Analyzing large-scale DNA Sequences on Multi-core Architectures

Rapid analysis of DNA sequences is important in preventing the evolution of different viruses and bacteria during an early phase, early diagnosis of genetic predispositions to certain diseases (cancer, cardiovascular diseases), and in DNA forensics. However, real-world DNA sequences may comprise several Gigabytes and the process of DNA analysis demands adequate computational resources to be completed within a reasonable time. In this paper we present a scalable approach for parallel DNA analysis that is based on Finite Automata, and which is suitable for analyzing very large DNA segments. We evaluate our approach for real-world DNA segments of mouse (2.7GB), cat (2.4GB), dog (2.4GB), chicken (1GB), human (3.2GB) and turkey (0.2GB). Experimental results on a dual-socket shared-memory system with 24 physical cores show speed-ups of up to 17.6x. Our approach is up to 3x faster than a pattern-based parallel approach that uses the RE2 library.Comment: The 18th IEEE International Conference on Computational Science and Engineering (CSE 2015), Porto, Portugal, 20 - 23 October 201

libcppa - Designing an Actor Semantic for C++11

Parallel hardware makes concurrency mandatory for efficient program execution. However, writing concurrent software is both challenging and error-prone. C++11 provides standard facilities for multiprogramming, such as atomic operations with acquire/release semantics and RAII mutex locking, but these primitives remain too low-level. Using them both correctly and efficiently still requires expert knowledge and hand-crafting. The actor model replaces implicit communication by sharing with an explicit message passing mechanism. It applies to concurrency as well as distribution, and a lightweight actor model implementation that schedules all actors in a properly pre-dimensioned thread pool can outperform equivalent thread-based applications. However, the actor model did not enter the domain of native programming languages yet besides vendor-specific island solutions. With the open source library libcppa, we want to combine the ability to build reliable and distributed systems provided by the actor model with the performance and resource-efficiency of C++11.Comment: 10 page

A multiprocessor parallel approach to bit-parallel approximate string matching

The purpose of this project is to present with empirical results that a parallel design with the use of multiple processors can be successfully applied along with bit-parallel approximate string matching algorithms to solve practical bioinformatics problems. It will demonstrate that nearly optimal speedup can be achieved with a cluster of between two and eight workstations using MPI (Message Passing Interface), directly decreasing the total latency required to perform a string matching problem

Ada as an implementation language for knowledge based systems

Debates about the selection of programming languages often produce cultural collisions that are not easily resolved. This is especially true in the case of Ada and knowledge based programming. The construction of programming tools provides a desirable alternative for resolving the conflict

Packet Inspection on Programmable Hardware

In the network security system, one of the issues that are being discussed is to conduct a quick inspection of all incoming and outgoing packet. In this paper, we make a design packet inspection systems using programmable hardware. We propose the packet inspection system using a Field Programmable Gate Array (FPGA). The system proposed consisting of two important parts. The first part is to scanning packet very fast and the second is for verifying the results of scanning the first part. On the first part, the system based on incoming packet contents, the packet can reduce the number of strings to be matched for each packet and, accordingly, feed the packet to a verifier in the second part to conduct accurate string matching. In this paper a novel multi-threading finite state machine is proposed, which improves the clock frequency and allows multiple packets to be examined by a single state machine simultaneously. Design techniques for high-speed interconnect and interface circuits are also presented. The results of our experiment show that the system performance depend on the string matching algorithm, design on FPGA, and the number of string to be matched. Keywords: Packet inspection, string matching, Field programmable gate array, Traffic classificatio