Search results for "Address space"

2016

The growth of next-generation sequencing (NGS) datasets poses a challenge to the alignment of reads to reference genomes in terms of alignment quality and execution speed. Some available aligners have been shown to obtain high quality mappings at the expense of long execution times. Finding fast yet accurate software solutions is of high importance to research, since availability and size of NGS datasets continue to increase. In this work we present an efficient parallelization approach for NGS short-read alignment on multi-core clusters. Our approach takes advantage of a distributed shared memory programming model based on the new UPC++ language. Experimental results using the CUSHAW3 alig…

parSRA: A framework for the parallel execution of short read aligners on compute clusters

2018

The growth of next generation sequencing datasets poses as a challenge to the alignment of reads to reference genomes in terms of both accuracy and speed. In this work we present parSRA, a parallel framework to accelerate the execution of existing short read aligners on distributed-memory systems. parSRA can be used to parallelize a variety of short read alignment tools installed in the system without any modification to their source code. We show that our framework provides good scalability on a compute cluster for accelerating the popular BWA-MEM and Bowtie2 aligners. On average, it is able to accelerate sequence alignments on 16 64-core nodes (in total, 1024 cores) with speedup of 10.48 …

The upgraded HADES trigger and data acquisition system

2011

The HADES experiment is a High Acceptance Di-Electron Spectrometer located at GSI in Darmstadt, Germany. Recently, its trigger and data acquisition system was upgraded. The main goal was to substantially increase the event rate capability by a factor of up to 20 to reach 100 kHz in light and 20 kHz in heavy ion reaction systems. The total data rate written to storage is about 400 MByte/s in peak.In this context, the complete read-out system was exchanged to FPGA-based platforms using optical communication. For data transport a general-purpose real-time network protocol was developed to meet the strong requirements of the system. In particular, trigger information has to reach all front-end …

UPC++ for bioinformatics: A case study using genome-wide association studies

2014

Modern genotyping technologies are able to obtain up to a few million genetic markers (such as SNPs) of an individual within a few minutes of time. Detecting epistasis, such as SNP-SNP interactions, in Genome-Wide Association Studies is an important but time-consuming operation since statistical computations have to be performed for each pair of measured markers. Therefore, a variety of HPC architectures have been used to accelerate these studies. In this work we present a parallel approach for multi-core clusters, which is implemented with UPC++ and takes advantage of the features available in the Partitioned Global Address Space and Object Oriented Programming models. Our solution is base…

Unified Parallel C++

2018

Abstract Although MPI is commonly used for parallel programming on distributed-memory systems, Partitioned Global Address Space (PGAS) approaches are gaining attention for programming modern multi-core CPU clusters. They feature a hybrid memory abstraction: distributed memory is viewed as a shared memory that is partitioned among nodes in order to simplify programming. In this chapter you will learn about Unified Parallel C++ (UPC++), a library-based extension of C++ that gathers the advantages of both PGAS and Object Oriented paradigms. The examples included in this chapter will help you to understand the main features of PGAS languages and how they can simplify the task of programming par…

Dependability-Based Reliability Analysis in URC Networks: Availability in the Space Domain

2019

Ultra-reliable low latency communication (URLLC), which refers to achieving almost 100% reliability at a certain (satisfactory) level of services and stringent latency, is one of the key requirements for 5G networks. However, most prior studies on reliable communication did not address space domain analysis. Neither were they pursued from a dependability perspective. This paper addresses the ultra-reliable communication (URC) aspect of URLLC and aims at advocating the concept of URC from a dependability perspective in the space domain. We perform in-depth analysis on URC considering both the spatial characteristics of cell deployment and user distributions, as well as service requirements. …

Large-scale genome-wide association studies on a GPU cluster using a CUDA-accelerated PGAS programming model

2015

[Abstract] Detecting epistasis, such as 2-SNP interactions, in genome-wide association studies (GWAS) is an important but time consuming operation. Consequently, GPUs have already been used to accelerate these studies, reducing the runtime for moderately-sized datasets to less than 1 hour. However, single-GPU approaches cannot perform large-scale GWAS in reasonable time. In this work we present multiEpistSearch, a tool to detect epistasis that works on GPU clusters. While CUDA is used for parallelization within each GPU, the workload distribution among GPUs is performed with Unified Parallel C++ (UPC++), a novel extension of C++ that follows the Partitioned Global Address Space (PGAS) model…

Detecting Kernel Vulnerabilities During the Development Phase

2015

Testing is one of the major problems in Linux kernel development cycle. Security analysis and ensuring no new vulnerabilities has been introduced is one of the toughest issues of testing. Kernel developers attempt to find as many security issues as possible before merging with the mainline branch. Failure to detect vulnerabilities will result in vulnerable kernel shipped by distribution and vulnerable systems. The kernel developers can choose between several industrial and open source tools to assist in the development process and shorten the development cycle. (Though not as many as user space developers. Kernel tools are limited and rare compared to user space tools) Some of these tools a…