Supporting automatic recovery in offloaded distributed programming models through MPI-3 techniques

In this paper we describe the design of fault tolerance capabilities for general-purpose offload semantics, based on the OmpSs programming model. Using ParaStation MPI, a production MPI-3.1 implementation, we explore the features that, being standard compliant, an MPI stack must support to provide the necessary fault tolerance guarantees, based on MPI's dynamic process management. Our results, including synthetic benchmarks and applications, reveal low runtime overhead and efficient recovery, demonstrating that the existing MPI standard provided us with sufficient mechanisms to implement an effective and efficient fault-tolerant solution.This research received funding from the European Community’s 7th Framework Programme via the DEEP-ER project under Grant Agreement no. 610476. This work has also been supported by the Spanish Ministry of Science and Innovation (contract TIN2012-34557) and by Generalitat de Catalunya (contracts 2014-SGR-1051 and 2014-SGR-1272). Antonio J. Peña is cofinanced by the Spanish Ministry of Economy and Competitiveness under Juan de la Cierva fellowship number IJCI-2015-23266. The authors thank Jorge Bell´on, from BSC, for his technical support with the Nanos++ internals.Peer ReviewedPostprint (author's final draft

Stress response of a clinical Enterococcus faecalis isolate subjected to a novel antimicrobial surface coating

Emerging antibiotic resistance among pathogenic bacteria, paired with their ability to form biofilms on medical and technical devices, represents a serious problem for effective and long-term decontamination in health-care environments and gives rise to an urgent need for new antimicrobial materials. Here we present the impact of AGXX®, a novel broad-spectrum antimicrobial surface coating consisting of micro-galvanic elements formed by silver and ruthenium, on the transcriptome of Enterococcus faecalis. A clinical E. faecalis isolate was subjected to metal stress by growing it for different periods in presence of the antimicrobial coating or silver-coated steel meshes. Subsequently, total RNA was isolated and next-generation RNA sequencing was performed to analyze variations in gene expression in presence of the antimicrobial materials with focus on known stress genes. Exposure to the antimicrobial coating had a large impact on the transcriptome of E. faecalis. After 24min almost 1/5 of the E. faecalis genome displayed differential expression. At each time-point the cop operon was strongly up-regulated, providing indirect evidence for the presence of free Ag+-ions. Moreover, exposure to the antimicrobial coating induced a broad general stress response in E. faecalis. Genes coding for the chaperones GroEL and GroES and the Clp proteases, ClpE and ClpB, were among the top up-regulated heat shock genes. Differential expression of thioredoxin, superoxide dismutase and glutathione synthetase genes indicates a high level of oxidative stress. We postulate a mechanism of action where the combination of Ag+-ions and reactive oxygen species generated by AGXX®results in a synergistic antimicrobial effect, superior to that of conventional silver coatings.</p

MPI Benchmarks: First release

Collection of MPI benchmark

MPIXternal: A Library for a Portable Adjustment of Parallel MPI Applications to Heterogeneous Environments

Nowadays, common systems in the area of high performance computing exhibit highly hierarchical architectures. As a result, achieving satisfactory application performance demands an adaptation of the respective parallel algorithm to such systems. This, in turn, requires knowledge about the actual hardware structure even at the application level. However, the prevalent Message Passing Interface (MPI) standard (at least in its current version 2.1) intentionally hides heterogeneity from the application programmer in order to assure portability. In this paper, we introduce the MPIXternal library which tries to circumvent this obvious semantic gap within the current MPI standard. For this purpose, the library offers the programmer additional features that should help to adapt applications to today’s hierarchical systems in a convenient and portable way. 1

Design and Implementation of a Service-integrated Session Layer for Efficient Message Passing in Grid Computing Environments

When running large parallel applications with demands for resources that exceed the capacity the local computing site offers, the deployment in a distributed Grid environment may help to satisfy these demands. However, since such an environment is a heterogeneous system by nature, there are some drawbacks that, if not taken into account, are limiting its applicability. First of all, one has to apply a meta-computing or Grid-enabled message-passing library in order to have the ability to route messages to remote sites as well as still being able to exploit fast site-local network facilities. Then, because the inter-site communication usually constitutes the system’s bottleneck, appropriate quality of service parameters should be provided and policed for those connections during the application’s execution. And finally, the parallel runtime environment of the distributed application should offer service interfaces in order to enable its interaction with Grid middleware. In this paper, we present a new library called ISI whose functionalities meet those requirements in terms of a session layer to be integrated into Grid-enabled message-passing implementations. 1

Allocation-Internal Co-Scheduling - Interaction and Orchestration of Multiple Concurrent MPI Sessions

Heading towards exascale, the challenges for process management with respect to flexibility and efficiency grow accordingly. Running more than one application simultaneously on a node can be the solution for better resource utilization. However, this approach of co-scheduling can also be the way to go for gaining a degree of flexibility with respect to process management that can enable some kind of interactivity even in the domain of high-performance computing. This chapter gives an introduction into such co-scheduling policies for running multiple MPI sessions concurrently and interactively within a single user allocation. The chapter initially introduces a taxonomy for classifying the different characteristics of such a flexible process management, and discusses actual manifestations thereof during the course of the reading. In doing so, real world examples are motivated and presented by means of ParaStation MPI, a high-performance MPI library supplemented by a complete framework comprising a scalable and dynamic process manager. In particular, four scheduling policies, implemented in ParaStation MPI, are detailed and evaluated by applying a benchmarking tool that has especially been developed for measuring interactivity and dynamicity metrics of job schedulers and process managers for high-performance computing