do not pro- vide a separate handle to track and complete the individual RMA opera- tions. They are guaranteed to be completed after either a shmem quiet(), shmem barrier() or a shmem barrier all() is called. These are global com- pletion and synchronization operations. Though this semantic is expected to achieve a higher message rate for the applications, the drawback is that it does not allow fine-grained control over the completion of RMA operations. In this paper, first, we introduce non-blocking RMA operations with requests, where each operation has an explicit request to track and com- plete the operation. Second, we introduce interfaces to merge multiple requests into a single request handle. The merged request tracks multiple user-selected RMA operations, which provides the flexibility of tracking related communication operations with one request handle. Lastly, we explore the implications in terms of performance, productivity, usability and the possibility of defining different patterns of communication via merging of requests. Our experimental results show that a well designed and implemented OpenSHMEM stack can hide the overhead of allocating and managing the requests. The latency of RMA operations with requests is similar to blocking and implicit non-blocking RMA operations. We test our implementation with the Scalable Synthetic Compact Applications (SSCA #1) benchmark and observe that using RMA operations with requests and merging of these requests outperform the implementation using blocking RMA operations and implicit non-blocking operations by 49% and 74% respectively.
Boehm, Swen↗
Fluorescent and Bioluminescent Reporter Mouse-Adapted Ebola Viruses Maintain Pathogenicity and Can Be Visualized in Vivo
Abstract Ebola virus (EBOV) causes lethal disease in humans but not in mice. Here, we generated recombinant mouse-adapted (MA) EBOVs, including 1 based on the previously reported serially adapted strain (rMA-EBOV), along with single-reporter rMA-EBOVs expressing either fluorescent (ZsGreen1 [ZsG]) or bioluminescent (nano-luciferase [nLuc]) reporters, and dual-reporter rMA-EBOVs expressing both ZsG and nLuc. No detriment to viral growth in vitro was seen with inclusion of MA-associated mutations or reporter proteins. In CD-1 mice, infection with MA-EBOV, rMA-EBOV, and single-reporter rMA-EBOVs conferred 100% lethality; infection with dual-reporter rMA-EBOV resulted in 73% lethality. Bioluminescent signal from rMA-EBOV expressing nLuc was detected in vivo and ex vivo using the IVIS Spectrum CT. Fluorescent signal from rMA-EBOV expressing ZsG was detected in situ using handheld blue-light transillumination and ex vivo through epi-illumination with the IVIS Spectrum CT. These data support the use of reporter MA-EBOV for studies of Ebola virus in animal disease models.
Immunology↗
UPC++: A High-Performance Communication Framework for Asynchronous Computation
© 2019 IEEE UPC++ is a C++ library that supports high-performance computation via an asynchronous communication framework. This paper describes a new incarnation that differs substantially from its predecessor, and we discuss the reasons for our design decisions. We present new design features, including future-based asynchrony management, distributed objects, and generalized Remote Procedure Call (RPC). We show microbenchmark performance results demonstrating that one-sided Remote Memory Access (RMA) in UPC++ is competitive with MPI-3 RMA; on a Cray XC40 UPC++ delivers up to a 25% improvement in the latency of blocking RMA put, and up to a 33% bandwidth improvement in an RMA throughput test. We showcase the benefits of UPC++ with irregular applications through a pair of application motifs, a distributed hash table and a sparse solver component. Our distributed hash table in UPC++ delivers near-linear weak scaling up to 34816 cores of a Cray XC40. Our UPC++ implementation of the sparse solver component shows robust strong scaling up to 2048 cores, where it outperforms variants communicating using MPI by up to 3.1x. UPC++ encourages the use of aggressive asynchrony in low-overhead RMA and RPC, improving programmer productivity and delivering high performance in irregular applications.
Bachan, John↗
Tracking ebolavirus genomic drift with a resequencing microarray
Filoviruses are emerging pathogens that cause acute fever with high fatality rate and present a global public health threat. During the 2013–2016 Ebola virus outbreak, genome sequencing allowed the study of virus evolution, mutations affecting pathogenicity and infectivity, and tracing the viral spread. In 2018, early sequence identification of the Ebolavirus as EBOV in the Democratic Republic of the Congo supported the use of an Ebola virus vaccine. However, field-deployable sequencing methods are needed to enable a rapid public health response. Resequencing microarrays (RMA) are a targeted method to obtain genomic sequence on clinical specimens rapidly, and sensitively, overcoming the need for extensive bioinformatic analysis. This study presents the design and initial evaluation of an ebolavirus resequencing microarray (Ebolavirus-RMA) system for sequencing the major genomic regions of four Ebolaviruses that cause disease in humans. The design of the Ebolavirus-RMA system is described and evaluated by sequencing repository samples of three Ebolaviruses and two EBOV variants. The ability of the system to identify genetic drift in a replicating virus was achieved by sequencing the ebolavirus glycoprotein gene in a recombinant virus cultured under pressure from a neutralizing antibody. Comparison of the Ebolavirus-RMA results to the Genbank database sequence file with the accession number given for the source RNA and Ebolavirus-RMA results compared to Next Generation Sequence results of the same RNA samples showed up to 99% agreement.
59 BASIC BIOLOGICAL SCIENCES↗
An implementation and evaluation of the MPI 3.0 one-sided communication interface
The Q1 Message Passing Interface (MPI) 3.0 standard includes a significant revision to MPI’s remote memory access (RMA) interface, which provides support for one-sided communication. MPI-3 RMA is expected to greatly enhance the usability and performance ofMPI RMA.We present the first complete implementation of MPI-3 RMA and document implementation techniques and performance optimization opportunities enabled by the new interface. Our implementation targets messaging-based networks and is publicly available in the latest release of the MPICH MPI implementation. Here using this implementation, we explore the performance impact of new MPI-3 functionality and semantics. Results indicate that the MPI-3 RMA interface provides significant advantages over the MPI-2 interface by enabling increased communication concurrency through relaxed semantics in the interface and additional routines that provide new window types, synchronization modes, and atomic operations.
97 MATHEMATICS AND COMPUTING↗
Phase Diagram of a Three-Dimensional Antiferromagnet with Random Magnetic Anisotropy
Three-dimensional (3D) antiferromagnets with random magnetic anisotropy (RMA) that were experimentally studied to date have competing two-dimensional and three-dimensional exchange interactions which can obscure the authentic effects of RMA. The magnetic phase diagram of Fe x Ni 1-x F 2 epitaxial thin films with true random single-ion anisotropy was deduced from magnetometry and neutron scattering measurements and analyzed using mean field theory. Regions with uniaxial, oblique and easy plane anisotropies were identified. A RMA-induced glass region was discovered where a Griffiths-like breakdown of long-range spin order occurs.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Exploring MPI Communication Models for Graph Applications Using Graph Matching as a Case Study
Traditional implementations of parallel graph operations on distributed memory platforms are written using Message Passing Interface (MPI) point to point communication primitives such as Send-Recv (blocking and nonblocking). Apart from this classical model, the MPI community has over the years added other communication models; however, their suitability for handling the irregular traffic workloads typical of graph operations remain comparatively less explored. Our aim in this paper is to study these relatively underutilized communication models of MPI for graph applications. More specifically, we evaluate MPI’s one-sided programming, or Remote Memory Access (RMA), and nearest neighborhood collectives using a process graph topology. There are features in these newer models that are intended to better map to irregular communication patterns, as exemplified in graph algorithms. As a concrete application for our case study, we use distributed memory implementations of a weighted graph matching algorithm to investigate performances of MPI-3 RMA and neighborhood collective operations compared to nonblocking Send- Recv. A matching in a graph is a subset of edges such that no two matched edges are incident on the same vertex. A maximum weight matching is a matching of maximum weight computed as the sum of the weights of matched edges. Algorithms for optimal matching have quadratic complexity and are difficult to parallelize. More importantly, execution of graph matching is dominated by high volume of irregular memory accesses, making it an ideal candidate for studying the effects of various MPI communication models on graph applications at scale. Our neighborhood collectives and RMA implementations yields up to 6× speedup over traditional optimized nonblocking Send-Recv implementations, on thousands of cores of the NERSC Cori supercomputer. We believe the lessons learned from this case study can be adopted to benefit a wider range of graph application codes.
Ghosh, Sayan↗
SU-F-BRD-01: A Novel 4D Robust Optimization Mitigates Interplay Effect in Intensity-Modulated Proton Therapy for Lung Cancer
Purpose: To compare the impact of interplay effect on 3D and 4D robustly optimized intensity-modulated proton therapy (IMPT) plans to treat lung cancer. Methods: Two IMPT plans were created for 11 non-small-cell-lung-cancer cases with 6–14 mm spots. 3D robust optimization generated plans on average CTs with the internal gross tumor volume density overridden to deliver 66 CGyE in 33 fractions to the internal target volume (ITV). 4D robust optimization generated plans on 4D CTs with the delivery of prescribed dose to the clinical target volume (CTV). In 4D optimization, the CTV of individual 4D CT phases received non-uniform doses to achieve a uniform cumulative dose. Dose evaluation software was developed to model time-dependent spot delivery to incorporate interplay effect with randomized starting phases of each field per fraction. Patient anatomy voxels were mapped from phase to phase via deformable image registration to score doses. Indices from dose-volume histograms were used to compare target coverage, dose homogeneity, and normal-tissue sparing. DVH indices were compared using Wilcoxon test. Results: Given the presence of interplay effect, 4D robust optimization produced IMPT plans with better target coverage and homogeneity, but slightly worse normal tissue sparing compared to 3D robust optimization (unit: Gy) [D95% ITV: 63.5 vs 62.0 (p=0.014), D5% - D95% ITV: 6.2 vs 7.3 (p=0.37), D1% spinal cord: 29.0 vs 29.5 (p=0.52), Dmean total lung: 14.8 vs 14.5 (p=0.12), D33% esophagus: 33.6 vs 33.1 (p=0.28)]. The improvement of target coverage (D95%,4D – D95%,3D) was related to the ratio RMA3/(TVx10−4), with RMA and TV being respiratory motion amplitude (RMA) and tumor volume (TV), respectively. Peak benefit was observed at ratios between 2 and 10. This corresponds to 125 – 625 cm3 TV with 0.5-cm RMA. Conclusion: 4D optimization produced more interplay-effect-resistant plans compared to 3D optimization. It is most effective when respiratory motion is modest compared to TV. NIH/NCI K25CA168984; Eagles Cancer Research Career Development; The Lawrence W. and Marilyn W. Matteson Fund for Cancer Research; Mayo ASU Seed Grant; The Kemper Marley Foundation.
60 APPLIED LIFE SCIENCES↗