Parallel Computing最新文献

{"title":"Task graph-based performance analysis of parallel-in-time methods","authors":"Matthias Bolten,&nbsp;Stephanie Friedhoff,&nbsp;Jens Hahne","doi":"10.1016/j.parco.2023.103050","DOIUrl":"https://doi.org/10.1016/j.parco.2023.103050","url":null,"abstract":"<div><p>In this paper, we present a performance model based on task graphs for various iterative parallel-in-time (PinT) methods. PinT methods have been developed to speed up the simulation time of time-dependent problems using modern parallel supercomputers<span>. The performance model is based on a data-driven notation of the methods, from which a task graph is generated. Based on this task graph and a distribution of time points across processes typical for PinT methods, a theoretical lower runtime bound for the method can be obtained, as well as a prediction of the runtime for a given number of processes. In particular, the model is able to cover the large parameter space of PinT methods and make predictions for arbitrary parameter settings. Here, we describe a general procedure for generating task graphs based on three iterative PinT methods, namely, Parareal, multigrid-reduction-in-time (MGRIT), and the parallel full approximation scheme in space and time (PFASST). Furthermore, we discuss how these task graphs can be used to analyze the performance of the methods. In addition, we compare the predictions of the model with parallel simulation times using five different PinT libraries.</span></p></div>","PeriodicalId":54642,"journal":{"name":"Parallel Computing","volume":"118 ","pages":"Article 103050"},"PeriodicalIF":1.4,"publicationDate":"2023-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49881776","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Distributed software defined network-based fog to fog collaboration scheme","authors":"Muhammad Kabeer ,&nbsp;Ibrahim Yusuf ,&nbsp;Nasir Ahmad Sufi","doi":"10.1016/j.parco.2023.103040","DOIUrl":"https://doi.org/10.1016/j.parco.2023.103040","url":null,"abstract":"<div><p><span><span>Fog computing was created to supplement the cloud in bridging the communication delay gap by deploying fog nodes nearer to </span>Internet of Things<span> (IoT) devices. Depending on the geographical location, computational resource and rate of IoT requests, fog nodes can be idle or saturated. The latter requires special mechanism to enable collaboration with other nodes through service offloading to improve resource utilization. Software Defined Network (SDN) comes with improved bandwidth, latency and understanding of </span></span>network topology<span>, which recently attracted researchers attention and delivers promising results in service offloading. In this study, a Hierarchical Distributed Software Defined Network-based (DSDN) fog to fog collaboration model is proposed; the scheme considers computational resources such as available CPU and network resources such as communication hops of a prospective offloading node. Fog nodes having limited resources coupled with the projected high demand for fog services in the near future, the model also accounts for extreme cases in which all nearby nodes in a fog domain are saturated, employing a supervisor controller to scale the collaboration to other domains. The results of the simulations carried out on Mininet shows that the proposed multi-controller DSDN solution outperforms the traditional single controller SDN solution, it also further demonstrate that increase in the number of fog nodes does not affect service offloading performance significantly when multiple controllers are used.</span></p></div>","PeriodicalId":54642,"journal":{"name":"Parallel Computing","volume":"117 ","pages":"Article 103040"},"PeriodicalIF":1.4,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49877856","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Optimizing massively parallel sparse matrix computing on ARM many-core processor","authors":"Jiang Zheng ,&nbsp;Jiazhi Jiang ,&nbsp;Jiangsu Du,&nbsp;Dan Huang,&nbsp;Yutong Lu","doi":"10.1016/j.parco.2023.103035","DOIUrl":"https://doi.org/10.1016/j.parco.2023.103035","url":null,"abstract":"<div><p><span><span>Sparse matrix multiplication is ubiquitous in many applications such as graph processing and numerical simulation. In recent years, numerous efficient sparse matrix multiplication algorithms and computational libraries have been proposed. However, most of them are oriented to x86 or GPU platforms, while the optimization on ARM many-core platforms has not been well investigated. Our experiments show that existing sparse matrix multiplication libraries for ARM many-core CPU cannot achieve expected parallel performance. Compared with traditional multi-core CPU, ARM many-core CPU has far more cores and often adopts </span>NUMA techniques to scale the </span>memory bandwidth. Its parallel efficiency tends to be restricted by NUMA configuration, memory bandwidth cache contention, etc.</p><p>In this paper, we propose optimized implementations for sparse matrix computing on ARM many-core CPU. We propose various optimization techniques for several routines of sparse matrix multiplication to ensure coalesced access<span> of matrix elements in the memory. In detail, the optimization techniques include a fine-tuned CSR-based format for ARM architecture, co-optimization of Gustavson’s algorithm with hierarchical cache and dense array strategy to mitigate performance loss caused by handling compressed storage formats. We exploit the coarse-grained NUMA-aware strategy for inter-node parallelism and the fine-grained cache-aware strategy for intra-node parallelism to improve the parallel efficiency of sparse matrix multiplication. The evaluation shows that our implementation consistently outperforms the existing library on ARM many-core processor.</span></p></div>","PeriodicalId":54642,"journal":{"name":"Parallel Computing","volume":"117 ","pages":"Article 103035"},"PeriodicalIF":1.4,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49877864","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Editorial on Advances in High Performance Programming","authors":"A. Marowka, Przemysław Stpiczyński","doi":"10.1016/j.parco.2023.103037","DOIUrl":"https://doi.org/10.1016/j.parco.2023.103037","url":null,"abstract":"","PeriodicalId":54642,"journal":{"name":"Parallel Computing","volume":"117 1","pages":"103037"},"PeriodicalIF":1.4,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"55107714","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Parallelizable efficient large order multiple recursive generators","authors":"L. Deng, Bryan R. Winter, J. H. Shiau, Henry Horng-Shing Lu, Nirman Kumar, Ching-Chi Yang","doi":"10.2139/ssrn.4344139","DOIUrl":"https://doi.org/10.2139/ssrn.4344139","url":null,"abstract":"","PeriodicalId":54642,"journal":{"name":"Parallel Computing","volume":"78 1","pages":"103036"},"PeriodicalIF":1.4,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73726981","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Finding inputs that trigger floating-point exceptions in heterogeneous computing via Bayesian optimization","authors":"Ignacio Laguna ,&nbsp;Anh Tran ,&nbsp;Ganesh Gopalakrishnan","doi":"10.1016/j.parco.2023.103042","DOIUrl":"https://doi.org/10.1016/j.parco.2023.103042","url":null,"abstract":"<div><p><span><span>Testing code for floating-point exceptions is crucial as exceptions can quickly propagate and produce unreliable numerical answers. The state-of-the-art to test for floating-point exceptions in heterogeneous systems<span> is quite limited and solutions require the application’s source code, which precludes their use in accelerated libraries where the source is not publicly available. We present an approach to find inputs that trigger floating-point exceptions in black-box CPU or </span></span>GPU functions, i.e., functions where the source code and information about input bounds are unavailable. Our approach is the first to use Bayesian optimization (BO) to identify such inputs and uses novel strategies to overcome the challenges that arise in applying BO to this problem. We implement our approach in the </span><span><span>Xscope</span></span> framework and demonstrate it on 58 functions from the CUDA Math Library and 81 functions from the Intel Math Library. <span><span>Xscope</span></span> is able to identify inputs that trigger exceptions in about 73% of the tested functions.</p></div>","PeriodicalId":54642,"journal":{"name":"Parallel Computing","volume":"117 ","pages":"Article 103042"},"PeriodicalIF":1.4,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49877859","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Parallelizable efficient large order multiple recursive generators","authors":"Lih-Yuan Deng ,&nbsp;Bryan R. Winter ,&nbsp;Jyh-Jen Horng Shiau ,&nbsp;Henry Horng-Shing Lu ,&nbsp;Nirman Kumar ,&nbsp;Ching-Chi Yang","doi":"10.1016/j.parco.2023.103036","DOIUrl":"https://doi.org/10.1016/j.parco.2023.103036","url":null,"abstract":"<div><p>The general multiple recursive generator (MRG) of maximum period has been thought of as an excellent source of pseudo random numbers. Based on a <span><math><mi>k</mi></math></span>th order linear recurrence modulo <span><math><mi>p</mi></math></span><span>, this generator produces the next pseudo random number based on a linear combination of the previous </span><span><math><mi>k</mi></math></span> numbers. General maximum period MRGs of order <span><math><mi>k</mi></math></span> have excellent empirical performance, and their strong mathematical foundations have been studied extensively.</p><p><span>For computing efficiency, it is common to consider special MRGs with some simple structure with few non-zero terms which requires fewer costly multiplications. However, such MRGs will not have a good “spectral test” property when compared with general MRGs with many non-zero terms. On the other hand, there are two potential problems of using general MRGs with many non-zero terms: (1) its efficient implementation (2) its efficient scheme for its parallelization. Efficient implementation of general MRGs of larger order </span><span><math><mi>k</mi></math></span> can be difficult because the <span><math><mi>k</mi></math></span>th order linear recurrence requires many costly multiplications to produce the next number. For its parallelization scheme, for a large <span><math><mi>k</mi></math></span>, the traditional scheme like “jump-ahead parallelization method” for general MRGs becomes highly computationally inefficient. We proposed implementing maximum period MRGs with many nonzero terms efficiently and in parallel by using a MCG constructed from the MRG. In particular, we propose a special class of large order MRGs with many nonzero terms that also have an efficient and parallel implementation.</p></div>","PeriodicalId":54642,"journal":{"name":"Parallel Computing","volume":"117 ","pages":"Article 103036"},"PeriodicalIF":1.4,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49877863","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An optimal scheduling algorithm considering the transactions worst-case delay for multi-channel hyperledger fabric network","authors":"Ou Wu ,&nbsp;Shanshan Li ,&nbsp;He Zhang ,&nbsp;Liwen Liu ,&nbsp;Haoming Li ,&nbsp;Yanze Wang ,&nbsp;Ziyi Zhang","doi":"10.1016/j.parco.2023.103041","DOIUrl":"https://doi.org/10.1016/j.parco.2023.103041","url":null,"abstract":"<div><p><span><span>As the most popular consortium blockchain platform, Hyperledger Fabric (Fabric for short) has released multiple versions that support different consensus protocols to address the risks faced in current and future network transactions. For example, Fabric v1.4 and v2.0 use Kafka and Raft mechanisms to complete consensus and ensure that the system can withstand failures such as crashes, </span>network partitions, or network shutdowns. In a multi-channel Fabric </span>network architecture, the system structure cannot guarantee the behavior of malicious nodes. Complex cooperation between peer groups on different channels can greatly affect the security and efficiency of the entire network architecture, which is challenging to estimate and optimize.</p><p><span><span>To address this challenge, we designed a Drift Plus Penalty Algorithm (DPPA) and a Transaction Worst-case Delay Algorithm (TWDA) based on peer node random scheduling using the Lyapunov optimization framework. The DPPA ensures the stability of the system and provides the maximum </span>transaction processing rate under the minimum safety probability. The numerical results show that this algorithm can achieve a good balance between system security probability and queue accumulation. The TWDA considers discarding transactions with excessively long </span>delay time by setting a worst-case transaction delay threshold. When considering both the security probability and queue accumulation of the Fabric system, the optimal scheduling of peer nodes is given. Numerical simulations were conducted on two types of algorithms, and the results showed that the security of the TWDA was slightly worse than that of the DPPA, but the system queue accumulation was significantly smaller. Therefore, the simulation results not only validate the effectiveness of the two types of algorithms but also provide operators with operational strategies that consider different factors.</p></div>","PeriodicalId":54642,"journal":{"name":"Parallel Computing","volume":"117 ","pages":"Article 103041"},"PeriodicalIF":1.4,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49877860","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Optimizing massively parallel sparse matrix computing on ARM many-core processor","authors":"Jiang Zheng, Jiazhi Jiang, Jiangsu Du, Dan-E Huang, Yutong Lu","doi":"10.1016/j.parco.2023.103035","DOIUrl":"https://doi.org/10.1016/j.parco.2023.103035","url":null,"abstract":"","PeriodicalId":54642,"journal":{"name":"Parallel Computing","volume":"117 1","pages":"103035"},"PeriodicalIF":1.4,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"55107333","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ESA: An efficient sequence alignment algorithm for biological database search on Sunway TaihuLight","authors":"Hao Zhang ,&nbsp;Zhiyi Huang ,&nbsp;Yawen Chen ,&nbsp;Jianguo Liang ,&nbsp;Xiran Gao","doi":"10.1016/j.parco.2023.103043","DOIUrl":"https://doi.org/10.1016/j.parco.2023.103043","url":null,"abstract":"<div><p>In computational biology, biological database search has been playing a very important role. Since the COVID-19 outbreak, it has provided significant help in identifying common characteristics of viruses and developing vaccines and drugs. Sequence alignment<span><span>, a method finding similarity, </span>homology<span> and other information between gene/protein sequences, is the usual tool in the database search. With the explosive growth of biological databases, the search process has become extremely time-consuming. However, existing parallel sequence alignment algorithms cannot deliver efficient database search due to low utilization of the resources such as cache memory and performance issues such as load imbalance and high communication overhead<span><span>. In this paper, we propose an efficient sequence alignment algorithm on Sunway TaihuLight, called ESA, for biological database search. ESA adopts a novel hybrid alignment algorithm combining local and global alignments, which has higher accuracy than other sequence alignment algorithms. Further, ESA has several optimizations including cache-aware sequence alignment, capacity-aware load balancing and bandwidth-aware data transfer. They are implemented in a heterogeneous processor SW26010 adopted in the world’s 6th fastest supercomputer<span><span>, Sunway TaihuLight. The implementation of ESA is evaluated with the Swiss-Prot database on Sunway TaihuLight and other platforms. Our experimental results show that ESA has a speedup of 34.5 on a single core group (with 65 cores) of Sunway TaihuLight. The strong and weak scalabilities of ESA are tested with 1 to 1024 core groups of Sunway TaihuLight. The results show that ESA has linear weak scalability and very impressive strong scalability. For strong scalability, ESA achieves a speedup of 338.04 with 1024 core groups compared with a single core group. We also show that our proposed optimizations are also applicable to GPU, Intel </span>multicore processors, and </span></span>heterogeneous computing platforms.</span></span></span></p></div>","PeriodicalId":54642,"journal":{"name":"Parallel Computing","volume":"117 ","pages":"Article 103043"},"PeriodicalIF":1.4,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49877449","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}