An increasingly large number of HPC systems rely on heterogeneous architectures combining traditional multi-core CPUs with power efficient accelerators. Designing efficient applications for these systems has been troublesome in the past as accelerators could usually be programmed using specific programming languages threatening maintainability, portability and correctness. Several new programming environments try to tackle this problem. Among them, OpenACC offers a high-level approach based on compiler directive clauses to mark regions of existing C, C++ or Fortran codes to run on accelerators. This approach directly addresses code portability, leaving to compilers the support of each different accelerator, but one has to carefully assess the relative costs of portable approaches versus computing efficiency. In this paper we address precisely this issue, using as a test-bench a massively parallel Lattice Boltzmann algorithm. We first describe our multi-node implementation and optimization of the algorithm, using OpenACC and MPI. We then benchmark the code on a variety of processors, including traditional CPUs and GPUs, and make accurate performance comparisons with other GPU implementations of the same algorithm using CUDA and OpenCL. We also asses the performance impact associated to portable programming, and the actual portability and performance-portability of OpenACC-based applications across several state-of-the- art architectures.
Over the years, LB codes have been written and optimized for large clusters of commodity CPUs @cite_15 , for application-specific machines @cite_18 @cite_5 @cite_31 and even for FPGAs @cite_27 . More recently work has focused on exploiting the parallelism of powerful traditional many-core processors @cite_19 , and of power-efficient accelerators such as GPUs @cite_2 @cite_3 or Xeon-Phi processors @cite_0 . As diversified HPC architectures emerge, it is becoming more and more important to have robust methodologies to port and maintain codes for several architectures. This need has sparked the development of frameworks, such as the Open Computing Language (OpenCL), allowing to write portable codes, that can be compiled (with varying degrees of efficiency) for several accelerator architectures. OpenCL is a low level approach: it usually obtains high performances at the price of substantial adjustments in the code implying large human efforts and seriously posing a threat to code correctness and maintainability.
@cite_18 @cite_31 @cite_3 @cite_0 @cite_19 @cite_27 @cite_2 @cite_5 @cite_15
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Producing high-performance implementations from simple, portable computation specifications is a challenge that compilers have tried to address for several decades. More recently, a relatively stable architectural landscape has evolved into a set of increasingly diverging and rapidly changing CPU and accelerator designs, with the main common factor being dramatic increases in the levels of parallelism available. The growth of architectural heterogeneity and parallelism, combined with the very slow development cycles of traditional compilers, has motivated the development of autotuning tools that can quickly respond to changes in architectures and programming models, and enable very specialized optimizations that are not possible or likely to be provided by mainstream compilers. In this paper we describe the new OpenCL code generator and autotuner OrCL and the introduction of detailed performance measurement into the autotuning process. OrCL is implemented within the Orio autotuning framework, which enables the rapid development of experimental languages and code optimization strategies aimed at achieving good performance on new platforms without rewriting or hand-optimizing critical kernels. The combination of the new OpenCL autotuning and TAU measurement capabilities enables users to consistently evaluate autotuning effectiveness across a range of architectures, including several NVIDIA and AMD accelerators and Intel Xeon Phi processors, and to compare the OpenCL and CUDA code generation capabilities. We present results of autotuning several numerical kernels that typically dominate the execution time of iterative sparse linear system solution and key computations from a 3-D parallel simulation of solid fuel ignition. Abstract Documents in computer-readable form can be used to provide information about other documents, i.e. those they cite. To do this efficiently requires procedures for computer recognition of citing statements. This is not easy, especially for multi-sentence citing statements. Computer recognition procedures have been developed which are accurate to the following extent: 73 of the words in statements selected by computer procedures as being citing statements are words which are correctly attributable to the corresponding documents. The retrieval effectiveness of computer-recognized citing statements was tested in the following way. First, for eight retrieval requests in inorganiic chemistry, average recall by search of Chemical Abstracts Service indexing and Chemical Abstracts abstract text words was found to be 50 . Words from citing statements referring to the papers to be retrieved were then added to the index terms and abstract words as additional access points, and searching was repeated. Average recall increased to 70 . Only words from citing statements published within a year of the cited papers were used. The retrieval effect of citing statement words alone (published within a year) without index or abstract terms was the following: average recall was 40 . When just the words of the titles of the cited papers were added to those citing statement words, average recall increased to 50 . A citing sentence is one that appears in a scientific article and cites previous work. Citing sentences have been studied and used in many applications. For example, they have been used in scientific paper summarization, automatic survey generation, paraphrase identification, and citation function classification. Citing sentences that cite multiple papers are common in scientific writing. This observation should be taken into consideration when using citing sentences in applications. For instance, when a citing sentence is used in a summary of a scientific paper, only the fragments of the sentence that are relevant to the summarized paper should be included in the summary. In this paper, we present and compare three different approaches for identifying the fragments of a citing sentence that are related to a given target reference. Our methods are: word classification, sequence labeling, and segment classification. Our experiments show that segment classification achieves the best results. Abstract In this paper we report on our early experience on porting, optimizing and benchmarking a Lattice Boltzmann (LB) code on the Xeon-Phi co-processor, the first generally available version of the new Many Integrated Core (MIC) architecture, developed by Intel. We consider as a test-bed a state-of-the-art LB model, that accurately reproduces the thermo-hydrodynamics of a 2D- fluid obeying the equations of state of a perfect gas. The regular structure of LB algorithms makes it relatively easy to identify a large degree of available parallelism. However, mapping a large fraction of this parallelism onto this new class of processors is not straightforward. The D2Q37 LB algorithm considered in this paper is an appropriate test-bed for this architecture since the critical computing kernels require high performances both in terms of memory bandwidth for sparse memory access patterns and number crunching capability. We describe our implementation of the code, that builds on previous experience made on other (simpler) many-core processors and GPUs, present benchmark results and measure performances, and finally compare with the results obtained by previous implementations developed on state-of-the-art classic multi-core CPUs and GP-GPUs. Purpose – The purpose of this paper is to suggest an alternative to the widely used Times Cited criterion for analysing citation networks. The approach involves taking account of the natures of the papers that cite a given paper, so as to differentiate between papers that attract the same number of citations.Design methodology approach – ArticleRank is an algorithm that has been derived from Google's PageRank algorithm to measure the influence of journal articles. ArticleRank is applied to two datasets – a citation network based on an early paper on webometrics, and a self‐citation network based on the 19 most cited papers in the Journal of Documentation – using citation data taken from the Web of Knowledge database.Findings – ArticleRank values provide a different ranking of a set of papers from that provided by the corresponding Times Cited values, and overcomes the inability of the latter to differentiate between papers with the same numbers of citations. The difference in rankings between Times Cited ... In a document network such as a citation network of scientific documents, web-logs, etc., the content produced by authors exhibits their interest in certain topics. In addition some authors influence other authors' interests. In this work, we propose to model the influence of cited authors along with the interests of citing authors. Moreover, we hypothesize that apart from the citations present in documents, the context surrounding the citation mention provides extra topical information about the cited authors. However, associating terms in the context to the cited authors remains an open problem. We propose novel document generation schemes that incorporate the context while simultaneously modeling the interests of citing authors and influence of the cited authors. Our experiments show significant improvements over baseline models for various evaluation criteria such as link prediction between document and cited author, and quantitatively explaining unseen text. Scholars are increasingly citing electronic “web references” which are not preserved in libraries or full text archives. WebCite is a new standard for citing web references. To “webcite” a document involves archiving the cited Web page through www.webcitation.org and citing the WebCite permalink instead of (or in addition to) the unstable live Web page. This journal has amended its “instructions for authors” accordingly, asking authors to archive cited Web pages before submitting a manuscript. Almost 200 other journals are already using the system. We discuss the rationale for WebCite, its technology, and how scholars, editors, and publishers can benefit from the service. Citing scholars initiate an archiving process of all cited Web references, ideally before they submit a manuscript. Authors of online documents and websites which are expected to be cited by others can ensure that their work is permanently available by creating an archived copy using WebCite and providing the citation information including the WebCite link on their Web document(s). Editors should ask their authors to cache all cited Web addresses (Uniform Resource Locators, or URLs) “prospectively” before submitting their manuscripts to their journal. Editors and publishers should also instruct their copyeditors to cache cited Web material if the author has not done so already. Finally, WebCite can process publisher submitted “citing articles” (submitted for example as eXtensible Markup Language [XML] documents) to automatically archive all cited Web pages shortly before or on publication. Finally, WebCite can act as a focussed crawler, caching retrospectively references of already published articles. Copyright issues are addressed by honouring respective Internet standards (robot exclusion files, no-cache and no-archive tags). Long-term preservation is ensured by agreements with libraries and digital preservation organizations. The resulting WebCite Index may also have applications for research assessment exercises, being able to measure the impact of Web services and published Web documents through access and Web citation metrics. @PARASPLIT [J Med Internet Res 2005;7(5):e60] In recent years scholars have built maps of science by connecting the academic fields that cite each other, are cited together, or that cite a similar literature. But since scholars cannot always publish in the fields they cite, or that cite them, these science maps are only rough proxies for the potential of a scholar, organization, or country, to enter a new academic field. Here we use a large dataset of scholarly publications disambiguated at the individual level to create a map of science-or research space-where links connect pairs of fields based on the probability that an individual has published in both of them. We find that the research space is a significantly more accurate predictor of the fields that individuals and organizations will enter in the future than citation based science maps. At the country level, however, the research space and citations based science maps are equally accurate. These findings show that data on career trajectories-the set of fields that individuals have previously published in-provide more accurate predictors of future research output for more focalized units-such as individuals or organizations-than citation based science maps. Emerging GPU architectures for high performance computing are well suited to a data-parallel programming model. This paper presents preliminary work examining a programming methodology that provides Fortran programmers with access to these emerging systems. We use array constructs in Fortran to show how this infrequently exploited, standardised language feature is easily transformed to lower-level accelerator code. The transformations in ForOpenCL are based on a simple mapping from Fortran to OpenCL. We demonstrate, using a stencil code solving the shallow-water fluid equations, that the performance of the ForOpenCL compiler-generated transformations is comparable with that of hand-optimised OpenCL code. Citation relationship between scientific publications has been successfully used for scholarly bibliometrics, information retrieval and data mining tasks, and citation-based recommendation algorithms are well documented. While previous studies investigated citation relations from various viewpoints, most of them share the same assumption that, if paper1 cites paper2 (or author1 cites author2), they are connected, regardless of citation importance, sentiment, reason, topic, or motivation. However, this assumption is oversimplified. In this study, we employ an innovative "context-rich heterogeneous network" approach, which paves a new way for citation recommendation task. In the network, we characterize 1) the importance of citation relationships between citing and cited papers, and 2) the topical citation motivation. Unlike earlier studies, the citation information, in this paper, is characterized by citation textual contexts extracted from the full-text citing paper. We also propose algorithm to cope with the situation when large portion of full-text missing information exists in the bibliographic repository. Evaluation results show that, context-rich heterogeneous network can significantly enhance the citation recommendation performance. A new form of document coupling called co-citation is defined as the frequency with which two documents are cited together. The co-citation frequency of two scientific papers can be determined by comparing lists of citing documents in the Science Citation Index and counting identical entries. Networks of co-cited papers can be generated for specific scientific specialties, and an example is drawn from the literature of particle physics. Co-citation patterns are found to differ significantly from bibliographic coupling patterns, but to agree generally with patterns of direct citation. Clusters of co-cited papers provide a new way to study the specialty structure of science. They may provide a new approach to indexing and to the creation of SDI profiles. Previous research indicates that during the past 20 years, the highest-quality work has been published in an increasingly diverse and larger group of journals. In this article, we examine whether this diversification has also affected the handful of elite journals that are traditionally considered to be the best. We examine citation patterns during the past 40 years of seven long-standing traditionally elite journals and six journals that have been increasing in importance during the past 20 years. To be among the top 5 or 1 cited papers, papers now need about twice as many citations as they did 40 years ago. Since the late 1980s and early 1990s, elite journals have been publishing a decreasing proportion of these top-cited papers. This also applies to the two journals that are typically considered as the top venues and often used as bibliometric indicators of "excellence": Science and Nature. On the other hand, several new and established journals are publishing an increasing proportion of the most-cited papers. These changes bring new challenges and opportunities for all parties. Journals can enact policies to increase or maintain their relative position in the journal hierarchy. Researchers now have the option to publish in more diverse venues knowing that their work can still reach the same audiences. Finally, evaluators and administrators need to know that although there will always be a certain prestige associated with publishing in "elite" journals, journal hierarchies are in constant flux. Historically, papers have been physically bound to the journal in which they were published; but in the digital age papers are available individually, no longer tied to their respective journals. Hence, papers now can be read and cited based on their own merits, independently of the journal's physical availability, reputation, or impact factor (IF). We compare the strength of the relationship between journals' IFs and the actual citations received by their respective papers from 1902 to 2009. Throughout most of the 20th century, papers' citation rates were increasingly linked to their respective journals' IFs. However, since 1990, the advent of the digital age, the relation between IFs and paper citations has been weakening. This began first in physics, a field that was quick to make the transition into the electronic domain. Furthermore, since 1990 the overall proportion of highly cited papers coming from highly cited journals has been decreasing and, of these highly cited papers, the proportion not coming from highly cited journals has been increasing. Should this pattern continue, it might bring an end to the use of the IF as a way to evaluate the quality of journals, papers, and researchers. © 2012 Wiley Periodicals, Inc. An overwhelming number of news articles are available every day via the internet. Unfortunately, it is impossible for us to peruse more than a handful; furthermore it is difficult to ascertain an article’s social context, i.e., is it popular, what sorts of people are reading it, etc. In this paper, we develop a system to address this problem in the restricted domain of political news by harnessing implicit and explicit contextual information from the blogosphere. Specifically, we track thousands of blogs and the news articles they cite, collapsing news articles that have highly overlapping content. We then tag each article with the number of blogs citing it, the political orientation of those blogs, and the level of emotional charge expressed in the blog posts that link to the news article. We summarize and present the results to the user via a novel visualization which displays this contextual information; the user can then find the most popular articles, the articles most cited by liberals, the articles most emotionally discussed in the political blogosphere, etc. This article challenges recent research (Evans, 2008) reporting that the concentration of cited scientific literature increases with the online availability of articles and journals. Using Thomson Reuters' Web of Science, the present article analyses changes in the concentration of citations received (2- and 5-year citation windows) by papers published between 1900 and 2005. Three measures of concentration are used: the percentage of papers that received at least one citation (cited papers); the percentage of papers needed to account for 20 , 50 , and 80 of the citations; and the Herfindahl-Hirschman index (HHI). These measures are used for four broad disciplines: natural sciences and engineering, medical fields, social sciences, and the humanities. All these measures converge and show that, contrary to what was reported by Evans, the dispersion of citations is actually increasing. © 2009 Wiley Periodicals, Inc. General purpose GPU based systems are highly attractive as they give potentially massive performance at little cost. Realizing such potential is challenging due to the complexity of programming. This paper presents a compiler based approach to automatically generate optimized OpenCL code from data-parallel OpenMP programs for GPUs. Such an approach brings together the benefits of a clear high level-language (OpenMP) and an emerging standard (OpenCL) for heterogeneous multi-cores. A key feature of our scheme is that it leverages existing transformations, especially data transformations, to improve performance on GPU architectures and uses predictive modeling to automatically determine if it is worthwhile running the OpenCL code on the GPU or OpenMP code on the multi-core host. We applied our approach to the entire NAS parallel benchmark suite and evaluated it on two distinct GPU based systems: Core i7 NVIDIA GeForce GTX 580 and Core 17 AMD Radeon 7970. We achieved average (up to) speedups of 4.51× and 4.20× (143× and 67×) respectively over a sequential baseline. This is, on average, a factor 1.63 and 1.56 times faster than a hand-coded, GPU-specific OpenCL implementation developed by independent expert programmers. Todays HPC systems are increasingly utilizing accelerators to lower time to solution for their users and reduce power consumption. To utilize the higher performance and energy efficiency of these accelerators, application developers need to rewrite at least parts of their codes. Taking the C++ flow solver ZFS as an example, we show that the directive-based programming model allows one to achieve good performance with reasonable effort, even for mature codes with many lines of code. Using OpenACC directives permitted us to incrementally accelerate ZFS, focusing on the parts of the program that are relevant for the problem at hand. The two new OpenACC 2.0 features, unstructured data regions and atomics, are required for this. OpenACC's interoperability with existing GPU libraries via the host_data use_device construct allowed to use CUDA-aware MPI to achieve multi-GPU scalability comparable to the CPU version of ZFS. Like many other codes, the data structures of ZFS have been designed with traditional CPUs and their relatively large private caches in mind. This leads to suboptimal memory access patterns on accelerators, such as GPUs. We show how the texture cache on NVIDIA GPUs can be used to minimize the performance impact of these suboptimal patterns without writing platform specific code. For the kernel most affected by the memory access pattern, we compare the initial array of structures memory layout with a structure of arrays layout. Many application developers need code that runs efficiently on multiple architectures, but cannot afford to maintain architecturally specific codes. With the addition of target directives to support offload accelerators, OpenMP now has the machinery to support performance portable code development. In this paper, we describe application ports of Kripke, Cardioid, and LULESH to OpenMP 4.5 and discuss our successes and failures. Challenges encountered include how OpenMP interacts with C++ including classes with virtual methods and lambda functions. Also, the lack of deep copy support in OpenMP increased code complexity. Finally, GPUs inability to handle virtual function calls required code restructuring. Despite these challenges we demonstrate OpenMP obtains performance within 10 of hand written CUDA for memory bandwidth bound kernels in LULESH. In addition, we show with a minor change to the OpenMP standard that register usage for OpenMP code can be reduced by up to 10 . The old Asian legend about the blind men and the elephant comes to mind when looking at how different authors of scientific papers describe a piece of related prior work. It turns out that different citations to the same paper often focus on different aspects of that paper and that neither provides a full description of its full set of contributions. In this article, we will describe our investigation of this phenomenon. We studied citation summaries in the context of research papers in the biomedical domain. A citation summary is the set of citing sentences for a given article and can be used as a surrogate for the actual article in a variety of scenarios. It contains information that was deemed by peers to be important. Our study shows that citation summaries overlap to some extent with the abstracts of the papers and that they also differ from them in that they focus on different aspects of these papers than do the abstracts. In addition to this, co-cited articles (which are pairs of articles cited by another article) tend to be similar. We show results based on a lexical similarity metric called cohesion to justify our claims. © 2008 Wiley Periodicals, Inc. Random program generation — fuzzing — is an effective technique for discovering bugs in compilers but successful fuzzers require extensive development effort for every language supported by the compiler, and often leave parts of the language space untested. We introduce DeepSmith, a novel machine learning approach to accelerating compiler validation through the inference of generative models for compiler inputs. Our approach infers a learned model of the structure of real world code based on a large corpus of open source code. Then, it uses the model to automatically generate tens of thousands of realistic programs. Finally, we apply established differential testing methodologies on them to expose bugs in compilers. We apply our approach to the OpenCL programming language, automatically exposing bugs with little effort on our side. In 1,000 hours of automated testing of commercial and open source compilers, we discover bugs in all of them, submitting 67 bug reports. Our test cases are on average two orders of magnitude smaller than the state-of-the-art, require 3.03× less time to generate and evaluate, and expose bugs which the state-of-the-art cannot. Our random program generator, comprising only 500 lines of code, took 12 hours to train for OpenCL versus the state-of-the-art taking 9 man months to port from a generator for C and 50,000 lines of code. With 18 lines of code we extended our program generator to a second language, uncovering crashes in Solidity compilers in 12 hours of automated testing.