Proceedings of the Second Annual PGAS Applications Workshop最新文献

{"title":"Incremental caffeination of a terrestrial hydrological modeling framework using Fortran 2018 teams","authors":"D. Rouson, J. McCreight, A. Fanfarillo","doi":"10.1145/3144779.3169110","DOIUrl":"https://doi.org/10.1145/3144779.3169110","url":null,"abstract":"We present Fortran 2018 teams (grouped processes) running a parallel ensemble of simulations built from a pre-existing Message Passing Interface (MPI) application. A challenge arises around the Fortran standard's eschewing any direct reference to lower-level communication substrates, such as MPI, leaving any interoperability between Fortran's parallel programming model, Coarray Fortran (CAF), and the supporting substrate to the quality of the compiler implmentation. Our approach introduces CAF incrementally, a process we term \"caffeination.\" By letting CAF initiate execution and exposing the underlying MPI communicator to the original application code, we create a one-to-one correspondence between MPI group colors and Fortran teams. We apply our approach to the National Center for Atmospheric Research (NCAR)'s Weather Research and Forcecasting Hydrological Model (WRF-Hydro). The newly caffeinated main program replaces batch job submission scripts and forms teams that each execute one ensemble member. To support this work, we developed the first compiler front-end and parallel runtime library support for teams. This paper describes the required modifications to a public GNU Compiler Collection (GCC) fork, an OpenCoarrays [1] application binary interface (ABI) branch, and a WRF-Hydro branch.","PeriodicalId":369424,"journal":{"name":"Proceedings of the Second Annual PGAS Applications Workshop","volume":"20 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116251793","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The UPC++ PGAS library for Exascale Computing","authors":"J. Bachan, D. Bonachea, Paul H. Hargrove, S. Hofmeyr, M. Jacquelin, A. Kamil, B. V. Straalen, S. Baden","doi":"10.1145/3144779.3169108","DOIUrl":"https://doi.org/10.1145/3144779.3169108","url":null,"abstract":"We describe UPC++ V1.0, a C++11 library that supports APGAS programming. UPC++ targets distributed data structures where communication is irregular or fine-grained. The key abstractions are global pointers, asynchronous programming via RPC, and futures. Global pointers incorporate ownership information useful in optimizing for locality. Futures capture data readiness state, are useful for scheduling and also enable the programmer to chain operations to execute asynchronously as high-latency dependencies become satisfied, via continuations. The interfaces for moving non-contiguous data and handling memories with different optimal access methods are composable and closely resemble those used in modern C++. Communication in UPC++ runs at close to hardware speeds by utilizing the low-overhead GASNet-EX communication library.","PeriodicalId":369424,"journal":{"name":"Proceedings of the Second Annual PGAS Applications Workshop","volume":"12 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130020269","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MerBench: PGAS Benchmarks for High Performance Genome Assembly","authors":"E. Georganas, Marquita Ellis, R. Egan, S. Hofmeyr, A. Buluç, B. Cook, L. Oliker, K. Yelick","doi":"10.1145/3144779.3169109","DOIUrl":"https://doi.org/10.1145/3144779.3169109","url":null,"abstract":"De novo genome assembly is one of the most important and challenging computational problems in modern genomics; further, it shares algorithms and communication patterns important to other graph analytic and irregular applications. Unlike simulations, it has no floating point arithmetic and is dominated by small memory transactions within and between computing nodes. In this work, we introduce MerBench, a compact set of PGAS benchmarks that capture the communication patterns of the parallel algorithms throughout HipMer, a parallel genome assembler pipeline that has been shown to scale to massive concurrencies. We also present results of these microbenchmarks on the Edison supercomputer and illustrate how these empirical results can be used to assess the scaling behavior of the pipeline.","PeriodicalId":369424,"journal":{"name":"Proceedings of the Second Annual PGAS Applications Workshop","volume":"120 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132169926","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Preliminary Performance Evaluation of Coarray-based Implementation of Fiber Miniapp Suite using XcalableMP PGAS Language","authors":"H. Murai, M. Nakao, H. Iwashita, M. Sato","doi":"10.1145/3144779.3144780","DOIUrl":"https://doi.org/10.1145/3144779.3144780","url":null,"abstract":"XcalableMP (XMP) is a Partitioned Global Address Space (PGAS) language that is defined by the XMP Specification Working Group of the PC Cluster Consortium. This paper provides the implementation and evaluation of the Fiber miniapp suite, which is primarily maintained by RIKEN Advanced Institute for Computational Science, on the basis of the local-view parallelization model using the coarray feature of XMP. In many cases, a coarray-based implementation can be obtained by replacing original Message Passing Interface (MPI) functions with coarray assignment statements. Herein, we demonstrate a method to rewrite irregular applications into the coarray-based style. Evaluation on the K computer using the Omni XMP compiler we have been developing shows that some XMP implementations are comparable to their original implementations, but there is performance degradation found in the others, which is due to the large overhead from allocating dynamic coarrays at runtime.","PeriodicalId":369424,"journal":{"name":"Proceedings of the Second Annual PGAS Applications Workshop","volume":"11 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121928341","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Performance portability of an intermediate-complexity atmospheric research model in coarray Fortran","authors":"D. Rouson, E. Gutmann, A. Fanfarillo, B. Friesen","doi":"10.1145/3144779.3169104","DOIUrl":"https://doi.org/10.1145/3144779.3169104","url":null,"abstract":"We examine the scalability and performance of an open-source, coarray Fortran (CAF) mini-application (mini-app) that implements the parallel, numerical algorithms that dominate the execution of The Intermediate Complexity Atmospheric Research (ICAR) [4] model developed at the the National Center for Atmospheric Research (NCAR). The Fortran 2008 mini-app includes one Fortran 2008 implementation of a collective subroutine defined in the Committee Draft of the upcoming Fortran 2018 standard. The ability of CAF to run atop various communication layers and the increasing CAF compiler availability facilitated evaluating several compilers, runtime libraries and hardware platforms. Results are presented for the GNU and Cray compilers, each of which offers different parallel runtime libraries employing one or more communication layers, including MPI, OpenSHMEM, and proprietary alternatives. We study performance on multi- and many-core processors in distributed memory. The results show promising scaling across a range of hardware, compiler, and runtime choices on up to ~100,000 cores.","PeriodicalId":369424,"journal":{"name":"Proceedings of the Second Annual PGAS Applications Workshop","volume":"101 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116336208","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cosmological Particle-Mesh Simulations in Chapel","authors":"N. Padmanabhan, Ben Albrecht","doi":"10.1145/3144779.3169105","DOIUrl":"https://doi.org/10.1145/3144779.3169105","url":null,"abstract":"1 EXTENDED ABSTRACT This presentation will describe the implementation and performance of a gravitational N-body particle-mesh (PM) code in Chapel. Our goal here is to go beyond simple benchmarks and kernels, and present a case-study on the readiness of Chapel to be used for end-to-end computations. Chapel is a next generation, high-productivity PGAS language being developed as an open source project at Cray Inc. Chapel grew out of the DARPA High Productivity Computing Systems (HPCS) program. Some of its key features include native parallelism in the core language, data and task locality, a multiresolution philosophy, and interoperability with C. Chapel supports parallelism and locality as first-class features allowing one to target a variety of hardware architectures under a single set of semantics. Chapel’s multiresolution design philosophy designates that Chapel exposes a spectrum of lower-level programming features under the higherlevel data-parallel approach, allowing users to customize or tune communication patterns as needed. Lastly, Chapel provides built-in 2-way interoperability with C, enabling users to wrap legacy codes in Chapel with relative ease. A key feature of Chapel is that the parallel and distributed abstractions are all implemented in Chapel itself, allowing it to easily be extended. We will discuss examples of these below. Our interest in implementing a gravitational N-body particlemesh code grew out of the research interests of the first author. The goal in cosmology is to use the Universe as a laboratory to probe fundamental physics on scales (both in energy and length) that are otherwise inaccessible to laboratories and experiments. However, unlike experiments that can be tailored to answer specific problems, cosmology must rely on modeling observations in their entirety to make the necessary inferences about the underlying physics. This process relies on being able to numerically simulate observations (since analytic calculations, while valuable for insight, often cannot reach the precision required) and is therefore is highly computational in nature. Furthermore, modern astrophysical datasets are getting large enough that they cannot be analyzed on single-core","PeriodicalId":369424,"journal":{"name":"Proceedings of the Second Annual PGAS Applications Workshop","volume":"127 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131962780","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Graph500 on OpenSHMEM: Using A Practical Survey of Past Work to Motivate Novel Algorithmic Developments","authors":"M. Grossman, H. Pritchard, Zoran Budimlic, Vivek Sarkar","doi":"10.1145/3144779.3144781","DOIUrl":"https://doi.org/10.1145/3144779.3144781","url":null,"abstract":"Graph500 is an open specification of a graph-based benchmark for high-performance computing (HPC). The core computational kernel of Graph500 is a breadth-first search of an undirected graph. Unlike many other HPC benchmarks, Graph500 is therefore characterized by heavily irregular and fine-grain computation, memory accesses, and network communication. Therefore, it can serve as a more realistic stress test of modern HPC hardware, software, and algorithmic techniques than other benchmarking efforts. On the other hand, OpenSHMEM is an open, PGAS, and SPMD specification of a communication model for communicating across large numbers of processing elements. OpenSHMEM explicitly focuses on applications characterized by fine-grain communication, of which Graph500 is one example. Therefore, there is a natural synergy between the communication patterns of Graph500 and the capabilities of OpenSHMEM. In this work we explore that synergy by developing several novel implementations of Graph500 on various OpenSHMEM implementations. We contribute a review of the state-of-the-art in distributed Graph500 implementations, as well as a performance and programmability comparison between the state-of-the-art and our own OpenSHMEM-based implementations. Our results demonstrate improved scaling of Graph500's BFS kernel out to 1,024 nodes of the Edison supercomputer, achieving ~2.5x performance improvement relative to the highest performing reference implementation at that scale.","PeriodicalId":369424,"journal":{"name":"Proceedings of the Second Annual PGAS Applications Workshop","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131164406","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}