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All sourcesNASA NTRSDOE OSTI
NASA NTRS2011

Local Estimators for Spacecraft Formation Flying

A formation estimation architecture for formation flying builds upon the local information exchange among multiple local estimators. Spacecraft formation flying involves the coordination of states among multiple spacecraft through relative sensing, inter-spacecraft communication, and control. Most existing formation flying estimation algorithms can only be supported via highly centralized, all-to-all, static relative sensing. New algorithms are needed that are scalable, modular, and robust to variations in the topology and link characteristics of the formation exchange network. These distributed algorithms should rely on a local information-exchange network, relaxing the assumptions on existing algorithms. In this research, it was shown that only local observability is required to design a formation estimator and control law. The approach relies on breaking up the overall information-exchange network into sequence of local subnetworks, and invoking an agreement-type filter to reach consensus among local estimators within each local network. State estimates were obtained by a set of local measurements that were passed through a set of communicating Kalman filters to reach an overall state estimation for the formation. An optimization approach was also presented by means of which diffused estimates over the network can be incorporated in the local estimates obtained by each estimator via local measurements. This approach compares favorably with that obtained by a centralized Kalman filter, which requires complete knowledge of the raw measurement available to each estimator.

Fathpour, Nanaz↗
NASA NTRS1993

Applications and accuracy of the parallel diagonal dominant algorithm

The Parallel Diagonal Dominant (PDD) algorithm is a highly efficient, ideally scalable tridiagonal solver. In this paper, a detailed study of the PDD algorithm is given. First the PDD algorithm is introduced. Then the algorithm is extended to solve periodic tridiagonal systems. A variant, the reduced PDD algorithm, is also proposed. Accuracy analysis is provided for a class of tridiagonal systems, the symmetric, and anti-symmetric Toeplitz tridiagonal systems. Implementation results show that the analysis gives a good bound on the relative error, and the algorithm is a good candidate for the emerging massively parallel machines.

Sun, Xian-He↗
NASA NTRS1996

A Fast parallel tridiagonal algorithm for a class of CFD applications

The parallel diagonal dominant (PDD) algorithm is an efficient tridiagonal solver. This paper presents for study a variation of the PDD algorithm, the reduced PDD algorithm. The new algorithm maintains the minimum communication provided by the PDD algorithm, but has a reduced operation count. The PDD algorithm also has a smaller operation count than the conventional sequential algorithm for many applications. Accuracy analysis is provided for the reduced PDD algorithm for symmetric Toeplitz tridiagonal (STT) systems. Implementation results on Langley's Intel Paragon and IBM SP2 show that both the PDD and reduced PDD algorithms are efficient and scalable.

Moitra, Stuti↗
NASA NTRS2000

Molecular Simulations in Astrobiology

One of the main goals of astrobiology is to understand the origin of cellular life. The most direct approach to this problem is to construct laboratory models of protocells. Such efforts, currently underway in the NASA Astrobiology Program, are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures that are capable of performing protocellular functions. Many of these functions, such as importing nutrients, capturing energy and responding to changes in the environment, are carried out by proteins bound to membranes. We use computer simulations to address the following questions about these proteins: (1) How do small proteins self-organize into ordered structures at water-membrane interfaces and insert into membranes? (2) How do peptides form membrane-spanning structures (e.g. channels)? (3) By what mechanisms do such structures perform their functions? The simulations are performed using the molecular dynamics method. In this method, Newton's equations of motion for each atom in the system are solved iteratively. At each time step, the forces exerted on each atom by the remaining atoms are evaluated by dividing them into two parts. Short-range forces are calculated in real space while long-range forces are evaluated in reciprocal space, using a particle-mesh algorithm which is of order O(NInN). With a time step of 2 femtoseconds, problems occurring on multi-nanosecond time scales (10(exp 6)-10(exp 8) time steps) are accessible. To address a broader range of problems, simulations need to be extended by three orders of magnitude, which requires algorithmic improvements and codes scalable to a large number of processors. Work in this direction is in progress. Two series of simulations are discussed. In one series, it is shown that nonpolar peptides, disordered in water, translocate to the nonpolar interior of the membrane and fold into helical structures (see Figure). Once in the membrane, the peptides exhibit orientational flexibility with changing conditions, which may have provided a mechanism of transmitting signals between the protocell and its environment. In another series of simulations, the mechanism by which a simple protein channel efficiently mediates proton transport across membranes was investigated. This process is a key step in cellular bioenergetics. In the channel under study, proton transport is gated by four histidines that occlude the channel pore. The simulations identify the mechanisms by which protons move through the gate.

Pohorille, Andrew↗
NASA NTRS2001

Molecular Simulations in Astrobiology

One of the main goals of astrobiology is to understand the origin of cellular life. In the absence of any record of the earliest ancestors of contemporary cells, protocells, the most direct way to test our understanding of their characteristics is to construct laboratory models of protocells. Such efforts, currently underway in the NASA Astrobiology Program, are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures and developing designs of molecules that are capable of performing protocellular functions. Many of these functions, such as importing nutrients, capturing and storing energy, and responding to changes in the environment, are carried out by proteins bound to membranes. We use computer simulations to address the following, questions about these proteins: (1) How do small proteins (peptides) organize themselves into ordered structures at water-membrane interfaces and insert into membranes? (2) How do peptides aggregate to form membrane-spannin(y structures (e.g., channels)? (3) By what mechanisms do such aggregates perform their functions? The simulations are performed using the molecular dynamics (MD) method. In this method, Newton's equations of motion for each atom in the system are solved iteratively. At each time step, the forces exerted on each atom by the remaining atoms are evaluated by dividing them into two parts. Short-range forces are calculated directly in real space while long-range forces are evaluated in reciprocal space, usually using a particle-mesh algorithm which is of order O(NlnN). Currently, a time step of 2 femtoseconds is typically used, thereby making studies of problems occurring on multi-nanosecond time scales (10(exp 6) - 10(exp 8) time steps) accessible. To address a broader range of problems, simulations need to be extended by three orders of magnitude. Such an extension requires both algorithmic improvements and codes scalable to a large number of parallel processors. Work in this direction is in progress. Two specific series of simulations that demonstrate how peptides self-organize and function in membranes are discussed. In one series of simulations, it was shown that nonpolar peptides, disordered in water, translocate to the nonpolar interior of the membrane and, simultaneously, fold into two different helical structures, which remain in equilibrium. Once in the membrane, the peptides can readily change their orientation, especially in response to local electric fields. This structural and orientational flexibility of peptides with changing conditions may have provided a mechanism of transmitting signals between the environment and the interior of the protocell. In another series of simulations, the mechanism by which a simple protein channel efficiently mediates proton transport across membranes was investigated. This process is a key step in cellular bioenergetics. In the channel under study, proton transport is gated by four histidines that occlude the channel pore. The simulations demonstrate that protons move through the gate by a "shuttle" mechanism, wherein one histidine is protonated on the extracellular side and, subsequently, the proton bound on the opposite side is released.

Pohorille, Andrew↗
NASA NTRS2002

A De-Centralized Scheduling and Load Balancing Algorithm for Heterogeneous Grid Environments

In the past two decades, numerous scheduling and load balancing techniques have been proposed for locally distributed multiprocessor systems. However, they all suffer from significant deficiencies when extended to a Grid environment: some use a centralized approach that renders the algorithm unscalable, while others assume the overhead involved in searching for appropriate resources to be negligible. Furthermore, classical scheduling algorithms do not consider a Grid node to be N-resource rich and merely work towards maximizing the utilization of one of the resources. In this paper we propose a new scheduling and load balancing algorithm for a generalized Grid model of N-resource nodes that not only takes into account the node and network heterogeneity, but also considers the overhead involved in coordinating among the nodes. Our algorithm is de-centralized, scalable, and overlaps the node coordination time of the actual processing of ready jobs, thus saving valuable clock cycles needed for making decisions. The proposed algorithm is studied by conducting simulations using the Message Passing Interface (MPI) paradigm.

Arora, Manish↗
NASA NTRS1995

Performance prediction: A case study using a multi-ring KSR-1 machine

While computers with tens of thousands of processors have successfully delivered high performance power for solving some of the so-called 'grand-challenge' applications, the notion of scalability is becoming an important metric in the evaluation of parallel machine architectures and algorithms. In this study, the prediction of scalability and its application are carefully investigated. A simple formula is presented to show the relation between scalability, single processor computing power, and degradation of parallelism. A case study is conducted on a multi-ring KSR1 shared virtual memory machine. Experimental and theoretical results show that the influence of topology variation of an architecture is predictable. Therefore, the performance of an algorithm on a sophisticated, heirarchical architecture can be predicted and the best algorithm-machine combination can be selected for a given application.

Sun, Xian-He↗
NASA NTRS2016

A Quantum Annealing Computer Team Addresses Climate Change Predictability

The near confluence of the successful launch of the Orbiting Carbon Observatory2 on July 2, 2014 and the acceptance on August 20, 2015 by Google, NASA Ames Research Center and USRA of a 1152 qubit D-Wave 2X Quantum Annealing Computer (QAC), offered an exceptional opportunity to explore the potential of this technology to address the scientific prediction of global annual carbon uptake by land surface processes. At UMBC,we have collected and processed 20 months of global Level 2 light CO2 data as well as fluorescence data. In addition we have collected ARM data at 2sites in the US and Ameriflux data at more than 20 stations. J. Dorband has developed and implemented a multi-hidden layer Boltzmann Machine (BM) algorithm on the QAC. Employing the BM, we are calculating CO2 fluxes by training collocated OCO-2 level 2 CO2 data with ARM ground station tower data to infer to infer measured CO2 flux data. We generate CO2 fluxes with a regression analysis using these BM derived weights on the level 2 CO2 data for three Ameriflux sites distinct from the ARM stations. P. Gentine has negotiated for the access of K34 Ameriflux data in the Amazon and is applying a neural net to infer the CO2 fluxes. N. Talik validated the accuracy of the BM performance on the QAC against a restricted BM implementation on the IBM Softlayer Cloud with the Nvidia co-processors utilizing the same data sets. G. Nearing and K. Harrison have extended the GSFC LIS model with the NCAR Noah photosynthetic parameterization and have run a 10 year global prediction of the net ecosystem exchange. C. Pellisier is preparing a BM implementation of the Kalman filter data assimilation of CO2 fluxes. At UMBC, R. Prouty is conducting OSSE experiments with the LISNoah model on the IBM iDataPlex to simulate the impact of CO2 fluxes to improve the prediction of global annual carbon uptake. J. LeMoigne and D. Simpson have developed a neural net image registration system that will be used for MODIS ENVI and will be converted to a BM algorithm implementation on the QAC. The first integer adder has been implemented on the D-Wave 2X by A. Shehab that will perform HAAR wavelets for image compression of MODIS scenes. Finally, based on the next generations of QACs, we are preparing a 5-year performance road map on the scalability of the current QAC algorithms.

Science Data Processing↗
NASA NTRS1994

Nonlinear structural response using adaptive dynamic relaxation on a massively-parallel-processing system

A parallel adaptive dynamic relaxation (ADR) algorithm has been developed for nonlinear structural analysis. This algorithm has minimal memory requirements, is easily parallelizable and scalable to many processors, and is generally very reliable and efficient for highly nonlinear problems. Performance evaluations on single-processor computers have shown that the ADR algorithm is reliable and highly vectorizable, and that it is competitive with direct solution methods for the highly nonlinear problems considered. The present algorithm is implemented on the 512-processor Intel Touchstone DELTA system at Caltech, and it is designed to minimize the extent and frequency of interprocessor communication. The algorithm has been used to solve for the nonlinear static response of two and three dimensional hyperelastic systems involving contact. Impressive relative speedups have been achieved and demonstrate the high scalability of the ADR algorithm. For the class of problems addressed, the ADR algorithm represents a very promising approach for parallel-vector processing.

Oakley, David R.↗
NASA NTRS1995

Slices: A Scalable Partitioner for Finite Element Meshes

A parallel partitioner for partitioning unstructured finite element meshes on distributed memory architectures is developed. The element based partitioner can handle mixtures of different element types. All algorithms adopted in the partitioner are scalable, including a communication template for unpredictable incoming messages, as shown in actual timing measurements.

partitioner finite element meshes parallel computi↗
NASA NTRS1993

Extending substructure based iterative solvers to multiple load and repeated analyses

Direct solvers currently dominate commercial finite element structural software, but do not scale well in the fine granularity regime targeted by emerging parallel processors. Substructure based iterative solvers--often called also domain decomposition algorithms--lend themselves better to parallel processing, but must overcome several obstacles before earning their place in general purpose structural analysis programs. One such obstacle is the solution of systems with many or repeated right hand sides. Such systems arise, for example, in multiple load static analyses and in implicit linear dynamics computations. Direct solvers are well-suited for these problems because after the system matrix has been factored, the multiple or repeated solutions can be obtained through relatively inexpensive forward and backward substitutions. On the other hand, iterative solvers in general are ill-suited for these problems because they often must restart from scratch for every different right hand side. In this paper, we present a methodology for extending the range of applications of domain decomposition methods to problems with multiple or repeated right hand sides. Basically, we formulate the overall problem as a series of minimization problems over K-orthogonal and supplementary subspaces, and tailor the preconditioned conjugate gradient algorithm to solve them efficiently. The resulting solution method is scalable, whereas direct factorization schemes and forward and backward substitution algorithms are not. We illustrate the proposed methodology with the solution of static and dynamic structural problems, and highlight its potential to outperform forward and backward substitutions on parallel computers. As an example, we show that for a linear structural dynamics problem with 11640 degrees of freedom, every time-step beyond time-step 15 is solved in a single iteration and consumes 1.0 second on a 32 processor iPSC-860 system; for the same problem and the same parallel processor, a pair of forward/backward substitutions at each step consumes 15.0 seconds.

Farhat, Charbel↗
NASA NTRS1995

Parallel adaptive mesh refinement within the PUMAA3D Project

To enable the solution of large-scale applications on distributed memory architectures, we are designing and implementing parallel algorithms for the fundamental tasks of unstructured mesh computation. In this paper, we discuss efficient algorithms developed for two of these tasks: parallel adaptive mesh refinement and mesh partitioning. The algorithms are discussed in the context of two-dimensional finite element solution on triangular meshes, but are suitable for use with a variety of element types and with h- or p-refinement. Results demonstrating the scalability and efficiency of the refinement algorithm and the quality of the mesh partitioning are presented for several test problems on the Intel DELTA.

Freitag, Lori↗
NASA NTRS2002

Program Instrumentation and Trace Analysis

Several attempts have been made recently to apply techniques such as model checking and theorem proving to the analysis of programs. This shall be seen as a current trend to analyze real software systems instead of just their designs. This includes our own effort to develop a model checker for Java, the Java PathFinder 1, one of the very first of its kind in 1998. However, model checking cannot handle very large programs without some kind of abstraction of the program. This paper describes a complementary scalable technique to handle such large programs. Our interest is turned on the observation part of the equation: How much information can be extracted about a program from observing a single execution trace? It is our intention to develop a technology that can be applied automatically and to large full-size applications, with minimal modification to the code. We present a tool, Java PathExplorer (JPaX), for exploring execution traces of Java programs. The tool prioritizes scalability for completeness, and is directed towards detecting errors in programs, not to prove correctness. One core element in JPaX is an instrumentation package that allows to instrument Java byte code files to log various events when executed. The instrumentation is driven by a user provided script that specifies what information to log. Examples of instructions that such a script can contain are: 'report name and arguments of all called methods defined in class C, together with a timestamp'; 'report all updates to all variables'; and 'report all acquisitions and releases of locks'. In more complex instructions one can specify that certain expressions should be evaluated and even that certain code should be executed under various conditions. The instrumentation package can hence be seen as implementing Aspect Oriented Programming for Java in the sense that one can add functionality to a Java program without explicitly changing the code of the original program, but one rather writes an aspect and compiles it into the original program using the instrumentation. Another core element of JPaX is an observation package that supports the analysis of the generated event stream. Two kinds of analysis are currently supported. In temporal analysis the execution trace is evaluated against formulae written in temporal logic. We have implemented a temporal logic evaluator on finite traces using the Maude rewriting system from SRI International, USA. Temporal logic is defined in Maude by giving its syntax as a signature and its semantics as rewrite equations. The resulting semantics is extremely efficient and can handle event streams of hundreds of millions events in few minutes. Furthermore, the implementation is very succinct. The second form of even stream analysis supported is error pattern analysis where an execution trace is analyzed using various error detection algorithms that can identify error-prone programming practices that may potentially lead to errors in some different executions. Two such algorithms focusing on concurrency errors have been implemented in JPaX, one for deadlocks and the other for data races. It is important to note, that a deadlock or data race potential does not need to occur in order for its potential to be detected with these algorithms. This is what makes them very scalable in practice. The data race algorithm implemented is the Eraser algorithm from Compaq, however adopted to Java. The tool is currently being applied to a code base for controlling a spacecraft by the developers of that software in order to evaluate its applicability.

Havelund, Klaus↗
NASA NTRS2010

Efficient Web Services Policy Combination

Large-scale Web security systems usually involve cooperation between domains with non-identical policies. The network management and Web communication software used by the different organizations presents a stumbling block. Many of the tools used by the various divisions do not have the ability to communicate network management data with each other. At best, this means that manual human intervention into the communication protocols used at various network routers and endpoints is required. Developing practical, sound, and automated ways to compose policies to bridge these differences is a long-standing problem. One of the key subtleties is the need to deal with inconsistencies and defaults where one organization proposes a rule on a particular feature, and another has a different rule or expresses no rule. A general approach is to assign priorities to rules and observe the rules with the highest priorities when there are conflicts. The present methods have inherent inefficiency, which heavily restrict their practical applications. A new, efficient algorithm combines policies utilized for Web services. The method is based on an algorithm that allows an automatic and scalable composition of security policies between multiple organizations. It is based on defeasible policy composition, a promising approach for finding conflicts and resolving priorities between rules. In the general case, policy negotiation is an intractable problem. A promising method, suggested in the literature, is when policies are represented in defeasible logic, and composition is based on rules for non-monotonic inference. In this system, policy writers construct metapolicies describing both the policy that they wish to enforce and annotations describing their composition preferences. These annotations can indicate whether certain policy assertions are required by the policy writer or, if not, under what circumstances the policy writer is willing to compromise and allow other assertions to take precedence. Meta-policies are specified in defeasible logic, a computationally efficient non-monotonic logic developed to model human reasoning. One drawback of this method is that at one point the algorithm starts an exhaustive search of all subsets of the set of conclusions of a defeasible theory. Although the propositional defeasible logic has linear complexity, the set of conclusions here may be large, especially in real-life practical cases. This phenomenon leads to an inefficient exponential explosion of complexity. The current process of getting a Web security policy from combination of two meta-policies consists of two steps. The first is generating a new meta-policy that is a composition of the input meta-policies, and the second is mapping the meta-policy onto a security policy. The new algorithm avoids the exhaustive search in the current algorithm, and provides a security policy that matches all requirements of the involved metapolicies.

Vatan, Farrokh↗
NASA NTRS2003

Scalability of a Low-Cost Multi-Teraflop Linux Cluster for High-End Classical Atomistic and Quantum Mechanical Simulations

Scalability of a low-cost, Intel Xeon-based, multi-Teraflop Linux cluster is tested for two high-end scientific applications: Classical atomistic simulation based on the molecular dynamics method and quantum mechanical calculation based on the density functional theory. These scalable parallel applications use space-time multiresolution algorithms and feature computational-space decomposition, wavelet-based adaptive load balancing, and spacefilling-curve-based data compression for scalable I/O. Comparative performance tests are performed on a 1,024-processor Linux cluster and a conventional higher-end parallel supercomputer, 1,184-processor IBM SP4. The results show that the performance of the Linux cluster is comparable to that of the SP4. We also study various effects, such as the sharing of memory and L2 cache among processors, on the performance.

Kikuchi, Hideaki↗
NASA NTRS2015

Achieving Agreement in Three Rounds With Bounded-Byzantine Faults

A three-round algorithm is presented that guarantees agreement in a system of K (nodes) greater than or equal to 3F (faults) +1 nodes provided each faulty node induces no more than F faults and each good node experiences no more than F faults, where, F is the maximum number of simultaneous faults in the network. The algorithm is based on the Oral Message algorithm of Lamport et al. and is scalable with respect to the number of nodes in the system and applies equally to the traditional node-fault model as well as the link-fault model. We also present a mechanical verification of the algorithm focusing on verifying the correctness of a bounded model of the algorithm as well as confirming claims of determinism.

Malekpour, Mahyar R.↗
NASA NTRS1993

The Automated Instrumentation and Monitoring System (AIMS) reference manual

Whether a researcher is designing the 'next parallel programming paradigm,' another 'scalable multiprocessor' or investigating resource allocation algorithms for multiprocessors, a facility that enables parallel program execution to be captured and displayed is invaluable. Careful analysis of execution traces can help computer designers and software architects to uncover system behavior and to take advantage of specific application characteristics and hardware features. A software tool kit that facilitates performance evaluation of parallel applications on multiprocessors is described. The Automated Instrumentation and Monitoring System (AIMS) has four major software components: a source code instrumentor which automatically inserts active event recorders into the program's source code before compilation; a run time performance-monitoring library, which collects performance data; a trace file animation and analysis tool kit which reconstructs program execution from the trace file; and a trace post-processor which compensate for data collection overhead. Besides being used as prototype for developing new techniques for instrumenting, monitoring, and visualizing parallel program execution, AIMS is also being incorporated into the run-time environments of various hardware test beds to evaluate their impact on user productivity. Currently, AIMS instrumentors accept FORTRAN and C parallel programs written for Intel's NX operating system on the iPSC family of multi computers. A run-time performance-monitoring library for the iPSC/860 is included in this release. We plan to release monitors for other platforms (such as PVM and TMC's CM-5) in the near future. Performance data collected can be graphically displayed on workstations (e.g. Sun Sparc and SGI) supporting X-Windows (in particular, Xl IR5, Motif 1.1.3).

Yan, Jerry↗
NASA NTRS1997

The Automated Instrumentation and Monitoring System (AIMS): Design and Architecture

Whether a researcher is designing the 'next parallel programming paradigm', another 'scalable multiprocessor' or investigating resource allocation algorithms for multiprocessors, a facility that enables parallel program execution to be captured and displayed is invaluable. Careful analysis of such information can help computer and software architects to capture, and therefore, exploit behavioral variations among/within various parallel programs to take advantage of specific hardware characteristics. A software tool-set that facilitates performance evaluation of parallel applications on multiprocessors has been put together at NASA Ames Research Center under the sponsorship of NASA's High Performance Computing and Communications Program over the past five years. The Automated Instrumentation and Monitoring Systematic has three major software components: a source code instrumentor which automatically inserts active event recorders into program source code before compilation; a run-time performance monitoring library which collects performance data; and a visualization tool-set which reconstructs program execution based on the data collected. Besides being used as a prototype for developing new techniques for instrumenting, monitoring and presenting parallel program execution, AIMS is also being incorporated into the run-time environments of various hardware testbeds to evaluate their impact on user productivity. Currently, the execution of FORTRAN and C programs on the Intel Paragon and PALM workstations can be automatically instrumented and monitored. Performance data thus collected can be displayed graphically on various workstations. The process of performance tuning with AIMS will be illustrated using various NAB Parallel Benchmarks. This report includes a description of the internal architecture of AIMS and a listing of the source code.

Yan, Jerry C.↗