2003 Abstracts of MCS Reports and Preprints |
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Reports |
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| S. Benson, L. C. McInnes, J. J. More', J. Sarich, "TAO Users Manual," Technical Memorandum ANL/MCS-TM-242, Nov. 2003. | The Toolkit for Advanced Optimization (TAO) focuses on the development
of algorithms and software for the solution of large-scale optimization problems on high-performance architectures. Areas of
interest include nonlinear least squares, unconstrained and bound-constrained optimization, and general nonlinear optimization. The development of TAO was motivated by the scattered support for parallel computations and the lack of reuse of external toolkits in current optimization software. Our aim is to use object-oriented techniques to produce high-quality optimization software for a range of computing environments ranging from serial workstations and laptops to massively parallel high-performance architectures. Our design decisions are strongly motivated by the challenges inherent in the use of large-scale distributed memory architectures and the reality of working with large, often poorly structured legacy codes for specific applications. This manual describes the use of TAO. Since TAO is still under development, changes in usage and calling sequences may occur. TAO is fully supported; see the web site http://www.mcs.anl.gov/tao for information on contacting the TAO developers. |
| R. Evard, P. Beckman, S. Bittner, R. Bradshaw, S. Coghlan, N. Desai, B. Finley, E. Rackow, J.-P. Navarro, "The Production Cluster Construction Checklist," Technical Memorandum ANL/MCS-TM-267, October 2003. |
This document is a detailed checklist of the steps that one must go through to bring up a production computing cluster. The list starts with planning activities and culminates in the activities necessary to operate and sustain a production computing facility. This checklist is derived from a number of experiences installing real-world, large-scale clusters. While each installation experience was unique, we were interested in determining the common characteristics across each deployment. We collected all of the to-do lists, presentations, notes, email messages, white board notes, and any other planning tools we could find from each of the installation activities. We combined them into a huge, messy diagram that was probably impossible to understand without having been involved in its creation but was excellent for identifying differences and commonalities. After organizing, checking, and distilling the information, we created the checklist presented here. Interesting is the fact that the high-level activities on the resulting list are neither cluster nor computer specific. Most of these activities would be followed when installing a production computer of any architecture or when installing any kind of complex facility that will eventually support users. The purpose of this list is not to give step-by-step instructions but rather to serve as a guide and a reminder. The items on the list are necessarily brief statements. Detailed explanations of these would go beyond the intended scope of the list. The list is organized in outline fashion. The major phases of construction are individual sections. Each of the subsections is a task or subtask in that phase. The items on this list are presented in a logical sequence, in approximately the order that one would follow if one were to start with a budget and an idea. However, every cluster is different, and every situation for using clusters is different. Most likely, no one would ever follow the steps here in this exact order; many things can be done in a different order, simultaneously, or skipped altogether. The list, for example, may place more emphasis on testing than many sites formally will. |
| M. Hereld, I. R. Judson, R. Stevens, "Application Performance Evaluation of the HTMT Architecture," Technical Memorandum ANL/MCS- TM-258, January 2003. | In
this report we summarize findings from a study of the predicted
performance of a suite of application codes taken from the research
environment and analyzed against a modeling framework for the HTMT
architecture. We find that the inward bandwidth of the data vortex may be
a limiting factor for some applications. We also find that available
memory in the cryogenic layer is a constraining factor in the partitioning
of applications into parcels. The architecture in several examples may be
inadequately exploited; in particular, applications typically did not
capitalize well on the available computational power or data
organizational capability in the PIM layers. The application suite
provided significant examples of wide excursions from the accepted (if
simplified) program execution model – in particular, by required complex
in-SPELL synchronization between parcels. The availability of the HTMT-C
emulation environment did not contribute significantly to the ability to
analyze applications, because of the large gap between the available
hardware descriptions and parameters in the modeling framework and the
types of data that could be collected via HTMT-C emulation runs. Detailed
analysis of application performance, and indeed further credible
development of the HTMT-inspired program execution model and system
architecture, requires development of much better tools. Chief among them
are cycle-accurate simulation tools for computational, network, and memory
components. Additionally, there is a critical need for a whole system
simulation tool to allow detailed programming exercises and performance
tests to be developed. |
| K. Keahey and K. Motawi, "The Taming of the Grid: Virtual Application Services," Technical Memorandum ANL/MCS-TM-262, May 2003. | In this report we develop a view of the Grid based on the application service provider (ASP) model. This view enables the user to see the Grid as a collection of application services that can be published, discovered, and accessed in a relatively straightforward manner, hiding much of the complexity involved in using computational Grids and thus making it simpler and more accessible to a wider range of users. However, in order to satisfy the requirements of real-time scientific application clients, we combine the ASP model with representation of quality of service about the execution of services and the results they produce. Specifically, we focus on real-time, deadline-bound execution as the quality of service derived by a client. We describe an architecture implementing these ideas and the role of client and server in the context of the functionality we develop. We also describe preliminary experiments using an equilibrium fitting application for magnetic fusion in our architecture. |
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O. S. Matlin, W. McCune, E. Lusk, "Methods to Model-Check Parallel
Systems Software," Technical Memorandum ANL/MCS-TM-261,
April 2003.
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We report on an effort to develop methodologies for formal verification of parts of the Multi-Purpose Daemon (MPD) parallel process management system. MPD is a distributed collection of communicating processes. While the individual components of the collection execute simple algorithms, their interaction leads to unexpected errors that are difficult to uncover by conventional means. Two verification approaches are discussed here: the standard model checking approach using the software model checker SPIN and the nonstandard use of a general-purpose first-order resolution-style theorem prover OTTER to conduct the traditional state space exploration. We compare modeling methodology and analyze performance and scalability of the two methods with respect to verification of MPD. |
| W. McCune, "OTTER 3.3 Reference Manual," Technical Memorandum ANL/MCS-TM-263, August 2003. | OTTER is a resolution-style theorem-proving program for first-order logic with equality. OTTER includes the inference rules binary resolution, hyperresolution, UR-resolution, and binary paramodulation. Some of its other abilities and features are conversion from first-order formulas to clauses, forward and back subsumption, factoring, weighting, answer literals, term ordering, forward and back demodulation, evaluable functions and predicates, Knuth-Bendix completion, and the hints strategy. OTTER is coded in ANSI C, is free, and is portable to many different kinds of computer. |
| W. McCune, "Mace4 Reference Manual and Guide," Technical Memorandum ANL/MCS-TM-264, August 2003. | Mace4 is a program that searches for finite models of first-order formulas. For a given domain size, all instances of the formulas over the domain are constructed. The result is a set of ground clauses with equality. Then, a decision procedure based on ground equational rewriting is applied. If satisfiability is detected, one or more models are printed. Mace4 is a useful complement to first-order theorem provers, with the prover searching for proofs and Mace4 looking for countermodels, and it is useful for work on finite algebras. Mace4 performs better on equational problems than did our previous model-searching program Mace2. |
| W. McCune, R. Padmanabhan, M. A. Rose, R. Veroff, "Short Equational Bases for Ortholattices: Proofs and Countermodels," Technical Memorandum ANL/MCS-TM-265, September 2003. | This document contains proofs and countermodels in support of the
paper "Short Equational Bases for Ortholattices'', by the same set of authors. In that paper, short single axioms for
ortholattices, orthomodular lattices, and modular ortholattices are presented, all in terms of the Sheffer stroke. The ortholattice axiom is the shortest possible. Other equational bases in terms of the Sheffer stroke and in terms of join, meet, and complement are presented. Computers were used extensively to find candidates, reject candidates, and search for proofs that candidates are single axioms. |
| U. Naumann and A. Walther, "An Introduction to Using Software Tools for Automatic Differentiation," Technical Memorandum ANL/MCS-TM-254, July 2003. | We give a gentle introduction to using various software tools for automatic differentiation (AD). Ready-to-use examples are discussed, and links to further information are presented. Our target audience includes all those who are looking for a straightforward way to get started using the available AD technology. The document is dynamic in the sense that its content will be updated as the AD software evolves. |
| Preprints | |
| A. Albrecht, P. Gottschling, and U. Naumann, "Markowitz-Type Heuristics for Computing Jacobian Matrices Efficiently, Proc. ICCS 2003, St. Petersburg, Russia, 6/2-4/2003, Springer LNCS 2658, pp. 575-584. Also Preprint ANL/MCS-P933-0202, February 2003. | We consider the problem of accumulating the Jacobian matrix of a nonlinear vector function by using a minimal number of arithmetic operations. Two new Markowitz-type heuristics are proposed for vertex elimination in linearized computational graphs, and their superiority over existing approaches is shown by several tests. Similar ideas are applied to drive new heuristics for edge elimination techniques. The well known superiority of edge over vertex elimination can be observed only partially for the heuristics discussed in this paper. Nevertheless, significant improvements can be achieved by the new heuristics both in terms of the quality of the results and their robustness with respect to different tiebreaking criteria. |
| M. Cohen, U. Naumann, J. Riehme, "Towards Differentiation-Enabled Fortran 95 Compiler Technology," Proc. ACM Symp. on Applied Computing, Melbourne, FL, 3/9-12/2003, pp. 143-147. Also Preprint ANL/MCS-P935-0202, May 2003. | We present a novel approach to generating derivative code for mathematical models implemented as Fortran 95 programs using Automatic Differentiation inside a compiler. This technique allows us to combine the advantages of both operator overloading and source transformation based tools for Automatic Differentiation. Furthermore, the compiler's infrastructure for syntactic, semantic, and static data flow analysis can be built on. |
| L. Hascoët, U. Naumann, and V. Pascual, "TBR Analysis in Reverse-Mode Automatic Differentiation," Preprint ANL/MCS-P936-0202, February 2003. | The automatic generation of adjoints of mathematical models
that are implemented as computer programs is receiving a increased attention in the scientific and engineering
communities. Reverse-mode automatic differentiation is of particular interest
for large-scale optimization problems. It allows the computation of gradients
at a small constant multiple of the cost for evaluating the objective function itself, that is independent of the number of input parameters.
Source-to-source transformation tools for automatic differentiation are available to generate adjoint codes based on the adjoint version of every statement that can be built by applying simple differentiation rules. Therefore, a reversal of the control flow of the original program becomes necessary. To guarantee correctness, certain values that are computed and overwritten in the original program must be made available in the adjoint program. They can be determined by performing a static data flow analysis, the so-called TBR analysis. Overestimation of this set must be kept minimal to get efficient adjoint codes. For many real-world applications the applicability of source-to-source transformation tools for automatic differentiation cannot be achieved without this efficiency. |
| U. Naumann, "Optimal Accumulation of Jacobian Matrices by Elimination Methods on the Dual Computational Graph," Preprint ANL/MCS-P943-0402, April 2003. | The accumulation of the Jacobian matrix $F'$ of a vector function F: R[sup n] -> R[sup m] can be regarded as a transformation of its linearized computational graph into a subgraph of the directed complete bipartite graph K[sub n,m]. This transformation can be performed by applying different elimination techniques that may lead to varying costs for computing F'. This paper introduces face elimination as the basic technique for accumulating Jacobian matrices by using a minimal number of arithmetic operations. Its superiority over both edge and vertex elimination methods is shown. The intention is to establish the conceptual basis for the ongoing development of algorithms for optimizing the computation of Jacobian matrices. |
| J. No, R. Thakur, A. Choudhary, "High-Performance Scientific Data Management System," Preprint ANL/MCS-P973-0502, April 2003. | Many scientific applications have large I/O requirements, in terms of both the size of data and the number of files or data sets. Management, storage, efficient access, and analysis of this data present an extremely challenging task. Traditionally, two different solutions have been used for this task: file I/O or databases. File I/O can provide high performance but is tedious to use with large numbers of files and large and complex data sets. Databases can be convenient, flexible, and powerful but do not perform and scale well for parallel supercomputing applications. We have developed a software system, called Scientific Data Manager (SDM), that combines the good features of both file I/O and databases. SDM provides a high-level API to the user and, internally, uses a parallel file system to store real data (using various I/O optimizations available in MPI-IO) and a database to store application-related metadata. In order to support I/O in irregular applications, SDM makes extensive use of MPI-IO's noncontiguous collective I/O functions. Moreover, SDM uses the concept of a history file to optimize the cost of the index distribution using the metadata stored in database. We describe the design and implementation of SDM and present performance results with two regular applications, ASTRO3D and an Euler solver, and with two irregular applications, a CFD code called FUN3D and a Rayleigh-Taylor instability code. |
| R. Butler, N. Desai, A. Lusk, and E. Lusk, "The Process Management Component of a Scalable Systems Software Environment," Preprint ANL/MCS-P987-0802, August 2003. | The systems software necessary to operate large-scale parallel computers presents a variety of research and development issues. One approach is to consider systems software as a collection of interacting components, with well-defined published interfaces. The Scalable Systems software SciDAC project is currently exploring the feasibility of architecting systems software this way. In this paper we present a prototype process manager component for such a system. We describe the component abstractly in terms of its functionality and the interface by which its functionality may be invoked. We propose a precise syntax for this interface and describe one implementation of the process manager component, based on an existing scalable process management system called MPD. We conclude with some experiences using this process manager component in conjunction with other systems software components on a medium-sized Linux cluster. |
| J. N. Lyness and T. Sorevik, "Four-Dimensional Lattice Rules Generated by Skew-circulant Matrices," Preprint ANL/MCS-P1012-0702, January 2002. | We introduce the class of skew-circulant lattice rules. These are s-dimensional lattice rules that may be generated by the rows of an s x s skew-circulant matrix. (This is a minor variant of the familiar circulant matrix.) We present briefly some of the underlying theory of these matrices and rules. We are particularly interested in finding rules of specified trigonometric degree d. We describe some of the results of computer-based searches for optimal four-dimensional skew-circulant rules. Besides determining optimal rules for \delta = d + 1 <= 47, we have constructed an infinite sequence of rules Q(4,\delta) that has a limit rho index of 27/34 ~~ 0.79. This index is an efficiency measure, which cannot exceed 1, and is inversely proportional to the abscissa count. |
| G. von Laszewski, J. Gawor, S. Krishnan, K. Jackson, "Commodity Grid Kits - Middleware for Building Grid Computing Environments," Preprint ANL/MCS-1016-0103, Jan. 2003. | Recent Grid projects, such as the Globus Project, provide a set of useful services such as authentication and remote access to resources, and information services to discover and query such remote resources. Unfortunately, these services may not be compatible with the commodity technologies used for application development by the software engineers and scientists. Instead, users may prefer accessing the Grid from a higher level of abstraction than what such toolkits provide. To bridge this gap, Commodity Grid (CoG) Kits provide the middleware for accessing the functionality of the Grid from a variety of commodity technologies, frameworks, and languages. It is important to recognize that these Commodity Grid Kits not only provide an interface to existing Grid technologies, but also bring Grid programming to a new level by leveraging the methodologies of the chosen commodity technology, thus helping the development of the next generation of Grid services. Based on these Commodity Grid Toolkits, a variety of higher level Grid services are far easier to design, maintain, and deploy. Several projects have successfully demonstrated the use of Commodity Grid Kits for the design of advanced Grid Services and Grid Computing Environments. |
| J. J. Evans, S. Baik, C. S. Hood, W. Gropp, "Toward Understanding Soft Faults in High Performance Cluster Networks," Preprint ANL/MCS-P1017-0103, Jan. 2003. | Fault management in high performance cluster networks has been focused on the notion of hard faults (i.e., link or node failures). Network degradations that negatively impact performance but do not result in failures often go unnoticed. In this paper, we classify such degradations as soft faults. In addition, we identify consistent performance as an important requirement in cluster networks. Using this service requirement, we describe a comprehensive strategy for cluster fault management. |
| U. Naumann and P. Heimbach, "Coupling Tangent-Linear and Adjoint Models," Preprint ANL/MCS-P1022-0203, June 2003. | We consider the solution of a (generalized) eigenvalue problem arising in physical oceanography that involves the evaluation of both the tangent-linear and adjoint versions of the underlying numerical model. Two different approaches are discussed. First, tangent-linear and adjoint models are generated by the software tool TAF and used separately. Second, the two models are combined into a single derivative model based on optimally preaccumulated local gradients of all scalar assignments. The coupled tangent-linear / adjoint model promises to be a good solution for small or medium sized problems. However, the simplicity of the example code at hand prevents us from observing considerable run time differences between the two approaches. |
| M. Anitescu, A. Miller, G. D. Hart, "Constraint Stabilization for Time-Stepping Approaches for Rigid Multibody Dynamics with Joints, Contact, and Friction," Proc. DETC'03 (to appear). Also Preprint ANL/MCS-P1023-0403, April 2003. | We present a method for achieving geometrical constraint stabilization for a linear-complementarity-based time-stepping scheme for rigid multibody dynamics with joints, contact, and friction. The method requires the solution of only one linear complementarity problem per step. The method depends on an adjustable parameter \gamma, but the constraint stabilization effect is shown to hold for any \gamma in (0,1]. Several examples are used to demonstrate the constraint stabilization effect. |
| V. Welch, F. Siebenlist, I.Foster, J.Bresnahan, K.Czajkowski, J.Gawor, C.Kesselman, S.Meder, L.Pearlman, S.Tuecke, "Security for Grid Services," Preprint ANL/MCS-P1024-0203, Feb. 2003. | Grid computing is concerned with the sharing and coordinated use of diverse resources in distributed "virtual organizations." The dynamic and multi-institutional nature of these environments introduces challenging security issues that demand new technical approaches. In particular, one must deal with diverse local mechanisms, support dynamic creation of services, and enable dynamic creation of trust domains. We describe how these issues are addressed in two generations of the Globus Toolkit®. First, we review the Globus Toolkit version 2 (GT2) approach; then, we describe new approaches developed to support the Globus Toolkit version 3 (GT3) implementation of the Open Grid Services Architecture, an initiative that is recasting Grid concepts within a service-oriented framework based on Web services. GT3's security implementation uses Web services security mechanisms for credential exchange and other purposes, and introduces a tight least-privilege model that avoids the need for any privileged network service. |
| S. Leyffer, "Mathematical Programs with Complementarity Constraints," Preprint ANL/MCS-P1026-0203, February 2003. | An exciting new application of nonlinear programming techniques is mathematical programs with complementarity constraints (MPCC). |
| S. Bhowmick, L. McInnes, B. Norris, P. Raghavan, "The Role of Multimethod Linear Solvers in PDE-Based Simulations," Preprint ANL/MCS-P1027-0203, Feb. 2003. | The solution of large-scale, nonlinear PDE-based simulations typically depends on the performance of sparse linear solvers, which may be invoked at each nonlinear iteration. We present a framework for using multimethod solvers in such simulations to potentially improve the execution time and reliability of linear system solution. We consider composite solvers, which provide reliable linear solution by using a sequence of preconditioned iterative methods on a given system until convergence is achieved. We also consider adaptive solvers, where the solution method is selected dynamically to match the attributes of linear systems as they change during the course of the nonlinear iterations. We demonstrate how such multimethod composite and adaptive solvers can be developed using advanced software architectures such as PETSc, and we report on their performance in a computational fluid dynamics application. |
| P. Hovland, K. Keahey, L. C. McInnes, B. Norris, L. Freitag, P. Raghavan, "A Quality-of-Service Architecture for High-Performance Numerical Components," Preprint ANL/MCS-P1028-0203, Feb. 2003. | We propose a model for QoS-based composition of high-performance numerical components. We define an architecture that relies on five key capabilities and services including component characterization, component proxy services, component replacement, a decision module, and archival run information processing. We describe quality metrics that are important for high-performance numerical simulations, including computational cost, accuracy, and rates of convergence and failure. We discuss the use of the architecture and quality metrics in the context of a driven cavity flow simulation, which has been shown to benefit from adaptive solution techniques that could be derived from a QoS architecture. |
| A. Rodriguez, D. Sulakhe, E. Marland, V. Nefedova, G. X. Yu, and N. Maltsev, "GADU - Genome Analysis and Database Update Pipeline," Preprint ANL/MCS-P1029-0203, February 2003. | Realizing the enormous scientific potential of exponentially growing biological information requires the development of high-throughput automated computational environments that integrate large amounts of genomic and experimental data, and powerful tools for knowledge discovery and data mining. To assist high-throughput analysis of the genomes, we have developed the Genome Analyssis and Databases Update system. GADU efficiently automates major steps of genome analysis: data acquisition and data analysis by a variety of tools and algorithms, as well as data storage and annotation. We are developing a TeraGrid technology-based backend for large-scale computations using GADU. GADU can function in either an automated or interactive mode via a Web-based user interface. Programs monitor every operation in GADU and report the status of the process. This architecture ensures GADU's robust performance and allows simultaneous processing of a large number of sequenced genomes regardless of their size. |
| N. T. Karonis, M. E. Papka, J. Binns, J. Bresnahan, J. A. Insley, D. Jones, J. M. Link, "High-Resolution Remote Rendering of Large Datasets in a Collaborative Environment," Future Generation Computer Systems 19 (2003), 900-917. Also Preprint ANL/MCS-P1030-0203, February 2003. | In a time when computational and data resources are distributed around the globe, users need to interact with these resources and each other easily and efficiently. The Grid, by definition, represents a connection of distributed resources that can be used regardless of the user's location. We have built a prototype visualization system using the Globus Toolkit, MPICH-G2, and the Access Grid in order to explore how future scientific collaborations may occur over the Grid. We describe our experience in demonstrating our system at iGrid2002, where the United States and the Netherlands were connected via a high-latency, high-bandwidth network. In particular, we focus on issues related to a grid-based application that couples a collaboration component (including a user interface to the Access Grid) with a high-resolution remote rendering component. |
| U. Naumann and P. Gottschling, "Simulated Annealing for Optimal Pivot Selection in Jacobian Accumulation," to appear in Proc. 2nd Symp. on Stochastic Algorithms, Foundations and Applications. Also Preprint ANL/MCS-P1032-0303, March 2003. | We report on new results in logarithmic simulated annealing
applied to the optimal Jacobian accumulation problem. This is a continuation
of work that was presented at the SAGA'01 conference in Berlin, Germany. We discuss the optimal edge elimination problem in linearized computational graphs in the context of linear algebra. We introduce row and column pivoting on the extended Jacobian as analogs to front and back edge elimination in linearized computational graphs. Neighborhood relations for simulated annealing are defined on a metagraph that is derived from the computational graph. All prerequisites for logarithmic simulated annealing are fulfilled for dyadic pivoting, which is equivalent to vertex elimination in linearized computational graphs. For row and column pivoting we cannot yet give a proof that the corresponding elimination sequences are polynomial in size. In practice, however, the likelihood for an exponential elimination sequence to occur is negligible. Numerical results are presented for algorithms based on both homogeneous and inhomogeneous Markov chains for all pivoting techniques. The superiority of row and column pivoting over dyadic pivoting can be observed when applying these techniques to Roe's numerical flux. |
| S. Vazhkudai and J. M. Schopf, "Using Regression Techniques to Predict Large Data Transfers," The International Journal of High Performance Computing Applications (IJHPCA), special issue on Grid Computing: Infrastructure and Applications, vol. 17, No. 3, August 2003. Also Preprint ANL/MCS-P1033-0303, March 2003. | The recent proliferation of Data Grids and the increasingly common practice of using resources as distributed data stores provide a convenient environment for communities of researchers to share, replicate, and manage access to copies of large datasets. This has led to the question of which replica can be accessed most efficiently. In such environments, fetching data from one of the several replica locations requires accurate predictions of end-to-end transfer times. The answer to this question can depend on many factors, including physical characteristics of the resources and the load behavior on the CPUs, networks, and storage devices that are part of the end-to-end data path linking possible sources and sinks. Our approach combines end-to-end application throughput observations with network and disk load variations and captures whole-system performance and variations in load patterns. Our predictions characterize the effect of load variations of several shared devices (network and disk) on file transfer times. We develop a suite of univariate and multivariate predictors that can use multiple data sources to improve the accuracy of the predictions as well as address Data Grid variations (availability of data and sporadic nature of transfers). We ran a large set of data transfer experiments using GridFTP and observed performance predictions within 15% error for our testbed sites, which is quite promising for a pragmatic system. |
| M. Anitescu, "A Fixed Time-Step Approach for Multibody Dynamics with Contact and Friction," Preprint ANL/MCS-P1034-0303, March 2003. | We present a fixed time-step algorithm for the simulation of multi-rigid-body dynamics with joints, contact, collision, and friction. The method solves a linear complementarity problem (LCP) at each step. We show that the algorithm can be obtained as the stiff limit of fixed time-step schemes applied to regularized contact models. We do not perform collision detection. Instead, a noninterpenetration constraint is replaced by its linearization, which, together with a judicious choice of the active constraints, guarantees geometrical constraint stabilization without the need to perform a reduction of the time step to detect new collision or stick-slip transition events. Partially elastic collisions are accommodated by a suitable modification of the free term of the LCP. |
| W. Allcock, J. Bresnahan, J. Bunn, S. Hedge, J. Insley, R. Kettimuthu, H. Newman, S. Ravot, T. Rimovsky, C. Steenberg, L. Winkler, "Grid-Enables Particle Physics Event Analysis: Experiences Using a 10 Gb, High-Latency Network for a High-Energy Physics Application," Future Generation Computer Systems 19(6) (2003), pp. 983-997. Also Preprint ANL/MCS-P1035-0303, March 2003. | This paper examines issues encountered attempting to exploit a high-bandwidth, high-latency link in support of a high-energy physics (HEP) analysis application. The primary issue was that the TCP additive increase/multiplicative decrease (AIMD) algorithm is not suitable for "long fat networks". While this is a known problem, the magnitude of the impact on application performance was much greater than anticipated. We were able to overcome much of the impact by altering the AIMD coefficients. Such an approach, of course, is non-TCP compliant, and there was insufficient time to test the network friendliness of these modifications. |
| A. Grimshaw and S. Tuecke, "Grid Services Extend Web Services," Web Services Journal (to appear Aug. 2003). Also Preprint ANL/MCS-P1036-0303, March 2003. | We are often asked by people who are trying to understand the value Grid technology brings to Web services, "what is the significance of Grid services? They look like Web services." The answer to this question is superficially straightforward: mechanically, the differences between Grid services (as defined in the Grid service specification) and Web services are few: to first order, a Grid service is simply a Web service that conforms to a particular set of conventions. For example, Grid services are defined in terms of standard WSDL (Web Services Definition Language) with minor extensions, and exploit standard Web service binding technologies such as SOAP (Simple Object Access Protocol) and WS-Security (Web Services Security). So yes, Grid services do look like Web services, etc. |
| L. A. Freitag and R. M. Loy, "Theoretical Cost Comparison of Remote Visualization Strategies," Preprint ANL/MCS-P1037-0303, March 2003. | We compare three remote visualization strategies used for interactive exploration of large data sets in distributed environments: image-based rendering, parallel visualization servers, and subsampling. To determine the regimes for which each approach is most cost-effective, we develop performance models to study the computation and communication costs associated with the common visualization task of isosurface generation. For one particular strategy, subsampling, we further investigate the tradeoffs between multiresolution and uniform grid methods in terms of performance and approximation errors. |
| R. Thakur and W. Gropp, "Improving the Performance of Collective Operations in MPICH," Preprint ANL/MCS-P1038-0403, April 2003. | We report on our work on improving the performance of collective operations in MPICH on clusters connected by switched networks. For each collective operation, we use multiple algorithms depending on the message size, with the goal of minimizing latency for short messages and minimizing bandwidth usage for long messages. Although we have implemented new algorithms for all MPI collective operations, because of limited space we describe only the algorithms for allgather, broadcast, reduce-scatter, and reduce. We present performance results using the SKaMPI benchmark on a Myrinet-connected Linux cluster and an IBM SP. In all cases, the new algorithms significantly outperform the old algorithms used in MPICH on the Myrinet cluster, and, in many cases, they outperform the algorithms used in IBM's MPI on the SP. |
| O. S. Matlin and W. McCune, "Encapsulation for Practical Simplification Procedures," Preprint ANL/MCS-P1039-0403, April 2003. | ACL2 was used to prove properties of two simplification procedures. The procedures differ in complexity but solve the same programming problem that arises in the context of a resolution/paramodulation theorem proving system. Term rewriting is at the core of the two procedures, but details of the rewriting procedure itself are irrelevant. The ACL2 encapsulate construct was used to assert the existence of the rewriting function and to state some of its properties. Termination, irreducibility, and soundness properties were established for each procedure. The availability of the encapsulation mechanism in ACL2 is considered essential to rapid and efficient verification of this kind of algorithm. |
| X. Zhang, J. Freschl, and J. M. Schopf, "A Performance Study of Monitoring and Information Services for Distribution Systems," Preprint ANL/MCS-P1040-0403, April 2003. | Monitoring
and information services form a key component of a distributed system, or
Grid. A quantitative study of such services can aid in understanding the
performance limitations, advise in the deployment of the systems, and help
evaluate future development work. To this end, we study the performance of
three monitoring and information services for distributed systems: the
Globus Toolkit’s Monitoring and Discovery Service (MDS), the European
Data Grid Relational Grid Monitoring Architecture (R-GMA) and Hawkeye,
part of the Condor project. We perform experiments to test their
scalability with respect to number of users, number of resources and
amount of data collected. Our study shows that each approach has different behaviors, often due to
their different design goals. In the four sets of experiments we conducted
to evaluate the performance of the service components under different
circumstances, we found a strong advantage to caching or pre-fetching the
data, as well as the need to have primary components at well connected
sites due to high load seen by all systems. |
| I. Lee, P. Raghavan, S. Schofield, and P. Fischer, "An O(n log n) Solution Algorithm for Spectral Element Methods," Preprint ANL/MCS-P1041-0403, April 2003. | Many three-dimensional flow problems in science and engineering feature geometries that are homogeneous in at least one flow direction. Two examples are the high-aspect-ratio domains in Fig. 1, which shows spectral element (SE) meshes currently being used for simulations of Rayleigh-Bénard convection (a) and reactor core cooling (b). In these cases, the numerical simulation costs can often be reduced by recasting the original problem (or subproblem) in terms of eigenvectors of the (discrete) one-dimensional operators to yield a set of decoupled problems of lower dimension. Here, we consider application of this approach to reduce three-dimensional problems to independent two-dimensional subproblems. The costs of performing the transformations and solving the subproblems is addressed, and we show that it is possible to achieve O(n log n) complexity for n-gridpoint problems in R3. |
| S. Byna, W. Gropp, X.-H. Sun, R. Thakur, "Improving the Performance of MPI Derived Datatypes by Optimizing Memory-Access Cost," Preprint ANL/MCS-P1045-0403, April 2003. | The MPI Standard supports derived datatypes, which allow users to describe noncontiguous memory layout and communicate noncontiguous data with a single communication function. This feature enables an MPI implementation to optimize the transfer of noncontiguous data. In practice, however, few MPI implementations implement derived datatypes in a way that performs better than what the user can achieve by manually packing data into a contiguous buffer and then calling an MPI function. In this paper, we present a technique for improving the performance of derived datatypes by automatically using packing algorithms that are optimized for memory-access cost. The packing algorithms are memory-optimization techniques that the user cannot apply easily without advanced knowledge of the memory architecture. We present performance results for a matrix-transpose example that demonstrate that our implementation of derived datatypes significantly outperforms both manual packing by the user and the existing derived-datatype code in the MPI implementation (MPICH). |
| S. Anand, S. Yoginath, G. von Laszewski, B. Alunkal, X.-H. Sun, "Flow-based Multistage Co-allocation Service," Preprint ANL/MCS-P1046-0403, April 2003. | The concept of co-allocation provides a simple mechanism to request and bind resources in a coordinated fashion in Grids across virtual organization boundaries. We have designed an advanced multistage co-allocation strategy based on resource hierarchies defined through user-specific patterns. The model manages simple flows between resources to perform managed job executions. We demonstrate the usefulness of our model on several examples and discuss advantages and disadvantages of the model. |
| G. von Laszewski, B. Alunkal, J. Gawor, R. Madduri, P. Plaszczak, X.-H. Sun, "A File Transfer Component for Grids," Preprint ANL/MCS-P1047-0403, April 2003. | Grids have become a critical asset in large-scale scientific and engineering research. Accessing to distributed data is typically as important as access to distributed computational resources. In this paper, we present the design of Java CoG Kit components and APIs that make handling of data accessed through Grids easier for the novice Grid user and programmer. We introduce the design and architecture of a component for file transfers that separates issues related to requesting, performing and visualizing the actual file transfer. The design of our component is based on object and component based methodologies. Hence, it is assembled from a collection of reusable components promoting customization and reuse. We integrated the drag-and-drop paradigm. Protocol-independent interfaces allow easy adaptation to a variety of data sources. Hence, we not only have developed a GUI but sophisticated middleware to develop advanced Grid file transfer services. These components are distributed with the Java CoG Kit. |
| J. Li, W.-K. Liao, A. Choudhary, R. Ross, R. Thakur, W. Gropp, R. Latham, "Parallel netCDF: A Scientific High-Performance I/O Interface," Preprint ANL/MCS-P1048-0503, May 2003. | Dataset storage, exchange, and access play a critical role in scientific applications. For such purposes netCDF serves as a portable and efficient file format and programming interface, which is popular in numerous scientific application domains. However, the original interface does not provide an efficient mechanism for parallel data storage and access. In this work, we present a new parallel interface for writing and reading netCDF datasets. This interface is derived with minimal changes from the serial netCDF interface but defines semantics for parallel access and is tailored for high performance. The underlying parallel I/O is achieved through MPI-IO, allowing for dramatic performance gains through the use of collective I/O optimizations. We compare the implementation strategies with HDF5 and analyze both. Our tests indicate programming convenience and significant I/O performance improvement with this parallel netCDF interface. |
| M. Grimsditch, G. K. Leaf, H. G. Kaper, D. A. Karpeev, R. E. Camley, "Normal Modes of Spin Excitations in Magnetic Nano-Particles," Preprint ANL/MCS-P1049-0503, May 2003. | This article describes a technique to compute magnetic normal modes of nano-sized particles. The technique is based on the Landau-Lifshitz formalism of micromagnetics and accounts fully for both the exchange and the dipolar field. It requires no more than the specification of the material parameters and the geometry of the sample; in particular, it does not require the specification of boundary conditions. It also allows the large-amplitude nonlinear regime to be probed. The technique is applied to a model of a polycrystalline iron particle, which is shown to possess a rich variety of normal modes. Some of these modes are reminiscent of standing waves while others are more or less localized in parts of the sample. The variation of the mode frequencies with the applied field is analyzed and compared with existing approximations. |
| A. Zagaris, H. G. Kaper, and T. J. Kaper, "Analysis of the Computational Singular Perturbation Reduction Method for Chemical Kinetics," J. of Nonlinear Sci. 14(1) (Jan./Feb. 2004), pp. 59-91. Also Preprint ANL/MCS-P1050-0503, May 2003. | This article is concerned with the asymptotic accuracy of the Computational Singular Perturbation (CSP) method developed by Lam and Goussis to reduce the dimensionality of a system of chemical kinetics equations. The method exploits the presence of disparate time scales to model the dynamics by an evolution equation on a lower-dimensional slow manifold. In this article it is shown that the successive applications of the CSP algorithm generate, order by order, the asymptotic expansion of a slow manifold. The results are illustrated on the Michaelis-Menten-Henri equations of enzyme kinetics. |
| J. W. Lottes and P. F. Fischer, "Hybrid Multigrid/Schwarz Algorithms for the Spectral Element Method," J. Sci. Comput. 24 (2005), pp. 45-78. Also Preprint ANL/MCS-P1052-0403, April 2003. | We study the performance of the multigrid method applied to spectral element (SE) discretizations of the Poisson equation. Smoothers based on finite element (FE) discretizations, overlapping Schwarz methods, and point-Jacobi are considered in conjunction with conjugate gradient and GMRES acceleration techniques. It is found that Schwarz methods based on restrictions of the originating SE matrices converge faster than FE-based methods and that weighting the Schwarz matrices by the inverse of the diagonal counting matrix is essential to effective Schwarz smoothing. Several of the methods considered achieve convergence rates comparable to those attained by classic multigrid on regular grids. |
| K. Keahey, V. Welch, S. Lang, B. Liu, S. Meder, "Fine-Grain Authorization Policies in the GRID: Design and Implementation," Concurrency Computat.: Pract. Exper. 16 (2004), pp. 477-488. Also Preprint ANL/MCS-P1053-0603, June 2003. | In thie paper we describe our work on enabling fine-grain authorization for resource usage and management. We address the need of Virtual Organizations (VOs) to enforce their own policies in addition to those of the resource owners, both in regard to resource consumption and job management. To implement this design we propose changes and extensions to the Globus Toolkit's version 2 (GT2) resource management mechanism. We describe the prototype and the policy language that we designed to express fine-grain policies. We then analyze our solution and describe plans for future work. |
| S. Leyffer, "Complementarity Constraints as Nonlinear Equations: Theory and Numerical Experience, Preprint ANL/MCS-P1054-0603, June 2003. | Recently, it has been shown that mathematical prgorams with complementarity constraints (MPCCs) can be solved efficiently and reliably as nonlinear programs. This paper examines various nonlinear formulations of the complementarity constraints. Several nonlinear complementarity functions are considered for use in MPCC. Unlike standard smoothing techniques, however, the reformulations do not require the control of a smoothing parameter. Thus they have the advantage taht the smoothing is exact in the sense that Karush-Kuhn-Tucker points of the reformulation correspond to strongly stationary points of the MPCC. A new exact smoothing of the well-known min function is also introduced and shown to possess desirable theoretical properties. It is shown how the new formulations can be integrated into a sequential quadratic programming solver, and their practical performance is compared on a range of test problems. |
| S. J. Benson and T. S. Munson, "Flexible Complementarity Solvers for Large-Scale Applications," Optimization Methods & Software 21, no. 1 (2006), pp. 155-168. Also Preprint ANL/MCS-P1055-0603, June 2003. | Discretizations of infinite-dimensional variational inequalities lead to linear and nonlinear complementarity problems with many degrees of freedom. To solve these problems in a parallel computing environment, we propose two active-set methods that solve only one linear system of equations per iteration. The linear solver, preconditioner, and matrix structures can be chosen by the user for a particular application to achieve high parallel performance. The parallel scalability of these methods is demonstrated for some discretizations of infinite-dimensional variational inequalities. |
| L. Pearlman, C. Kesselman, V. Welch, I. Foster, S. Tuecke, "The Community Authorization Service: Status and Future," Preprint ANL/MCS-P1056-0603, June 2003. | Virtual organizations (VOs) are communities of resource providers and users distributed over multiple policy domains. These VOs often wish to define and enforce consistent policies in addition to the policies of their underlying domains. This is challenging, not only because of the problems in distributing the policy to the domains, but also because of the fact that those domains may each have different capabilities for enforcing the policy. The Community Authorization Service (CAS) solves this problem by allowing resource providers to delegate some policy authority to the VO while maintaining ultimate control over their resources. In this paper we describe CAS and our past and current implementations of CAS, and we discuss our plans for CAS-related research. |
| M. R. Paul, K.-H. Chiam, M. C. Cross, P. F. Fischer, and H. S. Greenside, "Pattern Formation and Dynamics in Rayleigh-Bénard Convection: Numerical Simulations of Experimentally Realistic Geomtries," Preprint ANL/MCS-P1057-0603, June 2003. | Rayleigh-Bénard convection is studied and quantitative comparisons are made, where possible, between theory and experiment by performing numerical simulations of the Boussinesq equations for a variety of experimentally realistic situations. Rectangular and cylindrical geometries of varying aspect ratios for experimental boundary conditions, including fins and spatial ramps in plate separation, are examined with particular attention paid to the role of the mean flow. A small cylindrical convection layer bounded laterally either by a rigid wall, fin, or a ramp is investigated and our results suggest that the mean flow plays an important role in the observed wavenumber. Analytical results are developed quantifying the mean flow sources, generated by amplitude gradients, and its effect on the pattern wavenumber for a large-aspect-ratio cylinder with a ramped boundary. Numerical results are found to agree well with these analytical predictions. We gain further insight into the role of mean flow in pattern dynamics by employing a novel method of quenching the mean flow numerically. Simulations of a spiral defect chaos state where the mean flow is suddenly quenched is found to remove the time dependence, increase the wavenumber and make the pattern more angular in nature. |
| O. F. Rana, A. Shaikhali, and G. von Laszewski, "Creating and Managing Grid Services," in Grid Computing: A Practical Guide to Technology and Applications, ed. A. Abbas, Charles River Media, 2003. Also Preprint ANL/MCS-P1058-0603, June 2003. | There are many definitions of what constitutes a "Grid"---the most common of which identifies a Computational Grids as: "a collection of distributed computing resources available over local or wide area networks---and which appear to an end user as one large virtual computing system." A significant effort has been invested by the Grid community into building software systems that may be used to manage such a virtual computing system. The Grid approach is an important development for both the business and scientific community, and promotes a vision for sophisticated scientific and business collaborations. Until recently most of this effort was focused on managing resource ensembles, and coordinating access to such ensembles in a secure and efficient manner. The focus of this work was primarily driven by the need to handle differences between different kinds of hardware architectures (Intel vs. Sun vs. SGI), operating systems (Solaris vs. Win2000 vs. IRIX) and data repositories (structured databases vs. file systems). To establish a "virtual organization," it is also necessary to allow individual systems administrators---managing one or more resource ensembles---to exercise their individual authority. Each of these systems administrators would have control over their resources and would not allow some centralized system to override access rights that they have defined for external users coming to their system. The predominant interest within existing Grid systems remains on 'resources'---the hosting platforms and storage devices which may be combined together to establish a virtual system. Increasingly, here has been a recognition that it is also important to capture details about software programs and libraries which are run on such resources. |
| R. Stevens, M. E. Papka, T. Disz, "The Access Grid: Prototyping - Workspaces of the Future," Preprint ANL/MCS-P1064-0603, June 2003. |
Collaborative
immersive virtual reality technology has been in use since the late 1980s.
In the mid-1990s these systems were used to investigate multi-user
wide-area collaboration scenarios. While these efforts were pioneering in
many respects, they proved less suitable as work environments for everyday
use. People tire easily when spending extended time in the dark spaces
needed for projection virtual reality or when
being immersed in a completely synthetic world for hours at a time
without access to high-resolution text displays or high-quality
interactions devices. |
| S. Newhouse, J. MacLaren, K. Keahey, "Trading Grid Services within the UK e-Science Grid," in Grid Resource Management, eds. J. Nabrzyski, J. M. Schopf, and J. Weglarz, chatper 29, Kluwer Academic Publishers, 2003. Also Preprint ANL/MCS-P1065-0603, June 2003. | The Open Grid Services Architecture (OGSA) presents the Grid community with an opportunity to define standard interfaces to enable the construction of an interoperable Grid infrastructure. The provision of this infrastructure has, to date, come from the donation of time and effort from the research community primarily for their own use. The growing involvement of industry and commerce in Grid activity is accelerating the need to find business models that support their participation. It is therefore essential that an economic infrastructure be incorporated into the OGSA to support economic transactions between service providers and their clients. This chapter describes current standardization efforts taking place with the Global Grid Forum and the implementation of such an architecture within the UK e-Science Programme through the Computational Markets project. |
| U. Naumann, "Statement-Level Optimality of Tangent-Linear and Adjoint Models," Preprint ANL/MCS-P1066-0603, June 2003. | We discuss a combinatorial problem that arises in the optimization of first-derivative code generated by exploiting the associativity of the chain rule. Our objective is to minimize the arithmetic complexity of such codes. A hierarchical approach is taken that ensures optimality locally at the level of single scalar assignments. New optimal algorithms are presented for three important special cases that represent the main components of any derivative code. |
| R. Ross, N. Miller, and W. Gropp, "Implementing Fast and Reusable Datatype Processing," Proc. EuroPVM/MPI 2003, Venice, Sept. 2003. Also Preprint ANL/MCS-P1068-0603, July 2003. | Methods for describing structured data are a key aid in application development. The MPI standard defines a system for creating "MPI Types" at run time and using these types when passing messages, performing RMA operations, and accessing data in files. Similar capabilities are available in other middleware as well. Unfortunately, many implementations perform poorly when processing these structured data types. This leads application developers to avoid these components entirely, instead performing any necessary processing of data by hand. In this paper we describe an internal representation of types that aids in maintaining the highest possible performance during processing. The performance of this system, used in the MPICH2 implementation, is compared to well-written manual processing routines and other available MPI implementations. We show that performance for most tested types is comparable to manual processing. Finally we point to additional opportunities for optimization and other software where this implementation could be leveraged. |
| L. Yang, J. M. Schopf, and I. Foster, "Conservative Scheduling: Using Predicted Variance to Improve Scheduling Decisions in Dynamic Environments," Preprint ANL/MCS-P1069-0703, July 2003. |
In
heterogeneous and dynamic environments, efficient execution of parallel
computations can require mappings of tasks to processors that have both
irregular (due to heterogeneity) and time-varying (due to dynamicity)
performance. While adaptive domain decomposition techniques have been used
to address heterogeneous resource capabilities, temporal variations in those
capabilities have seldom been considered. We propose a conservative
scheduling policy that uses information about expected future variance in
resource capabilities to produce more efficient data mapping decisions. We
first present techniques, based on time series predictors that we developed
in previous work, for predicting CPU load at some future time point, average CPU load for some future time interval, and variation of CPU load over some future time interval.
We then present a family of stochastic scheduling algorithms that exploit
such predictions of future availability and variability when making data
mapping decisions. Finally, we describe experiments in which we apply our
techniques to an astrophysics application. The results of these experiments
demonstrate that conservative scheduling can produce execution times that
are significantly faster and less variable than other techniques.
|
| J. J. Evans, C. S. Hood, W. D. Gropp, "Exploring the Relationship Between Parallel Application Run-Time Variability and Network Performance in Clusters," Preprint ANL/MCS-P1071-0703, July 2003. | Highly variable parallel application execution time is a persistent issue in cluster computing environments, and can be particularly acute in systems composed of Networks of Workstations (NOWs). We are looking at this issue in terms of consistency. In particular, we are focusing on network performance. Before we can use techniques from fault management to attain consistency, this paper presents our preliminary analysis of run-time variability from logs and experiments, exposing important issues related to systemic inconsistency in NOW clusters. The characterization of application sensitivity can be used to set network performance goals, thereby defining operational requirements. Network performance depends on the virtual topology imposed by the scheduler's allocation of nodes and the communication patterns of the set of running applications. Therefore, it is important to look at both the network and the cluster's centralized node mapper (scheduler) as critical subsystems. |
| M. Hereld, "Local Methods for Measuring Tiled Display Alignment," Preprint ANL/MCS-P1072-0803, August 2003. | We describe a new method of accurately measuring the relationship between pixel coordinates of neighboring projectors in a tiled projection display. The method can be used to calibrate the alignment and distortions in the tiled display, and can be used to touch up existing calibrations with local corrections. Additionally, by simultaneously measuring the characteristic spacing of textural features on the screen surface, we show how an absolute measure of the screen coordinates might be derived. The techniques have application to information encoding in images, in situ measurement of projector distortions without interrupting display of image content, and commodity tile-aware smart projectors. We discuss the limits to precision of these measurements. |
| U. Naumann and J. Utke, "Reduction of Edge Labeled DAGs through Constant Folding," Preprint ANL/MCS-P1073-0803, Sept. 2003. | We present intermediate results for a discrete problem arising in the automatic generation of derivative code. Consider a directed acyclic graph (dag) G = (V,E) with vertex set V = X u Z u Y, where X is the set of minimal vertices, Z is the set of intermediate vertices, Y is the set of maximal vertices, and E is the set of edges (i,j) with i,j in V. X, Y, and Z are pairwise disjoint. The vertices are numbered such that they induce a dependency order, (i,j) in E => i < j. Each edge (i,j) is annotated with a label c[sub ji] in R. The c[sub ji] can be categorized as either variable or constant. G is transformed into a bipartite graph by using a sequence \sigma of edge (front and back) and vertex eliminations. |
| Y. Zhou, "Eigenvalue Computation from the Optimization Perspective: On Jacobi-Davidson, IIGD, RQI, and Newton Updates," Preprint ANL/MCS-P1074-0803, August 2003. | We discuss the close connection between eigenvalue computation and optimization using the Newton method and subspace methods. From the connection we derive a new class of Newton updates. The new update formulation is similar to the well-known Jacobi-Davidson method. This similarity leads to simplified versions of the Jacobi-Davidson method and the inverse iteration generalized Davidson (IIGD) method. We prove that the projection subspace augmented by the updating direction from each of these methods is able to include the Rayleigh quotient iteration (RQI) direction. Hence, the locally quadratic (cubic for normal matrices) convergence rate of the RQI method is retained and strengthened by the subspace methods. The theory is supported by extensive numerical results. Preconditioned formulations are also briefly discussed for large scale eigenvalue problems. |
| I. Foster and C. Kesselman, "The Grid in a Nutshell," in Grid Resource Management, ed. J. Nabrzyski, J. M. Schopf, and J. Weglarz, Kluwer Academic, Chap. 1 (to appear). Also Preprint ANL/MCS-P1075-0803, August 2003. | The emergence and widespread adoption of Grid computing has been fueled by continued growth in both our understanding of application requirements and the sophistication of the technologies used to meet these requirements. We provide an introduction to Grid applications and technologies and discuss the important role that resource management will play in future developments. |
| J. M. Schopf, "Ten Actions When Grid Scheduling," in Grid Resource Management, ed. J. Nabrzyski, J. M. Schopf, and J. Weglarz, Kluwer Academic, Chap. 2 (to appear). Also Preprint ANL/MCS-P1076-0803, August 2003. | In this chapter we present a general architecture or plan for scheduling on a Grid. A Grid scheduler (or broker) must make resource selection decisions in an environment where it has no control over the local resources, the resources are distributed, and information about the systems is often limited or dated. These interactions are also closely tied to the functionality of the Grid Information Services. This Grid scheduling approach has three phases: resource discovery, system selection, and job execution. We detail the steps involved in each phase. |
| H. Dail, O. Sievert, F. Berman, H. Casanova, A YarKhan, S. Vadhiyar, J. Dongarra, C.Liu, L.Yang, D.Angulo, I. Foster, "Scheduling in the Grid Application Development Software Project," in Grid Resource Management, ed. J. Nabrzyski et al., Kluwer Academic, Chap. 6 (to appear). Also Preprint ANL/MCS-P1077-0803, August 2003. | Developing Grid applications is a challenging endeavor that at the moment requires both extensive labor and expertise. The Grid Application Development Software Project (GrADS) provides a system to simplify Grid application development. This system incorporates tools at all stages of the application development and execution cycle. In this chapter we focus on application scheduling, and present the three scheduling approaches developed in GrADS: development of an initial application schedule (launch-time scheduling), modification of the execution platform during e3xecution (rescheduling), and negotiation between multiple applications in the system (metascheduling). These approaches have been developed and evaluated for platforms that consist of distributed networks of shared workstations, and applied to real-world parallel applications. |
| K. Czajkowski, I. Foster, C. Kesselman, and S. Tuecke, "Grid Service Level Agreements," in Grid Resource Management, eds. J. Nabrzyski, J. M. Schopf, and J. Weglarz, Kluwer Academic, Chap. 8 (to appear). Also Preprint ANL/MCS-P1078-0803, August 2003. | We present a reformulation of the well-known GRAM architecture based on the Service-Level Agreement (SLA) negotiation protocols defined within the Service Negotiation and Access Protocol (SNAP) framework. We illustrate how a range of local, distributed, and workflow scheduling mechanisms can be viewed as part of a cohesive yet open system in which new scheduling strategies and management policies can evolve without disrupting the infrastructure. This architecture remains neutral to, and in fact strives to mediate, the potentially conflicting resource, community, and user policies. |
| B. Nitzberg, J. M. Schopf, J. P. Jones, "PBS Pro: Grid Computing and Scheduling Attributes," in Grid Resource Management, eds. J. Nabrzyski, J. M. Schopf, and J. Weglarz, Kluwer Academic, Chap. 13 (to appear). Also Preprint ANL/MCS-P1079-0803, August 2003. | The PBS Pro software is a full-featured workload management and job scheduling system with capabilities that cover the entire Grid computing space: security, information, compute, and data. The security infrastructure includes user authentication, access control lists, X.509 certificate support, and cross-site user mapping facilities. Detailed status and usage information is maintained and available both programmatically and via a graphical interface. Compute Grids can be built to support advance reservations, harvest idle desktop compute cycles, and peer schedule work (automatically moving jobs across the room or across the globe). Data management in PBS Pro is handled via automatic stage-in and stage-out of files. The PBS Pro system has numerous site-tunable parameters and can provide access to available scheduling information, information about requesting resources, allocation properties, and information about how an allocation execution can be manipulated. |
| J. M. Schopf and L. Yang, "Using Predicted Variance for Conservative Scheduling on Shared Resources," in Grid Resource Management, eds. J. Nabrzyski, J. M. Schopf, and J. Weglarz, Kluwer Academic, Chap. 15 (to appear). Also Preprint ANL/MCS-P1080-0803, August 2003. | In heterogeneous and dynamic environments, efficient execution of parallel computations can require mappings of tasks to processors with performance that is both irregular and time varying. We propose a conservative scheduling policy that uses information about expected future variance in resource capabilities to produce more efficient data mapping decisions. We first present two techniques to estimate future load and variance, one based on normal distributions and another using tendency-based prediction methodologies. We then present a family of stochastic scheduling algorithms that exploit such predictions when making data mapping decisions. We describe experiments in which we apply our techniques to an astrophysics application. The results of these experiments demonstrate that conservative scheduling can produce execution times that are significantly faster and less variable than other techniques. |
| K. Ranganathan and I. Foster, "Computation Scheduling and Data Replication Algorithms for Data Grids," in Grid Resource Management, eds. J. Nabrzyski, J. M. Schopf, and J. Weglarz, Kluwer Academic, Chap. 22 (to appear). Also Preprint ANL/MCS-P1081-0803, August 2003. |
Data Grids seek to harness geographically distributed resources for large-scale data-intensive problems such as those encountered in high energy physics, bioinformatics, and other disciplines. These problems typically involve numerous, loosely coupled jobs that both access and generate large data sets. Effective scheduling in such environments is challenging, because of a need to address a variety of metrics and constraints (e.g., resource utilization, response time, global and local allocation policies) while dealing with multiple, potentially independent sources of jobs, and a large number of storage, compute, and network resources. We describe a scheduling framework that addresses these problems. Within this framework, data movement operations may be either tightly bound to job scheduling decisions or performed by a decoupled, asynchronous process on the basis of observed data access patterns and load. We develop a family of job scheduling and data movement (replication) algorithms and use simulation studies to evaluate various combinations. Our results suggest that while it is necessary to consider the impact of replication on the scheduling strategy, it is not always necessary to couple data movement and computation scheduling. Instead, these two activities can be addressed separately, thus significantly simplifying the design and implementation of the overall Data Grid system. |
| A. Iamnitchi and I. Foster, "A Peer-to-Peer Approach to Resource Location in Grid Environments," in Grid Resource Management, ed. J. Nabrzyski, J. M. Schopf, and J. Weglarz, Kluwer Academic, Chap. 25 (to appear). Also Preprint ANL/MCS-P1082-0803, August 2003. | Resource location (or discovery) is a fundamental service for resource-sharing environments: given desired resource attributes, the service returns locations of matching resources. Designing such a service for a Grid environment of the scale and volatility of today's peer-to-peer systems is not trivial. We explore part of the design space through simulations on an emulated Grid. To this end, we propose four axes that define the resource location design space, model and implement an emulated Grid, evaluate a set of resource discovery mechanisms, and discuss results. |
| G. G. Maisuradze, D. L. Thompson, A. F. Wagner, M. Minkoff, "Interpolating Moving Least Squares Methods for Fitting Potential Energy Surfaces: Detailed Analysis of One-Dimensional Applications," J. Chem. Phys. 119(19) (Nov. 15, 2003), pp. 10002-10014. Also Preprint ANL/MCS-P1083-0803, Aug. 2003. |
We present the
basic formal and numerical aspects of higher degree interpolated moving
least squares (IMLS) methods. For simplicity, applications of these
methods are restricted to two 1-D test cases: a Morse oscillator and a 1-D
slice of the HN{sub 2} -> H + N{sub 2} potential energy surface. For these two test cases, we
systematically examine the effect of parameters in the weight function
(intrinsic to IMLS methods), the degree of the IMLS fit, and the number
and placement of potential energy points.
From this systematic study, we discover compact and accurate
representations of potentials and their derivatives for first-degree and
higher-degree (up to nine degree) IMLS fits. We show how the number of ab
initio points needed to achieve a given accuracy declines with the degree
of the IMLS. We outline
automatic procedures for ab initio point selection that can optimize this
decline. |
| S. Benson, M. Krishnan, L. McInnes, J. Nieplocha, J. Sarich, "Using the GA and TAO Toolkits for Solving Large-Scale Optimization Problems on Parallel Computers," Preprint ANL/MCS-P1084-0903, Sept. 2003. | Challenges in the scalable solution of large-scale optimization problems include the development of innovative algorithms as well as efficient tools for parallel data manipulation. This paper discusses the combined use of two complementary toolkits from the collection of Advanced CompuTational Software (ACTS), namely Global Arrays (GA) for parallel data management and the Toolkit for Advanced Optimization (TAO). TAO uses abstractions for vectors and matrices, so that optimization algorithms can easily interface to the external linear algebra support provided by the GA library. The GA/TAO interfaces are available both in the traditional library mode and as components compliant with the Common Component Architecture (CCA). We highlight the design of each toolkit, describe the interfaces between them, and evaluate performance for model problems involving bound-constrained optimization. |
| A. Ching, A. Choudhary, K. Coloma, W.-K. Liao, R. Ross, W. Gropp, "Noncontiguous I/O Accesses Through MPI-IO," Preprint ANL/MCS-P1085-0903, Sept. 2003. | I/O performance remains a weakness of parallel computing systems today. While this weakness is partly attributed to rapid advances in other system components, I/O interfaces available to programmers and the I/O methods supported by file systems have traditionally not matched efficiently with the types of I/O operations that scientific applications perform, particularly noncontiguous accesses. The MPI-IO interface allows for rich descriptions of the I/O patterns desired for scientific applications and implementations such as ROMIO have taken advantage of this ability while remaining limited by underlying file system methods. A method of noncontiguous data access, list I/O, was recently implemented in the Parallel Virtual File System (PVFS). We implement support for this interface in the ROMIO MPI-IO implementation. Through a suite of noncontiguous I/O tests we compared ROMIO list I/O to current methods of ROMIO noncontiguous access and found that the list I/O interface provides performance benefits in many noncontiguous cases. |
| S. Benson, M. Krishnan, L. McInnes, J. Nieplocha, J. Sarich, "Using the GA and TAO Toolkits for Solving Large-Scale Optimization Problems on Parallel Computers," Preprint ANL/MCS-P1084-0903, September 2003. | Challenges in the scalable solution of large-scale optimization problems include the development of innovative algorithms as well as efficient tools for parallel data manipulation. This paper discusses the combined use of two complementary toolkits from the collection of Advanced CompuTational Software (ACTS), namely Global Arrays (GA) for parallel data management and the Toolkit for Advanced Optimization (TAO). TAO uses abstractions for vectors and matrices, so that optimization algorithms can easily interface to the external linear algebra support provided by the GA library. The GA/TAO interfaces are available both in the traditional library mode and as components compliant with the Common Component Architecture (CCA). We highlight the design of each toolkit, describe the interfaces between then, and evaluate performance for model problems involving bound-constrained optimization. |
| W. McCune, R. Padmanabhan, M. A. Rose, R. Veroff, "Short Equational Bases for Ortholattices," Preprint ANL/MCS-P1087-0903, September 2003. |
Short single axioms for ortholattices, orthomodular lattices, and modular ortholattices are presented, all in terms of the Sheffer
stroke. The ortholattice axiom is the shortest possible. Other equational bases in terms of the Sheffer stroke and in terms of join, meet, and complement are presented. Proofs are omitted but are available in an associated technical report. Computers were used extensively to find candidates, reject candidates, and search for proofs that candidates are single axioms. The notion of computer proof is addressed. |
| B.-D. Lee and J. M. Schopf, "Run-Time Prediction of Parallel Applications on Shared Environment," Preprint ANL/MCS-P1088-0903, September 2003. |
Application
run-time information is a fundamental component in application and job
scheduling, as well as in resource selection. However, accurate
predictions of run-times are difficult to achieve for parallel applications
running in shared environments where resource capacities can change
dynamically over time. In this paper, we propose a run-time prediction
technique for parallel applications that uses regression methods and
filtering techniques to derive the application execution time without using
standard performance models. The experimental results show that our
use of regression models delivers tolerable prediction accuracy and that we
can improve the accuracy dramatically by using appropriate filters. |
| N. Desai, A. Lusk, R. Bradshaw, R. Evard, "BCFD: A Configuration Management Tool for Heterogeneous Environments," Preprint ANL/MCS-P1089-0903, Sept. 2003. | Since clusters were first introduced, node counts have increased rapidly. Currently, a variety of clusters with more than one thousand nodes are listed on the TOP500 list. In the next three years, clusters with more than four thousand nodes are expected. Cluster management functionality has lagged behind all areas of system software. In order to effectively manage the clusters of today and tomorrow, the basic cluster management software model must change. Current techniques focus on the management of single nodes, as opposed to complete cluster configurations. This approach typically leads to automatic management of compute nodes, while using ad-hoc techniques to manage service nodes. |
| U. Naumann and J. Riehme, "A Differentiation-Enabled Fortran 95 Compiler," Preprint ANL/MCS-P1090-0903, Sept. 2003. | The availability of first derivatives of vector functions is crucial for the robustness and efficiency of a large number of numerical algorithms. A new differentiation-enabled Fortran 95 compiler is described that uses programming language extensions and a semantical code transformation known as automatic differentiation to provide Jacobians of numerical programs with machine accuracy. We describe the user interface as well as the relevant algorithmic details. The feasibility, robustness, and convenience of this approach is illustrated by various case studies. |
| S. Leyffer, "The Penalty Interior-Point Method Fails to Converge," Preprint ANL/MCS-P1091-0903, September 2003. | Equilibrium equations in the form of complementarity conditions often appear as constraints in optimization problems. Problems of this type are commonly referred to as mathematical programs with complementarity constraints (MPCCs). A popular method for solving MPCCs is the penalty interior-point algorithm (PIPA). This paper presents a small example for which PIPA converges to a nonstationary point, providing a counterexample to the established theory. The reasons for this adverse behavior are discussed. |
| M. Anitescu, W. J. Layton, F. Pahlevani, "Unconditional Stability for Numerical Scheme Combining Implicit Timestepping for Local Effects and Explicit Timestepping for Nonlocal Effects," Preprint ANL/MCS-P1093-0903, September 2003. | A combination of implicit and explicit timestepping is analyzed for a system of ODEs motivated by ones arising from spatial discretizations of evolutionary partial differential equations. Loosely speaking, the method we consider is implicit in local and stabilizing terms in the underlying PDE and explicit in nonlocal and unstabilizing terms. Unconditional stability and convergence of the numerical scheme are proven by the energy method and by algebraic techniques. This stability result is surprising because usually when different methods are combined, the stability properties of the least stable method plays a determining role in the combination. |
| K. Keahey, V. Welch, S. Lang, B. Liu, and S. Meder, "Fine-Grained Authorization for Job Execution in the Grid: Design and Implementation," Preprint ANL/MCS-P1094-0903, September 2003. | In this paper we describe our work on enabling fine-grained authorization for resource usage and management. We address the need of virtual organizations to enforce their own policies in addition to those of the resource owners, in regard to both resource consumption and job management. To implement this design, we propose changes and extensions to the Globus Toolkit's version 2 resource management mechanism. We describe the prototype and the policy language that we designed to express fine-grained policies, and we present an analysis of our solution. |
| M. R. Thompson, A. Essiari, K. Keahey, V. Welch, S. Lang, B. Liu, "Fine-Grained Authorization for Job and Resource Management Using Akenti and the Globus Toolkit," Preprint ANL/MCS-P1095-0903, September 2003. | As the Grid paradigm is adopted as a standard way of sharing remote resources across organizational domains, the need for fine-grained access control to these resources increases. This paper presents an authorization solution for job submission and control, developed as part of the National Fusion Collaboratory, that uses the Globus Toolkit 2 and the Akenti authorization service in order to perform fine-grained authorization of job and resource management requests in a Grid environment. At job startup, it allows the system to evaluate a user's Resource Specification Language request against authorization policies on resource usage (determining how many CPUs or memory a user can use on a given resource or which executables the user can run). Furthermore, based on authorization policies, it allows other virtual organization members to manage the user's job. |
| K. Keahey, M. Ripeanu, K. Koering, "Dynamic Creation and Management of Runtime Environments in the Grid," Preprint ANL/MCS-P1096-0903, Sept. 2003. | We describe abstractions for creation and management of distributed, dynamic runtime environments in Grids. We present how features of the Open Grid Services Infrastructure (OGSI) are leveraged to implement this architecture. We develop GSLab, a distributed, large-scale platform for deploying and experimenting with Grid Services and test these abstractions in practice. |
| G. von Laszewski, K. Amin, M. Hategan, N. J. Zaluzec, S. Hampton, A. Rossi, "GridAnt: A Client-Controllable Grid Workflow System," Preprint ANL/MCS-P1098-1003, October 2003. | Process management is an extremely important concept in both business and scientific communities. Several workflow management tools have been proposed in recent years offering advanced functionality in various domains. In the business world, workflow vendors offer commercial and customized solutions targeting specific users. In the scientific world, several open-source workflow management tools are freely available. However, they are directed toward service aggregation rather than distributed process management. Little consideration is given to the needs of the client in terms of mapping the process flow of the client. In the Grid community it is essential that the Grid users have such a tool available enabling them to orchestrate complex workflows on the fly without substantial help from the service providers. At the same time it is important that the Grid user not be burdened with the intricacies of the workflow system. With the perspective of the Grid user in mind, an extensible client-side workflow management system, called GridAnt, has been developed. This p |