A Migratable User-Level Process Package for PVM

Shared, multi-user, workstation networks are characterized by unpredictable variability in system load. Further, the concept of workstation ownership is typically present. For efficient and unobtrusive computing in such environments, applications must not only overlap their computation with communication but also redistribute their computations adaptively based on changes in workstation availability and load. Managing these issues at application level leads to programs that are difficult to write and debug. In this paper, we present a system that manages this dynamic multi-processor environment while exporting a simple message-based programming model of a dedicated, distributed memory multiprocessor to applications. Programmers are thus insulated from the many complexities of the dynamic environment at the same time are able to achieve the benefits of multi-threading, adaptive load distribution and unobtrusive computing. To support the dedicated multi-processor model efficiently, the system defines a new kind of virtual processor called User-Level Process (ULP) that can be used to implement efficient multi-threading and application-transparent migration. The viability of ULPs is demonstrated through UPVM, a prototype implementation of the PVM message passing interface using ULPs. Typically, existing PVM programs written in Single Program Multiple Data (SPMD) style need only be re-compiled to use this package. The design of the package is presented and the performance analyzed with respect to both micro-benchmarks and some complete PVM applications. Finally, we discuss aspects of the ULP package that affect its portability and its support for heterogeneity, application transparency, and application debugging

Parallel array classes and lightweight sharing mechanisms

ABSTRACT We discuss a set of parallel array classes, MetaMP, for distributed-memory architectures. The classes are implemented in C++ and interface to the PVM or Intel NX message-passing systems. An array class implements a partitioned array as a set of objects distributed across the nodes-a "collective" object. Object methods hide the low-level message-passing and implement meaningful array operations. These include transparent guard strips (or sharing regions) that support finite-difference stencils, reductions and multibroadcasts for support of pivoting and row operations, and interpolation/ contraction operations for support of multigrid algorithms. The concept of guard strips is generalized to an object implementation of lightweight sharing mechanisms for finite element method (FEM) and particle-in-cell (PIC) algorithms. The sharing is accomplished through the mechanism of weak memory coherence and can be efficiently implemented. The price of the efficient implementation is memory usage and the need to explicitly specify the coherence operations. An intriguing feature of this programming model is that it maps well to both distributed-memory and shared-memory architectures

Monte Carlo Methods in Lattice Gauge Theories

In this work, we study various Monte Carlo methods for lattice gauge theories. The mass of the 0+ glueball for SU(2) gauge theory in 4 dimensions is calculated. This computation was done on a prototype parallel processor and the implementation of gauge theories on this system is described in detail. Using an action of the purely Wilson form (trace of plaquette in the fundamental representation), we obtain results with high statistics . We conclude that these results are not consistent with scaling according to the continuum renormalization group. Using actions containing higher representations of the group, we search for one which is closer to the continuum limit. Our choice is based upon the phase structure of these extended theories and also upon the Migdal-Kadanoff approximation to the renormalization group on the lattice . We obtain the mass of the 0+ glueball for this improved action and find that the mass divided by the square root of the string tension is a constant as the lattice spacing is varied. We conclude that scaling has set in and that this lattice theory is closer to the continuum limit than the simple Wilson version. The other topic studied is the inclusion of dynamical fermions into Monte Carlo calculations via the pseudo fermion technique. Monte Carlo results obtained with this method are compared with those from an exact algorithm based on Gauss-Seidel inversion. We first apply the methods to the Schwinger model (QED in 1 + 1 dimensions) and show, in a coupling regime where the dynamical fermions have a nontrivial effect, that the mass gap is obtained with the correct value . After giving simple arguments explaining why the method works better than expected, we turn to a study of SU(3) in 4 dimensions (although on small lattices). Comparing with the exact algorithm, we again find encouraging agreement with the pseudo fermion technique. Evidence is given which shows that any systematic bias, associated with the breaking of the Markov process which generates the field configurations, is small.</p

Fast local fragment chaining using sum-of-pair gap costs

<p>Abstract</p> <p>Background</p> <p>Fast seed-based alignment heuristics such as <monospace>BLAST</monospace> and <monospace>BLAT</monospace> have become indispensable tools in comparative genomics for all studies aiming at the evolutionary relations of proteins, genes, and non-coding RNAs. This is true in particular for the large mammalian genomes. The sensitivity and specificity of these tools, however, crucially depend on parameters such as seed sizes or maximum expectation values. In settings that require high sensitivity the amount of short local match fragments easily becomes intractable. Then, fragment chaining is a powerful leverage to quickly connect, score, and rank the fragments to improve the specificity.</p> <p>Results</p> <p>Here we present a fast and flexible fragment chainer that for the first time also supports a sum-of-pair gap cost model. This model has proven to achieve a higher accuracy and sensitivity in its own field of application. Due to a highly time-efficient index structure our method outperforms the only existing tool for fragment chaining under the linear gap cost model. It can easily be applied to the output generated by alignment tools such as <monospace>segemehl</monospace> or <monospace>BLAST</monospace>. As an example we consider homology-based searches for human and mouse snoRNAs demonstrating that a highly sensitive <monospace>BLAST</monospace> search with subsequent chaining is an attractive option. The sum-of-pair gap costs provide a substantial advantage is this context.</p> <p>Conclusions</p> <p>Chaining of short match fragments helps to quickly and accurately identify regions of homology that may not be found using local alignment heuristics alone. By providing both the linear and the sum-of-pair gap cost model, a wider range of application can be covered. The software clasp is available at <url>http://www.bioinf.uni-leipzig.de/Software/clasp/</url>.</p

A User-Level Process Package for Concurrent Computing

A lightweight user-level process(ULP) package for parallel computing is described. Each ULP has its own register context, stack, data and heap space and communication with other ULPs is performed using locally synchronous, location transparent, message passing primitives. The aim of the package is to provide support for lightweight over-decomposition, optimized local communication and transparent dynamic migration. The package supports a subset of the Parallel Virtual Machine(PVM) interface[Sun90)

Analysis of EEC Regulation 2092/91 in relation to other national and international organic standards

This Deliverable 3.2 report presents an analysis of differences between EEC Regulation 2092/91 and other organic standards and their implementation, using a specially developed database (www.organicrules.org). It further reports on database development. The work was carried out as part of the “EEC 2092/91 (Organic) Revision” STREP project (No. SSPE-CT- 2004-502397) within the EU 6th Framework Programme. The main objective was to identify differences in organic standards in relation to Regulation (EEC) 2092/91 and to analyse selected national governmental and private organic standards with the aim of identifying specific areas in the (EEC) 2092/91 where revision in terms of harmonisation, regionalisation or simplification may be possible

Increasing Durability of Flame-Sprayed Strain Gauges

Thermally sprayed dielectric ceramic coatings are the primary means of attaching strain and temperature gauges to hot-section rotating parts of turbine engines. As hot-section temperatures increase, lifetimes of installed gauges decrease, and seldom exceed one hour above 2,000 F (approx.1,100 C). Advanced engine components are expected to operate at temperatures approaching 2,200 F (approx.1,200 C), and the required high-temperature lifetime is 10 hours minimum. Typically, to enable a ceramic coating to adhere to the smooth surface of an engine component, a thermally sprayed NiCrAlY or NiCoCrAlY bond coat is applied to the smooth surface, thereby providing a textured surface to which the ceramic coat can adhere. The main failure mechanism of this system is decohesion and/or delamination at the interface between the ceramic top coat and the bond coat, caused by oxidation of the bond coat and stresses from the mismatch between the coefficients of thermal expansion of the ceramic top coat and the metallic bond coat. The approach taken to increase the high-temperature lifetime of a gauge attached to an engine component by the method described above involves (1) selective oxidation of the bond coat by means of a heat treatment in reduced oxygen partial pressure followed by (2) the application of a noble-metal diffusion barrier. In experiments to test this approach, heat treatments of NiCoCrAlY bond coats were carried out in a tube furnace in which, in each case, the temperature was alternately (1) increased at a rate of 3 C per minute and (2) held steady for one hour until the desired temperature was reached. The tube furnace was continuously purged with dry nitrogen gas. A final heat-treatment temperature range of 1,600 to 1,800 F (871 to 982 C) proved most beneficial