Transactions On Parallel And Distributed Systems Research Articles

Guest Editorial: Special Section on SC19 Student Cluster Competition

Reproducibility is foundational to solid scientific and technical research, and the ability to repeat the research that produced is a key approach for confirming the validity of a new scientific discovery. The IEEE Transactions on Parallel and Distributed Systems (TPDS) is committed to enabling reproducible research through transparency and the availability and potential reuse of code. As part of its Reproducibility Initiative, TPDS is exploring post-publication peer review of code associated with articles published in TPDS. Authors who have published in TPDS can make their published article more reproducible and earn a reproducibility badge by submitting their associated code for post-publication peer review. However, the nature of the parallel and distributed systems research covered by TPDS makes it challenging to evaluate code and data challenging for reproducibility. This is because such an evaluation may require access to specific hardware, system architectures and scales, OS configurations, and so on, which may not be feasible or practical. Consequently, TPDS is exploring an alternate approach where members of the community can submit short, supplemental ‘critique’ papers that present their experiences in reproducing published results using the artifacts and/or evaluations or experiences with published artifacts. These supplemental paper submissions are reviewed and, if accepted, are linked to the original publication and are citable, serving to validate the reproducibility of the original publication. This special section, consisting of a primary paper and 6 critique papers that reproduce the results of the primary paper, is the initial pilot of this approach. The special section builds on the efforts of the SC19 Student Cluster Competition, which was part of the SC19 conference (https://sc19.supercomputing.org/) and represents a step forward in enabling reproducible research publications in parallel and distributed systems.

Leveraging the National Academies’ Reproducibility and Replication in Science Report to Advance Reproducibility in Publishing

The National Academies of Sciences, Engineering, and Medicine (NASEM) 2019 report Reproducibility and Replicability in Science addresses issues related to reproducibility and replicability across science. In this article, we explore the implications of this report and its recommendations in the publishing sphere using our experiences with the ongoing reproducibility pilot for the IEEE Transactions on Parallel and Distributed Systems (TPDS), which involves badging based on the postpublication peer review of code and other artifacts associated with articles published in TPDS, to explore key opportunities and challenges in implementing the report’s recommendations.

The Reproducibility Initiative

Reproducibility is a foundation of solid scientific and technical research. The ability to repeat research is key to confirming the validity of a scientific discovery. At IEEE Transactions on Parallel and Distributed Systems (TPDS), we are committed to enabling reproducible research through transparency and the availability and potential reuse of code. We have partnered with Code Ocean, New York, a cloud-based computational reproducibility platform, to pilot the post-publication peer review of code associated with papers published in TPDS. Authors who have published in TPDS can make their work more reproducible and earn a reproducibility badge by submitting their associated code for post-publication peer review.

Editor's Note: IEEE Transactions on Parallel and Distributed Systems (TPDS) Reproducibility Initiative, June 2019

Presents the introductory editorial for this issue of the publication.

State of the Journal

Welcome to 2018's first issue of the IEEE Transactions on Parallel and Distributed Systems (TPDS). I'm excited with my new role as incoming Editor-in-Chief (EIC) of TPDS and look forward to serving the community over the next few years. My goal as EIC is to continue to work on increasing the visibility and relevance and impact of TPDS, as well as the quality and timeliness of the review process, to ensure that TPDS is the premier Transactions in the field. The IEEE is a hallmark of quality for technical publication. The value TPDS brings to the international community is in its collection of the highest quality research that is relevant to academia, industry, and laboratories. I will investigate new opportunities for TPDS to capture the best research while maintaining its emphasis on highest quality papers. TPDS also needs to respond to a dynamic and rapidly evolving research and publication landscape. As EIC, I will work with the IEEE community to ensure that TPDS does respond appropriately, and will carefully work with the editorial board to revisit the scope and recruit new editorial board members as needed. An important and rapid growing conversation is related to the repeatability of published research and the submission of supplementary material such as code and data. I am part of this conversation, and will work with the EB and the community to explore how to bring these practices in meaningful and measured ways to TPDS.

Editor's Note

It is my great pleasure to announce that Professor Manish Parashar is appointed as the next Editor-in-Chief of the IEEE Transactions on Parallel and Distributed Systems (TPDS), with a term starting on 1 January 2018. Manish brings rich experience and leadership to TPDS, and provides significant continuity with his experience serving alongside me in his previous role as Associate Editor-in-Chief for TPDS. Manish has distinguished records of service and research leadership, and I'm pleased that he will provide excellent leadership and management of TPDS for our broad research community. Please join me in congratulating Manish on his new appointment. His brief biography appears below.

Editor's note

Summary form only given, as follows. Welcome to this year's first issue of IEEE Transactions on Parallel and Distributed Systems (TPDS). The author is privileged to serve our community proceeding into his third year as the editor-in-chief (EiC) of TPDS and looks forward to continuing his service to our growing community. Thank you to Prof. Manish Parashar from Rutgers University for his service role as the associate editor-in-chief of TPDS, and all of our associate editors. TPDS continues to be one of the healthiest IEEE Transactions. In the past 12 months, we've received 902 submissions, and reduced the time from submission to first decision from 75 days (as of January 2014) to 48 days on average now (as of November 2015). Our acceptance rate for the past 12 months is 24.4 % based upon our peer-review process and reflects a rigorous process for evaluating the top-tier research contributions in this area. TPDS is among the first IEEE Transactions to adopt the OnlinePlus publication model, and the abstract booklet and disk is distributed on a quarterly basis to subscribers. The EiC's goals are to increase the visibility and relevance of TPDS. IEEE is a hallmark of quality for technical publication. The value TPDS brings to the international community is in its collection of the highest quality research that is relevant to academia, industry, and laboratories. The topics covered by the leading research in the community change over time as technology rapidly changes in the parallel and distributed systems area, and the TPDS scope should be updated to reflect these areas of interest and 'hot topics' in the subfields of parallel and distributed systems. In 2014, the EiC worked with the community and the Computer Society to update and revise the Transaction's scope to highlight several new areas in exascale computing and big data. This revised scope brings these Transactions into better alignment with the IEEE Computer Society's flagship conferences in these areas.

State of the Journal

I am excited with my new role as incoming Editor-in-Chief (EiC) of IEEE Transactions on Parallel and Distributed Systems (TPDS) and look forward to serving the community over the next several years. As a brief introduction, I am a full professor at the Georgia Institute of Technology, and have a rich service record to the IEEE and the leading conferences and journals. One of my first official duties as incoming EIC is to recognize and thank Ivan Stojmen ovic for his dedication and service to TPDS. I'm inheriting a very healthy publication: As the former EIC, Ivan has been proactive to make TPDS one of the fastest growing among all of the transactions in the IEEE Computer and IEEE Communications Societies to accept and publish papers, within 36 weeks on average. TPDS was among the first of the IEEE transactions to adopt the OnlinePlus publication model, and the abstract booklet and disk are distributed on a quarterly basis to subscribers. My goals as EIC are to increase the visibility and relevance of TPDS. The IEEE is a hallmark of quality for technical publication. The value TPDS brings to the international community is in its collection of the highest quality research that is relevant to academia, industry, and laboratories. I will investigate new opportunities for TPDS to capture the best ideas and explore innovative ideas for partnerships with the leading parallel and distributed systems conferences in new mechanisms for publication. Last year, the scope of TPDS was updated to refl ect the latest and exciting developments in the area, such as manycore systems, network on chips, cloud computing, social networks, wireless networks, and cyber-physical systems. TPDS will continue to modify its scope to refl ect the state of the art in the research areas of parallel and distributed systems. I expect a very active discussion of the TPDS editorial board as we continue to modernize the scope by incorporating 'hot topic' areas.

Editor's Note: EIC Farewell and New EIC Introduction

IT is my great pleasure to announce that Professor David Bader has appointed as the next Editor-in-Chief of the IEEE Transactions on Parallel and Distributed Systems (TPDS), who will start his term on 1 January 2014. David has a highly distinguished academic career. I am quite sure that he will provide excellent leadership and bring a great deal of technical and managerial experience to TPDS. Please join me in congratulating David on his appointment. His brief biography appears below. As my term as Editor-in-Chief ends, I thought you would be interested in knowing how we are doing in TPDS. I have listed a few statistics during my term 2010-2013. The number of submissions doubled from 681 in 2009 to 1,272 in 2012 (and 1,322 for a year ending 31 August 2013). The number of editors also doubled, from 32 to the current number 66. The acceptance rate is approximately 25 percent. The average time from submission to the fi rst decision has been reduced from 4 months to 80 days, while it took, on average, 90 days from submission to the fi nal decision. The average time from submission to online publication has been reduced from 43 weeks to 36 weeks (median is 33 weeks), and each accepted paper has received at least three reviews. As you can see, we are a highly competitive journal with a fast turnaround time similar to conferences. However, the added advantage of submitting to our journal is getting detailed reviews with a possibility of addressing the drawbacks in a paper through a major revision. This does not happen in conferences. I attended three times each IPDPS and ICDCS, two main related conferences, to meet our editors and authors and attend steering committee meetings. To control the backlog (currently about one year from acceptance date to the scheduled publication date), I pioneered the division of papers into the main fi le plus supplementary one, with the main fi le restricted to currently 10 pages (reduced from 14) and with supplementary fi le with the text of practically unlimited size. A by-product of this conversion was increased readability of the main fi le; to help it further, one of my editorials was devoted to presenting articles with the goal of minimizing the time for a reader to understand the essence of the contribution. I was extremely lucky and honored to be given this leadership opportunity, and would like to thank many people who have made my tenure as Editor-in-Chief both rewarding and enjoyable. I am especially grateful to the staff in the publication offi ce of the IEEE Computer Society, Pam Gimzo and Carrie James for their help in day-to-day operation of the paper review and publication process, and Hilda Carman, Erin Espriu, Joyce Arnold, and Alicia Stickley for their help in many administrative and production matters related to TPDS. I often rely on their expertise to resolve diffi cult issues related to the paper review process. Last, but not the least, I would like to thank all of our authors, reviewers, and associate editors for their support and hard work for TPDS during the past four years. About 5,000 reviews were made in 2012, to select papers for TPDS, and efforts by reviewers receive little visibility due to the anonymous nature of reports. The IEEE CS started, at the end of 2012, the Reviewer Appreciation Program, to recognize distinguished reviewers for each transaction (see the April 2013 editorial of TPDS). The key enabler for this program is the reviewer statistics, which is made available by S1M, following my few requests in 2010 and 2011. I used it in making decisions on new TPDS editors (as one of factors). The information fi nally became available (for all CS transactions) in a reasonable size (excel) and sortable fi le during 2012. The scope of TPDS has been recently updated to refl ect the latest and exiting developments in the area, such as many-core systems, network on chips, cloud computing, social networks, wireless networks, and cyber-physical systems. I hope you will continue to submit your best papers to TPDS and continue our effort to keep TPDS the fl agship journal in the fi eld of parallel and distributed systems.

Editor's note: Reviewer appreciation program

The IEEE Computer Society (CS) established the Reviewer Appreciation Program (RAP) at the end of 2012, to recognize Distinguished Reviewers. The key enabler for this program is the reviewer statistics, which are made available by S1M. I requested these statistics in 2010 for IEEE Transactions on Parallel and Distributed Systems (TPDS) and used them in making decisions on new TPDS editors (as one of factors) in 2011. The information fi nally became available (for all CS transactions) in a reasonable size (Excel) file during 2012, sortable by any column. Therefore, EICs are able to see a list of reviewers sorted by the number of submitted reviews for any time period. RAP intends to recognize our Distinguished Reviewers at the end of each year. Editors were asked to nominate their top quality reviewers (which have no COI with them) for reviews made in 2012. Following 6 nominations by editors, 3 winners (Gilbert Hendry, Zubair Md. Fadlullah, and Ben Leong) were selected. The Outstanding Reviewer Service Award for the TPDS All-Time Most Prolific Reviewer is awarded to Yu-Kwong (Ricky) Kwok. He appears to be our star reviewer called by many editors, and was discovered only by this program (and was immediately invited to become a TPDS editor; please see his short biography). He made, by far, the most reviews (57; 44 as Yu-Kwong plus 13 as Ricky, which came as two separate entries in the file) made for TPDS. Other winners are Jelena Misic (37 reviews), Yu Wang (33), Yingshu Li (32), Jiangchuan Liu (32), Kui Ren (31), Chuan Wu (31), Weisong Shi (28), Haiying Shen (27), Nathalie Mitton (25), Govindarasu Manimaran (24), Song Jiang (23), Hongyi Wu (23), Tian He (22), Xue Liu (22), Henri Casanova (21), Bin Xiao (21), Hannes Frey (20), Mo Li (20), Hai Liu (20), Guoliang Xing (20), Wei Yu (20), Dror Feitelson (19), Stella Kafetzoglou (19), and Qun Li (19). Three of them are new TPDS editors and featured below.

Call for Papers for IEEE Transactions on Parallel and Distributed Systems (TPDS) Special Issue on Cloud Computing

Call for Papers for IEEE Transactions on Parallel and Distributed Systems (TPDS) Special Issue on Cloud Computing

Call for Papers for a Special Issue of IEEE Transactions on Parallel and Distributed Systems (TPDS) on Cyber-Physical Systems (CPS)

Call for Papers for a Special Issue of IEEE Transactions on Parallel and Distributed Systems (TPDS) on Cyber-Physical Systems (CPS)

Guest Editors' Introduction: Special Section on Many-Task Computing

IT is our honor to serve as guest editors of this special section of the IEEE Transactions on Parallel and Distributed Systems (TPDS) on many-task computing (MTC). This section focuses on the methods required to manage and execute large multiple program multiple data (MPMD) computations on large clusters, grids, clouds, and supercomputers. We are pleased to present 10 high-quality contributions chosen from 42 submissions, on resource management, data-intensive computing, applications, and MTC on supercomputers, grids, and clouds. We introduce the term many-task computing (MTC) [2] for computations that bridge the gap between high-performance computing (HPC) and high-throughput computing (HTC) [1]. MTC differs from HTC in its emphasis on using many computing resources over short periods of time to accomplish many computational tasks (both dependent and independent), for which primary metrics are measured in seconds (e.g., FLOPS, tasks/sec., MB/s I/O rates), as opposed to jobs per month. MTC computations comprise multiple distinct activities, coupled via files, shared memory, or message passing. Tasks may be small or large, uniprocessor or multiprocessor, or compute-intensive or data-intensive. The set of tasks may be static or dynamic, homogeneous or heterogeneous, or loosely coupled or tightly coupled. The number of tasks, quantity of computing, and volumes of data may be large. Today’sHPCsystemsareaviableplatformforMTC[3],but large MTC applications can stress HPC hardware and sotware. Challenges include local resource manager scalability and granularity, efficient utilization of raw hardware, parallel file system contention and scalability, data management, I/O management, reliability at scale, application scalability, and understanding the limitations of HPC systems in order to identify good candidate MTC applications [4]. MTC applications can also be executed on cloud systems, but face other challenges there, for example, relating to internode communication performance. Three recent MTC workshops (MTAGS, http://dsl.cs. uchicago.edu/MTAGS10/) and this special section attracted 142 abstracts and 110 paper submissions, from which 41 papers were accepted. Papers covered resource management, data-intensive computing, applications, and MTC on supercomputers, grids, and clouds. More than 1,000 people have participated as coauthors, program committee members, reviewers, and attendees in these venues. We are well beyond a critical mass for a new, thriving community, which is quickly expanding.

Editorial: EIC Farewell and New EIC Introduction

TPDS Editorial: EIC Farewell and New EIC Introduction

Editorial: Special Section on High-Performance Computational Biology

OVER the past decade, computational molecular biology has grown into a mature discipline with a well-defined body of core knowledge, and participation from a large and diverse group of researchers. To keep pace with the explosive growth in research in this field, a number of high quality journals and annual conferences have been established. Many universities are actively building academic programs and research centers and groups in computational biology. As a reflection of the maturing of the field, numerous textbooks on computational biology and its various subtopics have been written in recent years, and undergraduate programs are underway. Despite this progress, computational biology continues to be a vibrant discipline with many outstanding research problems and potential for new avenues of investigation for decades to come. We broadly view high-performance computational biology as the development and application of high-performance computing techniques for extending the reach or scale of investigations in computational biology. A major component of this is the development of parallel and distributed algorithms, and programming environments and systems for aiding biological investigations using highperformance parallel computers, grid computing, and emerging architectures. There is a compelling need for such research given the explosive growth in biological information, the complexity of interactions that underlie many biological processes, and the diversity and interconnectedness of organisms at the molecular level. However, research in high-performance computational biology has not grown as rapidly as computational biology itself. There are subfields of computational biology which have not seen significant influx of ideas from the high-performance computing community. This is perhaps a reflection of the confluence of expertise needed to conduct research in high-performance computational biology, which sets up a barrier to entry for new researchers. Efforts spent in transgressing the barrier are worthwhile given the opportunities for high impact research. By bringing together research in this area as a special section, we hope to provide a resource for IEEE Transactions on Parallel and Distributed Systems (TPDS) readers interested in this field and aid the entry of new researchers into the field. The arguments in favor of a sustained effort in highperformance computational biology are stronger than ever. New high-throughput sequencing machines introduced within the last year, such as those from 454 Life Sciences Inc., have significantly accelerated sequencing capabilities. Using 454 sequencing systems, it is possible to sequence as many as 200,000 short DNA fragments in a 4 hour experiment for a few thousand dollars. These machines are increasingly being used to sample transcriptomes of many organisms. The sequencing of several complex plant genomes is underway starting with maize and sorghum. Similar to large-scale genome sequencing projects, comprehensive gene expression profile measurement projects are underway to conduct large-scale microarray experiments on an organism spanning various organs, diesease/stress induced states, and developmental stages. Forays into personalized medicine, rational drug design, large-scale systems biology, such as the study of protein-protein interaction networks at the whole organism level, understanding evolutionary relationships and building the tree of life, all require processing vast amounts of data or carrying out highly complex computational tasks. In this special section, we showcase some of the recent work in high-performance computational biology. In addition to the open call for papers, authors whose work was published in the 2005 IEEE International Workshop on HighPerformance Computational Biology (HiCOMB, http:// www.hicomb.org) were solicited to submit extended versions of their papers. Each manuscript submitted to the special section was subjected to rigorous, independent peer review by three to four reviewers. We are extremely grateful to all the reviewers who agreed and delivered on providing thoughtful reviews within the time constraints imposed for the special issue. Based on the reviewer suggestions and our own reading of the manuscripts, six manuscripts were selected for publication in the special section. The first paper in this special issue is on a scalable implementation of the widely used BLAST search program for homology detection between a query sequence and a database of known sequences. In “ScalaBLAST: A Scalable Implementation of BLAST for High-Performance DataIntensive Bioinformatics Analysis,” Christopher Oehmen and Jarek Nieplocha report on ScalaBLAST, a high-performance sequence alignment program they developed to enable applications that require thousands to millions of queries to be performed simultaneously. Such queries are used in applications such as multiple genome/proteome comparisons, and in finding genes in newly sequenced genomes. By using a combination of techniques, including target database distribution, exploiting multilevel parallelism, parallel I/Os and latency hiding, the authors achieve a scalable implementation of this ubiquitous search program. IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS, VOL. 17, NO. 8, AUGUST 2006 737

Editorial: A Message from the New Editor-in-Chief

1045-9219/06/$20.00 © 2006 IEEE Published by the IEEE Computer Society For information on obtaining reprints of this article, please send e-mail to: tpds@computer.org. I T is a great privilege and honor to serve as the Editor-in-Chief (EIC) of the IEEE Transactions on Parallel and Distributed Systems (TPDS). TPDS is a relatively young journal that started in 1990, yet it has become the premier outlet for research publications in the parallel and distributed processing area. The credit for this accomplishment goes to all the four previous EICs, associate editors, reviewers, and the authors who submitted their papers to TPDS for publication. Currently, the first review turn around time for a submission is below six months, meaning that a paper can get accepted for TPDS as fast as a conference. At the same time, a paper submitted to TPDS can go through minor or major revision and, finally, get accepted, which is not possible in conferences. The timely review and publication of papers in TPDS is now possible because of the combined effort of the last EIC, Pen-Chung Yew, and his staff. While I am assuming the EIC job in a very comfortable position with regard to visibility and publication timing, there are a few challenges that need our urgent attention. TPDS was born while research in the area of parallel processing was at its peak. Also, the competition with other journals and conferences was not that fierce. Now, we need to take a closer look at the scope of TPDS and revise it to include emerging areas, technological advancements, and experimental results in the systems area to boost the number of submissions. I shall invite well-recognized researchers to organize special issues and appoint some of them to the editorial board. I also plan to appoint an associate Editor-in-Chief to help me in various areas. In order to reduce the delay in publication further, I would urge the associate editors to administratively reject submissions if the research is outdated, and cut down on major revisions, recommending some of them for new submission after revision. I would urge understanding on the part of authors if they are advised to do so. I would also request the associate editors to review some papers themselves instead of waiting for the reviewer’s response indefinitely. The TPDS staff will closely monitor the review time of a paper and bring it to our attention if such an action is needed. An IEEE Transactions cannot gain a good reputation without the active support and participation of the research community in the area. I invite you to send me your suggestions to further enhance the quality and visibility of the TPDS. I look forward to working with you during the next two years to take TPDS to the next level of excellence.