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Title: Efficient Execution of Electronic Structure Calculations on SMP Clusters

Abstract

Applications augmented with adaptive capabilities are becoming common in parallel computing environments. For large-scale scientific applications, dynamic adjustments to a computationally-intensive part may lead to a large pay-off in facilitating efficient execution of the entire application while aiming at avoiding resource contention. Application-specific knowledge, often best revealed during the run-time, is required to initiate and time these adjustments. In particular, General Atomic and Molecular Electronic Structure System (GAMESS) is a program for ab initio quantum chemistry that places significant demands on the high-performance computing platforms. Certain electronic structure calculations are characterized by high consumption of a particular resource, such as CPU, main memory, or disk I/O. This may lead to resource contention among concurrent GAMESS jobs and other programs in the dynamically changing environment. Thus, it is desirable to improve GAMESS calculations by means of dynamic adaptations. In this thesis, we show how an application- or algorithm-specific knowledge may play a significant role in achieving this goal. The choice of implementation is facilitated by a module-driven middleware easily integrated with GAMESS that assesses resource consumption and invokes GAMESS adaptations to the system environment. We show that the throughput of GAMESS jobs may be improved greatly as a result of suchmore » adaptations.« less

Authors:
 [1]
  1. Iowa State Univ., Ames, IA (United States)
Publication Date:
Research Org.:
Ames Lab., Ames, IA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
888952
Report Number(s):
IS-T 2595
TRN: US200619%%283
DOE Contract Number:
W-7405-Eng-82
Resource Type:
Thesis/Dissertation
Country of Publication:
United States
Language:
English
Subject:
99 GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE; CHEMISTRY; ELECTRONIC STRUCTURE; IMPLEMENTATION

Citation Formats

Ustemirov, Nurzhan. Efficient Execution of Electronic Structure Calculations on SMP Clusters. United States: N. p., 2006. Web. doi:10.2172/888952.
Ustemirov, Nurzhan. Efficient Execution of Electronic Structure Calculations on SMP Clusters. United States. doi:10.2172/888952.
Ustemirov, Nurzhan. Sun . "Efficient Execution of Electronic Structure Calculations on SMP Clusters". United States. doi:10.2172/888952. https://www.osti.gov/servlets/purl/888952.
@article{osti_888952,
title = {Efficient Execution of Electronic Structure Calculations on SMP Clusters},
author = {Ustemirov, Nurzhan},
abstractNote = {Applications augmented with adaptive capabilities are becoming common in parallel computing environments. For large-scale scientific applications, dynamic adjustments to a computationally-intensive part may lead to a large pay-off in facilitating efficient execution of the entire application while aiming at avoiding resource contention. Application-specific knowledge, often best revealed during the run-time, is required to initiate and time these adjustments. In particular, General Atomic and Molecular Electronic Structure System (GAMESS) is a program for ab initio quantum chemistry that places significant demands on the high-performance computing platforms. Certain electronic structure calculations are characterized by high consumption of a particular resource, such as CPU, main memory, or disk I/O. This may lead to resource contention among concurrent GAMESS jobs and other programs in the dynamically changing environment. Thus, it is desirable to improve GAMESS calculations by means of dynamic adaptations. In this thesis, we show how an application- or algorithm-specific knowledge may play a significant role in achieving this goal. The choice of implementation is facilitated by a module-driven middleware easily integrated with GAMESS that assesses resource consumption and invokes GAMESS adaptations to the system environment. We show that the throughput of GAMESS jobs may be improved greatly as a result of such adaptations.},
doi = {10.2172/888952},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Sun Jan 01 00:00:00 EST 2006},
month = {Sun Jan 01 00:00:00 EST 2006}
}

Thesis/Dissertation:
Other availability
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  • Modern quantum chemistry deals with electronic structure calculations of unprecedented complexity and accuracy. They demand full power of high-performance computing and must be in tune with the given architecture for superior e ciency. To make such applications resourceaware, it is desirable to enable their static and dynamic adaptations using some external software (middleware), which may monitor both system availability and application needs, rather than mix science with system-related calls inside the application. The present work investigates scienti c application interlinking with middleware based on the example of the computational chemistry package GAMESS and middleware NICAN. The existing synchronous model ismore » limited by the possible delays due to the middleware processing time under the sustainable runtime system conditions. Proposed asynchronous and hybrid models aim at overcoming this limitation. When linked with NICAN, the fragment molecular orbital (FMO) method is capable of adapting statically and dynamically its fragment scheduling policy based on the computing platform conditions. Signi cant execution time and throughput gains have been obtained due to such static adaptations when the compute nodes have very di erent core counts. Dynamic adaptations are based on the main memory availability at run time. NICAN prompts FMO to postpone scheduling certain fragments, if there is not enough memory for their immediate execution. Hence, FMO may be able to complete the calculations whereas without such adaptations it aborts.« less
  • The electronic structure of semiconductors, alloys, transition metal compounds, and the electronic states associated with surfaces are studied using the empirical pseudopotential and the tight-binding methods. Experimental data are extensively used to obtain information on the pseudopotential and tight-binding parameters, and to check the accuracy of the theoretical calculations. Reflectivity spectra, frequency dependent dielectric constants, densities of states and charge density distributions are calculated for a number of compounds and compared to corresponding experimental information when available.
  • This thesis consists of five chapters, each of which is a self-contained unit. The first chapter overviews methods for electronic-structure calculations. Chapter 2 introduces a new method to generate a rapidly converging configuration expansion. The approach iteratively combines (1) a least-squares fitting of a configuration expansion to a many-body wave function with (2) a transfer-matrix method for projecting out the ground state. Results are shown to be equivalent to multiconfiguration Hartree-Fock. Results from test calculations are given for a simple finite difference model of the helium atom. In Chapter 3 the use of the finite-element method in electronic structure calculationsmore » is discussed. Chapters 4 and 5 discuss developments in Monte Carlo methods based on Hubbard-Stratonovich transformations. Chapter 4 introduces a canonical ensemble formulation of the method, which is more appropriate than the usual grand canonical formulation for electronic structure. Chapter 5 considers problems in these types of simulations for systems with negative weights. Two methods - Langevin and molecular dynamics - are investigated for use in simulating fermion systems with real, non-positive definite probability functions.« less
  • Conventional implementations of collective communications are based on point-to-point communications, and their optimizations have been focused on efficiency of those communication algorithms. However, point-to-point communications are not the optimal choice for modern computing clusters of SMPs due to their two-level communication structure. In recent years, a few research efforts have investigated efficient collective communications for SMP clusters. This dissertation is focused on platform-independent algorithms and implementations in this area. There are two main approaches to implementing efficient collective communications for clusters of SMPs: using shared memory operations for intra-node communications, and overlapping inter-node/intra-node communications. The former fully utilizes the hardwaremore » based shared memory of an SMP, and the latter takes advantage of the inherent hierarchy of the communications within a cluster of SMPs. Previous studies focused on clusters of SMP from certain vendors. However, the previously proposed methods are not portable to other systems. Because the performance optimization issue is very complicated and the developing process is very time consuming, it is highly desired to have self-tuning, platform-independent implementations. As proven in this dissertation, such an implementation can significantly out-perform the other point-to-point based portable implementations and some platform-specific implementations. The dissertation describes in detail the architecture of the platform-independent implementation. There are four system components: shared memory-based collective communications, overlapping mechanisms for inter-node and intra-node communications, a prediction-based tuning module and a micro-benchmark based tuning module. Each component is carefully designed with the goal of automatic tuning in mind.« less
  • The term Logic Programming refers to a variety of computer languages and execution models based on the traditional concept of Symbolic Logic. The expressive power of these languages offers promise to be of great assistance in facing the programming challenges of present and future symbolic processing applications in artificial intelligence, knowledge-based systems, and many other areas of computing. This dissertation presents an efficient parallel execution model for logic programs. The model is described from the source language level down to an Abstract Machine level, suitable for direct implementation on existing parallel systems or for the design of special purpose parallelmore » architectures. Few assumptions are made at the source language level and, therefore, the techniques developed and the general Abstract Machine design are applicable to a variety of logic (and also functional) languages. These techniques offer efficient solutions to several areas of parallel Logic Programming implementation previously considered problematic or a source of considerable overhead, such as the detection and handling of variable binding conflicts in AND-parallelism, the specification of control and management of the execution tree, the treatment of distributed backtracking, and goal scheduling and memory management issues, etc. A parallel Abstract Machine design is offered, specifying data areas, operation, and a suitable instruction set.« less