A Study of Disk Performance Optimization.

Response time is one of the most important performance measures associated with a typical multi-user system. Response time, in turn, is bounded by the performance of the input/output (I/O) subsystem. Other than the end user and some external peripherals, the slowest component of the I/O subsystem is the disk drive. One standard strategy for improving I/O subsystem performance uses high-performance hardware like Small Computer Systems Interface (SCSI) drives to improve overall response time. SCSI hardware, unfortunately, is often too expensive to use in low-end multi-user systems. The low-end multi-user systems commonly use inexpensive Integrated Drive Electronics (IDE) disk drives to keep overall costs low. On such IDE based multi-user systems, reducing the Central Processing Unit (CPU) overhead associated with disk I/O is critical to system responsiveness. This thesis explores the impact of PCI bus mastering Direct Memory Access (DMA) on the performance of systems with IDE drives. DMA is a data transfer protocol that allows data to be sent directly from an attached device to a computer system’s main memory, thereby reducing CPU overhead. PCI bus mastering allows modern IDE disk controllers to manipulate main memory without utilizing motherboard-resident DMA controllers. Using a series of experiments, this thesis examines the impact of PCI bus mastering DMA on IDE performance for synchronous I/O, relative to Programmed Input/Output (PIO) and SCSI performance. Experiment results show that PCI bus mastering DMA, when used properly, improves the responsiveness and throughput of IDE drives by as much as a factor of seven. The magnitude of this improvement shows the importance of operating system support for DMA in low-end multi-user systems. Additionally, experimental results demonstrate that performance gains associated with SCSI are dependent on system usage and operating system support for advanced SCSI capabilities. Therefore, under many circumstances, high-performance SCSI drives are not cost effective when compared with IDE bus mastering DMA capable drives

CRAID: Online RAID upgrades using dynamic hot data reorganization

Current algorithms used to upgrade RAID arrays typically require large amounts of data to be migrated, even those that move only the minimum amount of data required to keep a balanced data load. This paper presents CRAID, a self-optimizing RAID array that performs an online block reorganization of frequently used, long-term accessed data in order to reduce this migration even further. To achieve this objective, CRAID tracks frequently used, long-term data blocks and copies them to a dedicated partition spread across all the disks in the array. When new disks are added, CRAID only needs to extend this process to the new devices to redistribute this partition, thus greatly reducing the overhead of the upgrade process. In addition, the reorganized access patterns within this partition improve the array’s performance, amortizing the copy overhead and allowing CRAID to offer a performance competitive with traditional RAIDs. We describe CRAID’s motivation and design and we evaluate it by replaying seven real-world workloads including a file server, a web server and a user share. Our experiments show that CRAID can successfully detect hot data variations and begin using new disks as soon as they are added to the array. Also, the usage of a dedicated partition improves the sequentiality of relevant data access, which amortizes the cost of reorganizations. Finally, we prove that a full-HDD CRAID array with a small distributed partition (<1.28% per disk) can compete in performance with an ideally restriped RAID-5 and a hybrid RAID-5 with a small SSD cache.Peer ReviewedPostprint (published version

Operating System Concepts for Reconfigurable Computing: Review and Survey

One of the key future challenges for reconfigurable computing is to enable higher design productivity and a more easy way to use reconfigurable computing systems for users that are unfamiliar with the underlying concepts. One way of doing this is to provide standardization and abstraction, usually supported and enforced by an operating system. This article gives historical review and a summary on ideas and key concepts to include reconfigurable computing aspects in operating systems. The article also presents an overview on published and available operating systems targeting the area of reconfigurable computing. The purpose of this article is to identify and summarize common patterns among those systems that can be seen as de facto standard. Furthermore, open problems, not covered by these already available systems, are identified

Self-organization via active exploration in robotic applications

We describe a neural network based robotic system. Unlike traditional robotic systems, our approach focussed on non-stationary problems. We indicate that self-organization capability is necessary for any system to operate successfully in a non-stationary environment. We suggest that self-organization should be based on an active exploration process. We investigated neural architectures having novelty sensitivity, selective attention, reinforcement learning, habit formation, flexible criteria categorization properties and analyzed the resulting behavior (consisting of an intelligent initiation of exploration) by computer simulations. While various computer vision researchers acknowledged recently the importance of active processes (Swain and Stricker, 1991), the proposed approaches within the new framework still suffer from a lack of self-organization (Aloimonos and Bandyopadhyay, 1987; Bajcsy, 1988). A self-organizing, neural network based robot (MAVIN) has been recently proposed (Baloch and Waxman, 1991). This robot has the capability of position, size rotation invariant pattern categorization, recognition and pavlovian conditioning. Our robot does not have initially invariant processing properties. The reason for this is the emphasis we put on active exploration. We maintain the point of view that such invariant properties emerge from an internalization of exploratory sensory-motor activity. Rather than coding the equilibria of such mental capabilities, we are seeking to capture its dynamics to understand on the one hand how the emergence of such invariances is possible and on the other hand the dynamics that lead to these invariances. The second point is crucial for an adaptive robot to acquire new invariances in non-stationary environments, as demonstrated by the inverting glass experiments of Helmholtz. We will introduce Pavlovian conditioning circuits in our future work for the precise objective of achieving the generation, coordination, and internalization of sequence of actions

Murasaki: A Fast, Parallelizable Algorithm to Find Anchors from Multiple Genomes

BACKGROUND: With the number of available genome sequences increasing rapidly, the magnitude of sequence data required for multiple-genome analyses is a challenging problem. When large-scale rearrangements break the collinearity of gene orders among genomes, genome comparison algorithms must first identify sets of short well-conserved sequences present in each genome, termed anchors. Previously, anchor identification among multiple genomes has been achieved using pairwise alignment tools like BLASTZ through progressive alignment tools like TBA, but the computational requirements for sequence comparisons of multiple genomes quickly becomes a limiting factor as the number and scale of genomes grows. METHODOLOGY/PRINCIPAL FINDINGS: Our algorithm, named Murasaki, makes it possible to identify anchors within multiple large sequences on the scale of several hundred megabases in few minutes using a single CPU. Two advanced features of Murasaki are (1) adaptive hash function generation, which enables efficient use of arbitrary mismatch patterns (spaced seeds) and therefore the comparison of multiple mammalian genomes in a practical amount of computation time, and (2) parallelizable execution that decreases the required wall-clock and CPU times. Murasaki can perform a sensitive anchoring of eight mammalian genomes (human, chimp, rhesus, orangutan, mouse, rat, dog, and cow) in 21 hours CPU time (42 minutes wall time). This is the first single-pass in-core anchoring of multiple mammalian genomes. We evaluated Murasaki by comparing it with the genome alignment programs BLASTZ and TBA. We show that Murasaki can anchor multiple genomes in near linear time, compared to the quadratic time requirements of BLASTZ and TBA, while improving overall accuracy. CONCLUSIONS/SIGNIFICANCE: Murasaki provides an open source platform to take advantage of long patterns, cluster computing, and novel hash algorithms to produce accurate anchors across multiple genomes with computational efficiency significantly greater than existing methods. Murasaki is available under GPL at http://murasaki.sourceforge.net