PARALLEL, SPACE-EFFICIENT HASH TABLE RESIZE

Methods, systems, and apparatus, including computer programs encoded on a computer storage medium, for parallel, space-efficient hash table resize. An aspect may include a hash table that may be resized by incrementally de-allocating buckets of an old hash table and incrementally allocating buckets of a new hash table. Additionally or alternatively, an aspect may include a hash table that may be resized by re-allocating buckets from the old hash table to the new hash table and then re-arranging the buckets of the new hash table. Additionally or alternatively, an aspect may include a hash table with chaining that may be resized by copying the elements of the old hash table to corresponding buckets of the new hash table and indicating which elements are not necessarily in a final position. After copying, final positions may be determined for the buckets that are indicated as not necessarily in a final position. Additionally or alternatively, an aspect may include parallezing algorithms for resizing hash tables

Sparse Tensor Transpositions

We present a new algorithm for transposing sparse tensors called Quesadilla. The algorithm converts the sparse tensor data structure to a list of coordinates and sorts it with a fast multi-pass radix algorithm that exploits knowledge of the requested transposition and the tensors input partial coordinate ordering to provably minimize the number of parallel partial sorting passes. We evaluate both a serial and a parallel implementation of Quesadilla on a set of 19 tensors from the FROSTT collection, a set of tensors taken from scientific and data analytic applications. We compare Quesadilla and a generalization, Top-2-sadilla to several state of the art approaches, including the tensor transposition routine used in the SPLATT tensor factorization library. In serial tests, Quesadilla was the best strategy for 60% of all tensor and transposition combinations and improved over SPLATT by at least 19% in half of the combinations. In parallel tests, at least one of Quesadilla or Top-2-sadilla was the best strategy for 52% of all tensor and transposition combinations.Comment: This work will be the subject of a brief announcement at the 32nd ACM Symposium on Parallelism in Algorithms and Architectures (SPAA '20

High quality graph-based similarity search

SimRank is an influential link-based similarity measure that has been used in many fields of Web search and sociometry. The best-of-breed method by Kusumoto et. al., however, does not always deliver high-quality results, since it fails to accurately obtain its diagonal correction matrix D. Besides, SimRank is also limited by an unwanted "connectivity trait": increasing the number of paths between nodes a and b often incurs a decrease in score s(a,b). The best-known solution, SimRank++, cannot resolve this problem, since a revised score will be zero if a and b have no common in-neighbors. In this paper, we consider high-quality similarity search. Our scheme, SR#, is efficient and semantically meaningful: (1) We first formulate the exact D, and devise a "varied-D" method to accurately compute SimRank in linear memory. Moreover, by grouping computation, we also reduce the time of from quadratic to linear in the number of iterations. (2) We design a "kernel-based" model to improve the quality of SimRank, and circumvent the "connectivity trait" issue. (3) We give mathematical insights to the semantic difference between SimRank and its variant, and correct an argument: "if D is replaced by a scaled identity matrix, top-K rankings will not be affected much". The experiments confirm that SR# can accurately extract high-quality scores, and is much faster than the state-of-the-art competitors

RadixInsert, a much faster stable algorithm for sorting floating-point numbers

The problem addressed in this paper is that we want to sort an array a[] of n floating point numbers conforming to the IEEE 754 standard, both in the 64bit double precision and the 32bit single precision formats on a multi core computer with p real cores and shared memory (an ordinary PC). This we do by introducing a new stable, sorting algorithm, RadixInsert, both in a sequential version and with two parallel implementations. RadixInsert is tested on two different machines, a 2 core laptop and a 4 core desktop, outperforming the not stable Quicksort based algorithms from the Java library – both the sequential Arrays.sort() and a merge-based parallel version Arrays.parallelsort() for 500. The RadixInsert algorithm resembles in many ways the Shell sorting algorithm [1]. First, the array is pre-sorted to some degree – and in the case of Shell, Insertion sort is first used with long jumps and later shorter jumps along the array to ensure that small numbers end up near the start of the array and the larger ones towards the end. Finally, we perform a full insertion sort on the whole array to ensure correct sorting. RadixInsert first uses the ordinary right-to-left LSD Radix for sorting some left part of the floating-point numbers, then considered as integers. Finally, as with Shell sort, we perform a full Insertion sort on the whole array. This resembles in some ways a proposal by Sedgewick [10] for integer sorting and will be commented on later. The IEE754 standard was deliberately made such that positive floating-point numbers can be sorted as integers (both in the 32 and 64 bit format). The special case of a mix of positive and negative numbers is also handled in RadixInsert. One other main reason why Radix-sort is so well suited for this task is that the IEEE 754 standard normalizes numbers to the left side of the representation in a 64bit double or a 32bit float. The Radix algorithm will then in the same sorting on the leftmost bits in n floating-point numbers, sort both large and small numbers simultaneously. Finally, Radix is cache-friendly as it reads all its arrays left-to right with a small number of cache misses as a result, but writes them back in a different location in b[] in order to do the sorting. And thirdly, Radix-sort is a fast O(n) algorithm – faster than quicksort O(nlogn) or Shell sort O(n1.5). RadixInsert is in practice O(n), but as with Quicksort it might be possible to construct numbers where RadixInsert degenerates to an O(n2) algorithm. However, this worst case for RadixInsert was not found when sorting seven quite different distributions reported in this paper. Finally, the extra memory used by RadixInsert is n + some minor arrays whereas the sequential Quicksort in the Java library needs basically no extra memory. However, the merge based Arrays.parallelsort() in the Java library needs the same amount of n extra memory as RadixInsert

Removing duplicate reads using graphics processing units

Background: During library construction polymerase chain reaction is used to enrich the DNA before sequencing. Typically, this process generates duplicate read sequences. Removal of these artifacts is mandatory, as they can affect the correct interpretation of data in several analyses. Ideally, duplicate reads should be characterized by identical nucleotide sequences. However, due to sequencing errors, duplicates may also be nearly-identical. Removing nearly-identical duplicates can result in a notable computational effort. To deal with this challenge, we recently proposed a GPU method aimed at removing identical and nearly-identical duplicates generated with an Illumina platform. The method implements an approach based on prefix-suffix comparison. Read sequences with identical prefix are considered potential duplicates. Then, their suffixes are compared to identify and remove those that are actually duplicated. Although the method can be efficiently used to remove duplicates, there are some limitations that need to be overcome. In particular, it cannot to detect potential duplicates in the event that prefixes are longer than 27 bases, and it does not provide support for paired-end read libraries. Moreover, large clusters of potential duplicates are split into smaller with the aim to guarantees a reasonable computing time. This heuristic may affect the accuracy of the analysis. Results: In this work we propose GPU-DupRemoval, a new implementation of our method able to (i) cluster reads without constraints on the maximum length of the prefixes, (ii) support both single- and paired-end read libraries, and (iii) analyze large clusters of potential duplicates. Conclusions: Due to the massive parallelization obtained by exploiting graphics cards, GPU-DupRemoval removes duplicate reads faster than other cutting-edge solutions, while outperforming most of them in terms of amount of duplicates reads

Design and Control of Warehouse Order Picking: a literature review

Order picking has long been identified as the most labour-intensive and costly activity for almost every warehouse; the cost of order picking is estimated to be as much as 55% of the total warehouse operating expense. Any underperformance in order picking can lead to unsatisfactory service and high operational cost for its warehouse, and consequently for the whole supply chain. In order to operate efficiently, the orderpicking process needs to be robustly designed and optimally controlled. This paper gives a literature overview on typical decision problems in design and control of manual order-picking processes. We focus on optimal (internal) layout design, storage assignment methods, routing methods, order batching and zoning. The research in this area has grown rapidly recently. Still, combinations of the above areas have hardly been explored. Order-picking system developments in practice lead to promising new research directions.Order picking;Logistics;Warehouse Management

Algorithms versus architectures for computational chemistry

The algorithms employed are computationally intensive and, as a result, increased performance (both algorithmic and architectural) is required to improve accuracy and to treat larger molecular systems. Several benchmark quantum chemistry codes are examined on a variety of architectures. While these codes are only a small portion of a typical quantum chemistry library, they illustrate many of the computationally intensive kernels and data manipulation requirements of some applications. Furthermore, understanding the performance of the existing algorithm on present and proposed supercomputers serves as a guide for future programs and algorithm development. The algorithms investigated are: (1) a sparse symmetric matrix vector product; (2) a four index integral transformation; and (3) the calculation of diatomic two electron Slater integrals. The vectorization strategies are examined for these algorithms for both the Cyber 205 and Cray XMP. In addition, multiprocessor implementations of the algorithms are looked at on the Cray XMP and on the MIT static data flow machine proposed by DENNIS