Yoginder S. Dandass

MPI/FT/sup TM/: architecture and taxonomies for fault-tolerant, message-passing middleware for performance-portable parallel computing

MPI has proven effective for parallel applications in situations with neither QoS nor fault handling. Emerging environments motivate fault-tolerant MPI middleware. Environments include space-based, wide-area/web/meta computing and scalable clusters. MPI/FT, the system described in the paper, trades off sufficient MPI fault coverage against acceptable parallel performance, based on mission requirements and constraints. MPI codes are evolved to use MPI/FT features. Non-portable code for event handlers and recovery management is isolated. User-coordinated recovery, checkpointing, transparency and event handling, as well as evolvability of legacy MPI codes form key design criteria. Parallel self-checking threads address four levels of MPI implementation robustness, three of which are portable to any multithreaded MPI. A taxonomy of application types provides six initial fault-relevant models; user-transparent parallel nMR computation is thereby considered. Key concepts from MPI/RT-real-time MPI-are also incorporated into MPI/FT, with further overt support for MPI/RT and MPI/FT in applications possible in future.

MPI/FT: A Model-Based Approach to Low-Overhead Fault Tolerant Message-Passing Middleware

Fault tolerance in parallel systems has traditionally been achieved through a combination of redundancy and checkpointing methods. This notion has also been extended to message-passing systems with user-transparent process checkpointing and message logging. Furthermore, studies of multiple types of rollback and recovery have been reported in literature, ranging from communication-induced checkpointing to pessimistic and synchronous solutions. However, many of these solutions incorporate high overhead because of their inability to utilize application level information.This paper describes the design and implementation of MPI/FT, a high-performance MPI-1.2 implementation enhanced with low-overhead functionality to detect and recover from process failures. The strategy behind MPI/FT is that fault tolerance in message-passing middleware can be optimized based on an applications execution model derived from its communication topology and parallel programming semantics. MPI/FT exploits the specific characteristics of two parallel application execution models in order to optimize performance. MPI/FT also introduces the self-checking thread that monitors the functioning of the middleware itself. User aware checkpointing and user-assisted recovery are compatible with MPI/FT and complement the techniques used here.This paper offers a classification of MPI applications for fault tolerant MPI purposes and MPI/FT implementation discussed here provides different middleware versions specifically tailored to each of the two models studied in detail. The interplay of various parameters affecting the cost of fault tolerance is investigated. Experimental results demonstrate that the approach used to design and implement MPI/FT results in a low-overhead MPI-based fault tolerant communication middleware implementation.

Genome Sequence of the Solvent-Producing Bacterium Clostridium carboxidivorans Strain P7T

Clostridium carboxidivorans strain P7(T) is a strictly anaerobic acetogenic bacterium that produces acetate, ethanol, butanol, and butyrate. The C. carboxidivorans genome contains all the genes for the carbonyl branch of the Wood-Ljungdahl pathway for CO(2) fixation, and it encodes enzymes for conversion of acetyl coenzyme A into butanol and butyrate.

Engineering future cyber-physical energy systems: Challenges, research needs, and roadmap

Cyber-physical energy systems require the integration of a heterogeneous physical layers and decision control networks, mediated by decentralized and distributed local sensing/actuation structures backed by an information layer. With the North American Electric Reliability Corporation (NERC) Critical Infrastructure Protection (CIP) [1] requirements and presidents visions of more secure, reliable and controllable cyber-physical system, a new paradigm for modeling and research investigation is needed. In this paper, we present common challenges and our vision of solutions to design advanced Cyber-physical energy systems with embedded security and distributed control. Finally, we present a survey of our research results in this domain.

A testbed for SCADA control system cybersecurity research and pedagogy

This paper describes the Mississippi State University Supervisory Control and Data Acquisition (SCADA) security laboratory and Power and Energy Research laboratory. This laboratory combines process control systems from multiple critical infrastructure industries to create a testbed with functional physical processes controlled by commercial hardware and software over common industrial control system routable and non-routable networks. The testbed enables a research process in which cybersecurity vulnerabilities are discovered, exploits are used to understand the implications of the vulnerability on controlled physical processes, identified problems are classified by criticality and similarities in type and effect, and finally cybersecurity mitigations are developed and validated against the testbed. The testbed also enables control system security workforce development through integration into the classroom of laboratory exercises, functional demonstrations, and research outcomes.

Accelerating String Set Matching in FPGA Hardware for Bioinformatics Research

BackgroundThis paper describes techniques for accelerating the performance of the string set matching problem with particular emphasis on applications in computational proteomics. The process of matching peptide sequences against a genome translated in six reading frames is part of a proteogenomic mapping pipeline that is used as a case-study. The Aho-Corasick algorithm is adapted for execution in field programmable gate array (FPGA) devices in a manner that optimizes space and performance. In this approach, the traditional Aho-Corasick finite state machine (FSM) is split into smaller FSMs, operating in parallel, each of which matches up to 20 peptides in the input translated genome. Each of the smaller FSMs is further divided into five simpler FSMs such that each simple FSM operates on a single bit position in the input (five bits are sufficient for representing all amino acids and special symbols in protein sequences).ResultsThis bit-split organization of the Aho-Corasick implementation enables efficient utilization of the limited random access memory (RAM) resources available in typical FPGAs. The use of on-chip RAM as opposed to FPGA logic resources for FSM implementation also enables rapid reconfiguration of the FPGA without the place and routing delays associated with complex digital designs.ConclusionExperimental results show storage efficiencies of over 80% for several data sets. Furthermore, the FPGA implementation executing at 100 MHz is nearly 20 times faster than an implementation of the traditional Aho-Corasick algorithm executing on a 2.67 GHz workstation.

A Retrofit Network Intrusion Detection System for MODBUS RTU and ASCII Industrial Control Systems

MODBUS RTU/ASCII Snort is software to retrofit serial based industrial control systems to add Snort intrusion detection and intrusion prevention capabilities. This article discusses the need for such a system by describing 4 classes of intrusion vulnerabilities (denial of service, command injection, response injection, and system reconnaissance) which can be exploited on MODBUS RTU/ASCII industrial control systems. The article provides details on how Snort rules can detect and prevent such intrusions. Finally, the article describes the MODBUS RTU/ASCII Snort implementation, provides details on placement of a MODBUS RTU/ASCII Snort host within a control system to maximize intrusion detection and prevention capabilities, and discusses the systems validation.

The Proteogenomic Mapping Tool

BackgroundHigh-throughput mass spectrometry (MS) proteomics data is increasingly being used to complement traditional structural genome annotation methods. To keep pace with the high speed of experimental data generation and to aid in structural genome annotation, experimentally observed peptides need to be mapped back to their source genome location quickly and exactly. Previously, the tools to do this have been limited to custom scripts designed by individual research groups to analyze their own data, are generally not widely available, and do not scale well with large eukaryotic genomes.ResultsThe Proteogenomic Mapping Tool includes a Java implementation of the Aho-Corasick string searching algorithm which takes as input standardized file types and rapidly searches experimentally observed peptides against a given genome translated in all 6 reading frames for exact matches. The Java implementation allows the application to scale well with larger eukaryotic genomes while providing cross-platform functionality.ConclusionsThe Proteogenomic Mapping Tool provides a standalone application for mapping peptides back to their source genome on a number of operating system platforms with standard desktop computer hardware and executes very rapidly for a variety of datasets. Allowing the selection of different genetic codes for different organisms allows researchers to easily customize the tool to their own research interests and is recommended for anyone working to structurally annotate genomes using MS derived proteomics data.

An Approach to Model Network Exploitations Using Exploitation Graphs

In this article, a modeling process is defined to address challenges in analyzing attack scenarios and mitigating vulnerabilities in networked environments. Known system vulnerability data, system configuration data, and vulnerability scanner results are considered to create exploitation graphs (e-graphs) that are used to represent attack scenarios. Experiments carried out in a cluster computing environment showed the usefulness of proposed techniques in providing in-depth attack scenario analyses for security engineering. Critical vulnerabilities can be identified by employing graph algorithms. Several factors were used to measure the difficulty in executing an attack. A cost/benefit analysis was used for more accurate quantitative analysis of attack scenarios. The authors also show how the attack scenario analyses better help deployment of security products and design of network topologies.

Research toward a Partially-Automated, and Crime Specific Digital Triage Process Model

The digital forensic process as traditionally laid out begins with the collection, duplication, and authentication of every piece of digital media prior to examination. These first three phases of the digital forensic process are by far the most costly. However, complete forensic duplication is standard practice among digital forensic laboratories. The time it takes to complete these stages is quickly becoming a serious problem. Digital forensic laboratories do not have the resources and time to keep up with the growing demand for digital forensic examinations with the current methodologies. One solution to this problem is the use of pre-examination techniques commonly referred to as digital triage. Pre-examination techniques can assist the examiner with intelligence that can be used to prioritize and lead the examination process. This work discusses a proposed model for digital triage that is currently under development at Mississippi State University.