2171593
Proactive fault tolerance for HPC with Xen virtualization
Large-scale parallel computing is relying increasingly on clusters with thousands of processors. At such large counts of compute nodes, faults are becoming common place. Current techniques to tolerate faults focus on reactive schemes to recover from faults and generally rely on a checkpoint/restart mechanism. Yet, in today's systems, node failures can often be anticipated by detecting a deteriorating health status.
 Instead of a reactive scheme for fault tolerance (FT), we are promoting a proactive one where processes automatically migrate from "unhealthy" nodes to healthy ones. Our approach relies on operating system virtualization techniques exemplified by but not limited to Xen. This paper contributes an automatic and transparent mechanism for proactive FT for arbitrary MPI applications. It leverages virtualization techniques combined with health monitoring and load-based migration. We exploit Xen's live migration mechanism for a guest operating system (OS) to migrate an MPI task from a health-deteriorating node to a healthy one without stopping the MPI task during most of the migration. Our proactive FT daemon orchestrates the tasks of health monitoring, load determination and initiation of guest OS migration. Experimental results demonstrate that live migration hides migration costs and limits the overhead to only a few seconds making it an attractive approach to realize FT in HPC systems. Overall, our enhancements make proactive FT a valuable asset for long-running MPI application that is complementary to reactive FT using full checkpoint/restart schemes since checkpoint frequencies can be reduced as fewer unanticipated failures are encountered. In the context of OS virtualization, we believe that this is the first comprehensive study of proactive fault tolerance where live migration is actually triggered by health monitoring.
61605137
Proactive process-level live migration in HPC environments
As the number of nodes in high-performance computing environments keeps increasing, faults are becoming common place. Reactive fault tolerance (FT) often does not scale due to massive I/O requirements and relies on manual job resubmission. This work complements reactive with proactive FT at the process level. Through health monitoring, a subset of node failures can be anticipated when one's health deteriorates. A novel process-level live migration mechanism supports continued execution of applications during much of processes migration. This scheme is integrated into an MPI execution environment to transparently sustain health-inflicted node failures, which eradicates the need to restart and requeue MPI jobs. Experiments indicate that 1-6.5 seconds of prior warning are required to successfully trigger live process migration while similar operating system virtualization mechanisms require 13-24 seconds. This self-healing approach complements reactive FT by nearly cutting the number of checkpoints in half when 70% of the faults are handled proactively.
2529194
Improving WCET by optimizing worst-case paths
It is advantageous to perform compiler optimizations to lower the WCET of a task since tasks with lower WCETs are easier to schedule and more likely to meet their deadlines. Compiler writers in recent years have used profile information to detect the frequently executed paths in a program and there has been much effort to develop compiler optimizations to improve these paths in order to reduce average-case execution time. In this paper we describe our approach to reduce WCET by adapting and applying optimizations designed for frequent paths to the worst-case paths in an application. Our compiler uses feedback from our timing analyzer to detect the WCET paths through a function that will be subject to aggressive optimizations, reflect subsequent effects on the WCET of the paths due to these optimizations, and to also ensure that the worst-case path optimizations actually improve the WCET before committing to a code size increase. We evaluate a number of WC path optimizations and present results showing the decrease in WCET versus the increase in code size.
200398
Prioritized token-based mutual exclusion for distributed systems
A number of solutions have been proposed for the problem of mutual exclusion in distributed systems. Some of these approaches have since been extended to a prioritized environment suitable for real-time applications but impose a higher message passing overhead than our approach. We present a new protocol for prioritized mutual exclusion in a distributed environment. Our approach uses a token-based model working on a logical tree structure, which is dynamically modified. In addition, we utilize a set of local queues whose union would resemble a single global queue. Furthermore, our algorithm is designed for out-of-order message delivery, handles messages asynchronously and supports multiple requests from one node for multi-threaded nodes. The prioritized algorithm has an average overhead of O(log(n)) messages per request for mutual exclusion with a worst-case overhead of O(n), where n represents the number of nodes in the system. Thus, our prioritized algorithm matches the message complexity of the best non-prioritized algorithms while previous prioritized algorithms have a higher message complexity, to our knowledge. Our concept of local queues can be incorporated into arbitrary token-based protocols with or without priority support to reduce the amount of messages. Performance results indicate that the additional functionality of our algorithm comes at the cost of 30% longer response times within our test environment for distributed execution when compared with an unprioritized algorithm. This result suggests that the algorithm should be used when strict priority ordering is required.
2354214
2006 WCET Preface - Proceedings of the 6th Intl. Workshop on Worst-Case Execution Time Analysis (WCET'06)
On the 4th of July, 2006, the 6th International Workshop onWorst-Case Execution Time Analysis (WCET'06) 
was held in Dresden, Germany, co-located with the 18th Euromicro International Conference on Real-Time 
Systems (ECRTS'06), both with support of Euromicro Technical Committee. The goal of the workshop was 
to bring together people from academia, tool vendors and users in industry that are interested in all aspects 
of timing analysis for real-time systems. The workshop provided a relaxed forum to present and discuss 
new ideas, new research directions, and to review current trends in this area. The workshop was based on 
short presentations that should encourage discussion by the attendees.
3256210
MOLAR: adaptive runtime support for high-end computing operating and runtime systems
MOLAR is a multi-institutional research effort that concentrates on adaptive, reliable, and efficient operating and runtime system (OS/R) solutions for ultra-scale high-end scientific computing on the next generation of supercomputers. This research addresses the challenges outlined in FAST-OS (forum to address scalable technology for runtime and operating systems) and HECRTF (high-end computing revitalization task force) activities by exploring the use of advanced monitoring and adaptation to improve application performance and predictability of system interruptions, and by advancing computer reliability, availability and serviceability (RAS) management systems to work cooperatively with the OS/R to identify and preemptively resolve system issues. This paper describes recent research of the MOLAR team in advancing RAS for high-end computing OS/Rs.
10691387
Penumbra: an Eclipse plugin for introductory programming
Eclipse is a full-featured and easily extensible integrated development environment. As such, it has grown to include a large degree of functionality that may be overwhelming to the novice programmer. Nevertheless, we believe Eclipse is an environment that students of programming will come to find useful and empowering once they become familiar with it. The trick is easing them into using Eclipse without them feeling overwhelmed at the outset. Penumbra is an Eclipse plug-in developed at Purdue University for use in our introductory programming classes. It is intended to ease the transition to use of the full-featured functionality of Eclipse. Penumbra presents an Eclipse perspective that hides all but the basic actions of Eclipse's existing Java perspective, while packaging elements of other perspectives (e.g., the CVS perspective) into simpler actions that ease the downloading and turn-in of programming assignments, and adding new code views inspired by other environments for introductory programmers. Our experiences using Eclipse with a small group of introductory programming students in the Spring of 2003 have guided the development of Penumbra, which is now being rolled out for general use by the full class of 230 students in the Fall of 2003.
15056437
Analysis assistant for single-molecule force spectroscopy data on membrane proteins - MPTV
UNLABELLED
Force-distance (F-D) curves of single membrane proteins reveal information on inter- and intramolecular interactions occurring within a protein and between proteins. However, the analysis of single-molecule force spectroscopy data is a time consuming and complex process requiring objective criteria. In most cases the user requires additional information to interpret F-D curves. Therefore we developed a software assistant representing the force or molecular interaction pattern and the topology or the 3D structure of the membrane protein. This representation establishes a basis for detailed interpretation of the protein structure and its underlying molecular interactions. Various integrated bioinformatic features further assist in the interpretation of measured and assigned molecular interactions that determine membrane protein folding, structure, stability and function. Web queries and programs about the topology are directly linked. Motifs, helix types, representation of Venn diagrams and the complete functionality of the program Jmol belong to it.


AVAILABILITY
The program MPTV is freely available from the website at http://www.bioforscher.de/mptv.htm/.