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Raja Appuswamy

Publications and source records attributed to Raja Appuswamy.

8 recordsLinked to original sources

From Custom-Fit to Portable: Bridging the Gap Between Synthesized and Engineered GPU Query Execution

GPUs are increasingly used for analytical query processing, but developing GPU-based database engines that achieve the peak performance of the underlying hardware requires substantial research and engineering effort. A recent line of work argues that query processing should be synthesized, not engineered. In this scenario, instead of tuning a general-purpose engine to fit a workload, a large language model (LLM) generates code specialized to one query, one dataset, and one machine, thereby achieving an order-of-magnitude improvement in performance. This thesis, however, has so far been tested only on CPUs. In this work, we revisit the synthesize-versus-engineer debate for GPU analytics by answering three questions: (i) how good is synthesized GPU code?, (ii) why is it faster than engineered engines?, and (iii) how much of its advantage can be transferred back into a single, performance-portable engine? To answer the first question, we present SHADB, an LLM-based synthesis framework that generates optimized CUDA or HIP kernels using an automated, profile-guided optimization loop. Using SHADB, we show that the synthesized code approaches the memory-bandwidth ceiling and outperforms a state-of-the-art JIT-compiled GPU database engine (HeavyDB) by 7.4$\times$ on SSB SF100. To answer the second question, we decompose this performance gap and systematically classify optimizations as generalizable or workload-specific. Finally, to answer the third question, we integrate these generalizable optimizations into SYCLDB, a performance-portable engine written entirely in the open SYCL programming model. Using optimized SYCLDB, we show that it is possible to substantially bridge the gap to synthesized code (within 1.27$\times$ total execution time) while retaining workload-level generality and hardware-level performance portability.

cs.DB

Adaptive Sampling for Storage of Progressive Images on DNA

The short lifespan of traditional data storage media, coupled with an exponential increase in storage demand, has made long-term archival a fundamental problem in the data storage industry and beyond. Consequently, researchers are looking for innovative media solutions that can store data over long time periods at a very low cost. DNA molecules, with their high density, long lifespan, and low energy needs, have emerged as a viable alternative to digital data archival. However, current DNA data storage technologies are facing challenges with respect to cost and reliability. Thus, coding rate and error robustness are critical to scale DNA storage and make it technologically and economically achievable. Moreover, the molecules of DNA that encode different files are often located in the same oligo pool. Without random access solutions at the oligo level, it is very impractical to decode a specific file from these mixed pools, as all oligos need to first be sequenced and decoded before a target file can be retrieved, which greatly deteriorates the read cost. This paper introduces a solution to efficiently encode and store images into DNA molecules, that aims at reducing the read cost necessary to retrieve a resolution-reduced version of an image. This image storage system is based on the Progressive Decoding Functionality of the JPEG2000 codec but can be adapted to any conventional progressive codec. Each resolution layer is encoded into a set of oligos using the JPEG DNA VM codec, a DNA-based coder that aims at retrieving a file with a high reliability. Depending on the desired resolution to be read, the set of oligos as well as the portion of the oligos to be sequenced and decoded are adjusted accordingly. These oligos will be selected at sequencing time, with the help of the adaptive sampling method provided by the Nanopore sequencers, making it a PCR-free random access solution.

eess.IV

Combining Progressive Image Compression and Random Access in DNA Data Storage

The exponential increase in storage demand and low lifespan of data storage devices has resulted in long-term archival and preservation emerging as a critical bottlenecks in data storage. In order to meet this demand, researchers are now investigating novel forms of data storage media. The high density, long lifespan and low energy needs of synthetic DNA make it a promising candidate for long-term data archival. However, current DNA data storage technologies are facing challenges with respect to cost (writing data to DNA is expensive) and reliability (reading and writing data is error prone). Thus, data compression and error correction are crucial to scale DNA storage. Additionally, the DNA molecules encoding several files are very often stored in the same place, called an oligo pool. For this reason, without random access solutions, it is relatively impractical to decode a specific file from the pool, because all the oligos from all the files need to first be sequenced, which greatly deteriorates the read cost. This paper introduces PIC-DNA - a novel JPEG2000-based progressive image coder adapted to DNA data storage. This coder directly includes a random access process in its coding system, allowing for the retrieval of a specific image from a pool of oligos encoding several images. The progressive decoder can dynamically adapt the read cost according to the user's cost and quality constraints at decoding time. Both the random access and progressive decoding greatly improve on the read-cost of image coders adapted to DNA.

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Hardware Acceleration for Knowledge Graph Processing: Challenges & Recent Developments

Knowledge graphs (KGs) have achieved significant attention in recent years, particularly in the area of the Semantic Web as well as gaining popularity in other application domains such as data mining and search engines. Simultaneously, there has been enormous progress in the development of different types of heterogeneous hardware, impacting the way KGs are processed. The aim of this paper is to provide a systematic literature review of knowledge graph hardware acceleration. For this, we present a classification of the primary areas in knowledge graph technology that harnesses different hardware units for accelerating certain knowledge graph functionalities. We then extensively describe respective works, focusing on how KG related schemes harness modern hardware accelerators. Based on our review, we identify various research gaps and future exploratory directions that are anticipated to be of significant value both for academics and industry practitioners.

cs.IR

CMOSS: A Reliable, Motif-based Columnar Molecular Storage System

The surge in demand for cost-effective, durable long-term archival media, coupled with density limitations of contemporary magnetic media, has resulted in synthetic DNA emerging as a promising new alternative. Despite its benefits, storing data on DNA poses several challenges as the technology used for reading/writing data and achieving random access on DNA are highly error prone. In order to deal with such errors, it is important to design efficient pipelines that can carefully use redundancy to mask errors without amplifying overall cost. In this work, we present Columnar MOlecular Storage System (CMOSS), a novel, end-to-end DNA storage pipeline that can provide error-tolerant data storage at low read/write costs. CMOSS differs from SOTA on three fronts (i) a motif-based, vertical layout in contrast to nucleotide-based horizontal layout used by SOTA, (ii) merged consensus calling and decoding enabled by the vertical layout, and (iii) a flexible, fixed-size, block-based data organization for random access over DNA storage in contrast to the variable-sized, object-based access used by SOTA. Using an in-depth evaluation via simulation studies and real wet-lab experiments, we demonstrate the benefits of various CMOSS design choices. We make the entire pipeline together with the read datasets openly available to the community for faithful reproduction and furthering research.

cs.DB

Universal Layout Emulation for Long-Term Database Archival

Research on alternate media technologies, like film, synthetic DNA, and glass, for long-term data archival has received a lot of attention recently due to the media obsolescence issues faced by contemporary storage media like tape, Hard Disk Drives (HDD), and Solid State Disks (SSD). While researchers have developed novel layout and encoding techniques for archiving databases on these new media types, one key question remains unaddressed: How do we ensure that the decoders developed today will be available and executable by a user who is restoring an archived database several decades later in the future, on a computing platform that potentially does not even exist today? In this paper, we make the case for Universal Layout Emulation (ULE), a new approach for future-proof, long-term database archival that advocates archiving decoders together with the data to ensure successful recovery. In order to do so, ULE brings together concepts from Data Management and Digital Preservation communities by using emulation for archiving decoders. In order to show that ULE can be implemented in practice, we present the design and evaluation of Micr'Olonys, an end-to-end long-term database archival system that can be used to archive databases using visual analog media like film, microform, and archival paper.

cs.DB

Cold Storage Data Archives: More Than Just a Bunch of Tapes

The abundance of available sensor and derived data from large scientific experiments, such as earth observation programs, radio astronomy sky surveys, and high-energy physics already exceeds the storage hardware globally fabricated per year. To that end, cold storage data archives are the---often overlooked---spearheads of modern big data analytics in scientific, data-intensive application domains. While high-performance data analytics has received much attention from the research community, the growing number of problems in designing and deploying cold storage archives has only received very little attention. In this paper, we take the first step towards bridging this gap in knowledge by presenting an analysis of four real-world cold storage archives from three different application domains. In doing so, we highlight (i) workload characteristics that differentiate these archives from traditional, performance-sensitive data analytics, (ii) design trade-offs involved in building cold storage systems for these archives, and (iii) deployment trade-offs with respect to migration to the public cloud. Based on our analysis, we discuss several other important research challenges that need to be addressed by the data management community.

cs.DB

A biologically constrained encoding solution for long-term storage of images onto synthetic DNA

Living in the age of the digital media explosion, the amount of data that is being stored increases dramatically. However, even if existing storage systems suggest efficiency in capacity, they are lacking in durability. Hard disks, flash, tape or even optical storage have limited lifespan in the range of 5 to 20 years. Interestingly, recent studies have proven that it was possible to use synthetic DNA for the storage of digital data, introducing a strong candidate to achieve data longevity. The DNA's biological properties allows the storage of a great amount of information into an extraordinary small volume while also promising efficient storage for centuries or even longer with no loss of information. However, encoding digital data onto DNA is not obvious, because when decoding, we have to face the problem of sequencing noise robustness. Furthermore, synthesizing DNA is an expensive process and thus, controlling the compression ratio by optimizing the rate-distortion trade-off is an important challenge we have to deal with. This work proposes a coding solution for the storage of digital images onto synthetic DNA. We developed a new encoding algorithm which generates a DNA code robust to biological errors coming from the synthesis and the sequencing processes. Furthermore, thanks to an optimized allocation process the solution is able to control the compression ratio and thus the length of the synthesized DNA strand. Results show an improvement in terms of coding potential compared to previous state-of-the-art works.

eess.IV