An exploration of CUDA and CBEA for a gravitational wave data-analysis application (Einstein@Home)

We present a detailed approach for making use of two new computer hardware architectures -- CBEA and CUDA -- for accelerating a scientific data-analysis application (Einstein@Home). Our results suggest that both the architectures suit the application quite well and the achievable performance in the same software developmental time-frame, is nearly identical.Comment: Accepted for publication in International Conference on Parallel Processing and Applied Mathematics (PPAM 2009

Testing systems of identical components

We consider the problem of testing sequentially the components of a multi-component reliability system in order to figure out the state of the system via costly tests. In particular, systems with identical components are considered. The notion of lexicographically large binary decision trees is introduced and a heuristic algorithm based on that notion is proposed. The performance of the heuristic algorithm is demonstrated by computational results, for various classes of functions. In particular, in all 200 random cases where the underlying function is a threshold function, the proposed heuristic produces optimal solutions

Inclusive Cost Attribution for Cache Use Profiling

AbstractFor performance analysis tools to be useful, they need to show the relation of detected bottlenecks to source code. To this end, it often makes sense to use the instruction triggering a problematic event. However for cache line utilization, information on usage is only available at eviction time, but may be better attributed to the instruction which loaded the line. Such attribution is impossible with current processor hardware. Callgrind, a cache simulator part of the open-source Valgrind tool, can do this. However, it only provides Self Costs. In this paper, we extend the cost attribution of cache use metrics to inclusive costs which helps for top-down analysis of complex workloads. The technique can be used for all event types where collected metrics should to be attributed to instructions executing earlier in a program run to be useful

Building community broadband: Barriers and opportunities for community‐based organizations in the federal BTOP and BIP broadband development programs

Despite $7.2 billion of recent federal investments in broadband infrastructure through the Broadband Technology Opportunities and Broadband Initiatives Programs (BTOP and BIP), questions around the effectiveness of such national‐scale initiatives at the local level remain. Drawing on ethnographic interviews, observation, and documentary evidence, this paper charts the experience of twenty‐seven grassroots and community‐based organizations (CBOs) from around the country that have engaged the BTOP and BIP process. We explore the challenges CBOs have faced in initiating, developing partnerships, and executing BTOP and BIP grant applications. We find that CBOs often struggled to define the effective scope of potential BTOP projects; to align these with traditional organizational goals; to develop effective project partnerships, including with larger and more institutionalized partners; and to meet the formal evaluation, reporting, and management requirements of a large‐scale and sensitive federal program. Despite these barriers, several community‐based organizations have engaged in successful BTOP and BIP applications, which are now moving into operational stage. This paper documents these experiences, and concludes with recommendations for reform of the BTOP, BIP, or possible successor programs that could improve the inclusion and effectiveness of community‐based organizations as agents of broadband development and social change.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/90169/1/14504801169_ftp.pd

On the Ballot for Nov. 2, 2021: the Constitutional Amendment on Redistricting

On November 2, 2021, New York State voters will be asked to approve a constitutional amendment revising the redistricting process to be based on the 2020 census. If the constitutional amendment is approved, the changes will take effect on January 1, 2022. This amendment is necessary to address delays in the census created by the pandemic and to accommodate New York State’s change from a September primary to an earlier June primary for both federal and state elections. These changes compressed the time needed to complete the redistricting. Without these changes, it is possible that the new districts will not be ready in time for the political process to function

On the size of binary decision diagrams representing Boolean functions

AbstractWe consider the size of the representation of Boolean functions by several classes of binary decision diagrams (BDDs) (also called branching programs), namely the classes of arbitrary BDDs of real time BDD (RBDD) (i.e. BDDs where each computation path is limited to the number of variables), of free BDDs (FBDDs) (also called read-once-only branching programs), of ordered BDDs (OBDDS) i.e. FBDDs where variables are tested in the same order along all paths), and binary decision trees (BDTs).Using well-known techniques, we first establish asymptotically sharp bounds as a function of n on the minimum size of arbitrary BDDs representing almost all Boolean functions of n variables and provide asymptotic lower and upper bounds, differing only by a factor of two, on the minimum size OBDDs representing almost all Boolean functions of n variables.We then, using a method to obtain exponential lower bounds on complexity of computation of Boolean functions by RBDD, FBDD and OBDD that originated in (Breitbart, 1968), present the highest such bounds to date and also present improved bounds on the relative economy of description of particular Boolean functions by the above classes of BDDs. For each nontrivial pair of BDD classes considered, we exhibit infinite families of Boolean functions representable much more concisely by BDDs in one class than by BDDs in the other

The Role of Social Anarchism and Geography in Constructing a Radical Agenda: A Response to David Harvey

David Harvey’s response to Simon Springer (2014) raises important questions about the places from which to draw ideas for a radical geography agenda. Nevertheless, Harvey ignores critical contributions that social anarchists (including social geographers) have made to understanding both the theory and practice of social transformation. We draw on studies of the anarchist movement in Spain before and during the Spanish Civil War to explore some of what social anarchism has to contribute to geography and contemporary struggles for a more equitable society

RNA Viral Community in Human Feces: Prevalence of Plant Pathogenic Viruses

The human gut is known to be a reservoir of a wide variety of microbes, including viruses. Many RNA viruses are known to be associated with gastroenteritis; however, the enteric RNA viral community present in healthy humans has not been described. Here, we present a comparative metagenomic analysis of the RNA viruses found in three fecal samples from two healthy human individuals. For this study, uncultured viruses were concentrated by tangential flow filtration, and viral RNA was extracted and cloned into shotgun viral cDNA libraries for sequencing analysis. The vast majority of the 36,769 viral sequences obtained were similar to plant pathogenic RNA viruses. The most abundant fecal virus in this study was pepper mild mottle virus (PMMV), which was found in high concentrations—up to 10(9) virions per gram of dry weight fecal matter. PMMV was also detected in 12 (66.7%) of 18 fecal samples collected from healthy individuals on two continents, indicating that this plant virus is prevalent in the human population. A number of pepper-based foods tested positive for PMMV, suggesting dietary origins for this virus. Intriguingly, the fecal PMMV was infectious to host plants, suggesting that humans might act as a vehicle for the dissemination of certain plant viruses

The Third Age of Phage

The third age of phage has begun with the recognition that phages may be key to the great planetary biogeochemical cycles and represent the greatest potential genetic resource in the biospher

FastGroupII: A web-based bioinformatics platform for analyses of large 16S rDNA libraries

BACKGROUND: High-throughput sequencing makes it possible to rapidly obtain thousands of 16S rDNA sequences from environmental samples. Bioinformatic tools for the analyses of large 16S rDNA sequence databases are needed to comprehensively describe and compare these datasets. RESULTS: FastGroupII is a web-based bioinformatics platform to dereplicate large 16S rDNA libraries. FastGroupII provides users with the option of four different dereplication methods, performs rarefaction analysis, and automatically calculates the Shannon-Wiener Index and Chao1. FastGroupII was tested on a set of 16S rDNA sequences from coral-associated Bacteria. The different grouping algorithms produced similar, but not identical, results. This suggests that 16S rDNA datasets need to be analyzed in multiple ways when being used for community ecology studies. CONCLUSION: FastGroupII is an effective bioinformatics tool for the trimming and dereplication of 16S rDNA sequences. Several standard diversity indices are calculated, and the raw sequences are prepared for downstream analyses