Quantitative analysis of vector code

In this paper we present the results of a detailed simulation study of the execution of vector programs on a single processor of a Convex C3480 machine, using a subset of the Perfect Club benchmarks. We are interested in evaluating several cost/performance tradeoffs that the machine designers made in order to assess which features of the architecture severely limit the performance attainable. We present the detailed usage of the vector functional units and a study of the kinds of resource conflicts that stall the machine. The results obtained show that the resources of the vector architecture are not efficiently used mainly due to the single bus memory architecture. Other severe limitations of the machine turn out to be the lack of chaining between vector loads and vector computations, and the lack of a second general purpose functional unit. We also present some data about the port pressure on the vector register file and we see that stalls due to port conflicts are relatively high. We also consider the slow-down introduced by spill code and find that the limited number of vector registers also limits performance.Peer ReviewedPostprint (published version

Parallel machine architecture and compiler design facilities

The objective is to provide an integrated simulation environment for studying and evaluating various issues in designing parallel systems, including machine architectures, parallelizing compiler techniques, and parallel algorithms. The status of Delta project (which objective is to provide a facility to allow rapid prototyping of parallelized compilers that can target toward different machine architectures) is summarized. Included are the surveys of the program manipulation tools developed, the environmental software supporting Delta, and the compiler research projects in which Delta has played a role

Semiannual final report, 1 October 1991 - 31 March 1992

A summary of research conducted at the Institute for Computer Applications in Science and Engineering in applied mathematics, numerical analysis, and computer science during the period 1 Oct. 1991 through 31 Mar. 1992 is presented

Detecting Stable Communities In Large Scale Networks

A network is said to exhibit community structure if the nodes of the network can be easily grouped into groups of nodes, such that each group is densely connected internally but sparsely connected with other groups. Most real world networks exhibit community structure. A popular technique for detecting communities is based on computing the modularity of the network. Modularity reflects how well the vertices in a group are connected as opposed to being randomly connected. We propose a parallel algorithm for detecting modularity in large networks. However, all modularity based algorithms for detecting community structure are affected by the order in which the vertices in the network are processed. Therefore, detecting communities in real world graphs becomes increasingly difficult. We introduce the concept of stable community, that is, a group of vertices that are always partitioned to the same community independent of the vertex perturbations to the input. We develop a preprocessing step that identifies stable communities and empirically show that the number of stable communities in a network affects the range of modularity values obtained. In particular, stable communities can also help determine strong communities in the network. Modularity is a widely accepted metric for measuring the quality of a partition identified by various community detection algorithms. However, a growing number of researchers have started to explore the limitations of modularity maximization such as resolution limit, degeneracy of solutions and asymptotic growth of the modularity value for detecting communities. In order to address these issues we propose a novel vertex-level metric called permanence. We show that our metric permanence as compared to other standard metrics such as modularity, conductance and cut-ratio performs as a better community scoring function for evaluating the detected community structures from both synthetic networks and real-world networks. We demonstarte that maximizing permanence results in communities that match the ground-truth structure of networks more accurately than modularity based and other approaches. Finally, we demonstrate how maximizing permanence overcomes limitations associated with modularity maximization

Distribuert fellesminne i software over SCI

Denne oppgaven diskuterer utnyttelse av SCI i et system for distribuert fellesminne implementert i software. Foruten å benytte SCI som et medium for rask meldingsutveksling, er også muligheten for å skrive direkte til minnet i en annen maskin via SCI-kortet testet. Konklusjonen er at man har mulighet til å oppnå bedre ytelse ved å utnytte SCI og den ekstra funksjonaliteten. Dette krever dog at programmereren har kjennskap til programmets datastrukturer og bruk av data for å få en effektiv utnyttelse

On the design of architecture-aware algorithms for emerging applications

This dissertation maps various kernels and applications to a spectrum of programming models and architectures and also presents architecture-aware algorithms for different systems. The kernels and applications discussed in this dissertation have widely varying computational characteristics. For example, we consider both dense numerical computations and sparse graph algorithms. This dissertation also covers emerging applications from image processing, complex network analysis, and computational biology. We map these problems to diverse multicore processors and manycore accelerators. We also use new programming models (such as Transactional Memory, MapReduce, and Intel TBB) to address the performance and productivity challenges in the problems. Our experiences highlight the importance of mapping applications to appropriate programming models and architectures. We also find several limitations of current system software and architectures and directions to improve those. The discussion focuses on system software and architectural support for nested irregular parallelism, Transactional Memory, and hybrid data transfer mechanisms. We believe that the complexity of parallel programming can be significantly reduced via collaborative efforts among researchers and practitioners from different domains. This dissertation participates in the efforts by providing benchmarks and suggestions to improve system software and architectures.Ph.D.Committee Chair: Bader, David; Committee Member: Hong, Bo; Committee Member: Riley, George; Committee Member: Vuduc, Richard; Committee Member: Wills, Scot

Parallel Lagrangian particle transport : application to respiratory system airways

This thesis is focused on particle transport in the context of high computing performance (HPC) in its widest range, from the numerical modeling to the physics involved, including its parallelization and post-process. The main goal is to obtain a general framework that enables understanding all the requirements and characteristics of particle transport using the Lagrangian frame of reference. Although the idea is to provide a suitable model for any engineering application that involves particle transport simulation, this thesis uses the respiratory system framework. This means that all the simulations are focused on this topic, including the benchmarks for testing, verifying and optimizing the results. Other applications, such as combustion, ocean residuals, or automotive, have also been simulated by other researchers using the same numerical model proposed here. However, they have not been included here in the interest of allowing the project to advance in a specific direction, and facilitate the structure and comprehension of this work. Human airways and respiratory system simulations are of special interest for medical purposes. Indeed, human airways can be significantly different in every individual. This complicates the study of drug delivery efficiency, deposition of polluted particles, etc., using classic in-vivo or in-vitro techniques. In other words, flow and deposition results may vary depending on the geometry of the patient and simulations allow customized studies using specific geometries. With the help of the new computational techniques, in the near future it may be possible to optimize nasal drugs delivery, surgery or other medical studies for each individual patient though a more personalized medicine. In summary, this thesis prioritizes numerical modeling, wide usability, performance, parallelization, and the study of the physics that affects particle transport. In addition, the simulation of the respiratory system should carry out interesting biological and medical results. However, the interpretation of these results will be only done from a pure numerical point of view.Aquesta tesi se centra en el transport de partícules dins el context de la computació d'alt rendiment (HPC), en el seu ventall més ampli; des del model numèric fins a la física involucrada, incloent-hi la part de paral·lelització del codi i de post-procés. L'objectiu principal és obtenir un esquema general que permeti entendre tant els requeriments com les característiques del transport de partícules fent servir el marc de referència Lagrangià. Encara que la idea sigui definir un model capaç¸ de simular qualsevol aplicació en el camp de l'enginyeria que involucri el transport de partícules, aquesta tesi utilitza el sistema respiratori com a temàtica de referència. Això significa que totes les simulacions estan emmarcades en aquest camp d'estudi, incloent-hi els tests de referència, verificacions i optimitzacions de resultats. L'estudi d'altres aplicacions, com ara la combustió, els residus oceànics, l'automoció o l'aeronàutica també han estat dutes a terme per altres investigadors utilitzant el mateix model numèric proposat aquí. Tot i així, aquests resultats no han estat inclosos en aquesta tesi per simplificar-la i avançar en una sola direcció; facilitant així l'estructura i millor comprensió d'aquest treball. Pel que fa al sistema respiratori humà i les seves simulacions, tenen especial interès per a propòsits mèdics. Particularment, la geometria dels conductes respiratoris pot variar de manera considerable en cada persona. Això complica l'estudi en aspectes com el subministrament de medicaments o la deposició de partícules contaminants, per exemple, utilitzant les tècniques clàssiques de laboratori (in-vivo o in-vitro). En altres paraules, tant el flux com la deposició poden canviar en funció de la geometria del pacient i aquí és on les simulacions permeten estudis adaptats a geometries concretes. Gràcies a les noves tècniques de computació, en un futur proper és probable que puguem optimitzar el subministrament de medicaments per via nasal, la cirurgia o altres estudis mèdics per a cada pacient mitjançant una medicina més personalitzada. En resum, aquesta tesi prioritza el model numèric, l'amplitud d'usos, el rendiment, la paral·lelització i l'estudi de la física que afecta directament a les partícules. A més, el fet de basar les nostres simulacions en el sistema respiratori dota aquesta tesi d'un interès biològic i mèdic pel que fa als resultats

Software for Exascale Computing - SPPEXA 2016-2019

This open access book summarizes the research done and results obtained in the second funding phase of the Priority Program 1648 "Software for Exascale Computing" (SPPEXA) of the German Research Foundation (DFG) presented at the SPPEXA Symposium in Dresden during October 21-23, 2019. In that respect, it both represents a continuation of Vol. 113 in Springer’s series Lecture Notes in Computational Science and Engineering, the corresponding report of SPPEXA’s first funding phase, and provides an overview of SPPEXA’s contributions towards exascale computing in today's sumpercomputer technology. The individual chapters address one or more of the research directions (1) computational algorithms, (2) system software, (3) application software, (4) data management and exploration, (5) programming, and (6) software tools. The book has an interdisciplinary appeal: scholars from computational sub-fields in computer science, mathematics, physics, or engineering will find it of particular interest