Austrian Grid Project [SEE-Grid]

Project Description

This is a project in the frame of the Austrian Grid initiative. Its goal is the development of a grid-enabled version of the SEE++ simulation software for eye-surgery developed by Upper Austrian Research in collaboration with the Upper Austria University of Applied Sciences at Hagenberg.

Project Lead

Project Duration

01/09/2004 - 31/12/2006

Project URL

Go to Website

Publications

2009

Automated Reasoning

Tudor Jebelean, Bruno Buchberger, Temur Kutsia, Nikolaj Popov, Wolfgang Schreiner, Wolfgang Windsteiger

In: Hagenberg Research, B. Buchberger, M. Affenzeller, A. Ferscha, M. Haller, T. Jebelean, E.P. Klement, P. Paule, G. Pomberger, W. Schreiner, R. Stubenrauch, R. Wagner, G. Weiss, W. Windsteiger (ed.), pp. 63-101. 2009. Springer Dordrecht Heidelberg London New York, ISBN 978-3-642-02126-8. [url]
[bib]
@incollection{RISC3844,
author = {Tudor Jebelean and Bruno Buchberger and Temur Kutsia and Nikolaj Popov and Wolfgang Schreiner and Wolfgang Windsteiger},
title = {{Automated Reasoning}},
booktitle = {{Hagenberg Research}},
language = {english},
pages = {63--101},
publisher = {Springer Dordrecht Heidelberg London New York},
isbn_issn = {ISBN 978-3-642-02126-8},
year = {2009},
annote = {2009-00-00-B},
editor = {B. Buchberger and M. Affenzeller and A. Ferscha and M. Haller and T. Jebelean and E.P. Klement and P. Paule and G. Pomberger and W. Schreiner and R. Stubenrauch and R. Wagner and G. Weiss and W. Windsteiger},
refereed = {no},
length = {39},
url = {http://www.springer.com/computer/programming/book/978-3-642-02126-8}
}

Evaluation of Cluster Middleware in a Heterogeneous Computing Environment

Stefan Georgiev

Internationaler Universitätslehrgang Informatics: Engineering & Management (ISI Hagenberg). Diploma Thesis. July 2009. [pdf]
[bib]
@mastersthesis{RISC3855,
author = {Stefan Georgiev},
title = {{Evaluation of Cluster Middleware in a Heterogeneous Computing Environment}},
language = {english},
abstract = {Deploying a Beowulf-type high-performance cluster is a challenging task. Many problems,regarding the underlying hardware infrastructure and the used software components need to besolved in order to make a set of machines work as a single computer. The task becomes even morecomplicated when heterogeneous commodity hardware platforms are utilized. This research isprovoked by the idea of using a company’s old desktop computers for achieving computingperformance at a low cost. While the existing cluster middleware provides many solutions forutilizing distributed resources, it still fails to be suitable for some cluster setups. This thesisrepresents the results of an evaluation in the field of heterogeneous high-performance computing. Asystematic analysis of available tools for high-performance clustering aims to reveal both theirstrong and their weak sides. In addition, a detailed evaluation is provided from the point of view ofadministrators and users. The thesis describes the process of building a fully-functioning parallelenvironment using three different tools for cluster deployment - OSCAR v6.0.2, ROCKS v5.1 andCAOS-NSA v 1.0. These tools are compared in detail, so that the most suitable one can bedetermined. As a result two test environments are built. Numerous examples of tests runs, executedon the two environments, are described. Usability, with regards to different tools like resourcemanagers, schedulers, and MPI, is assessed taking into consideration the underlying hardwareplatforms. The capabilities of the clusters are evaluated against a parallel application for routeoptimization.},
year = {2009},
month = {July},
translation = {0},
school = {Internationaler Universitätslehrgang Informatics: Engineering & Management (ISI Hagenberg)},
length = {94}
}

2007

A Grid Software for Virtual Eye Surgery Based on Globus 4 and gLite

Karoly Bosa, Wolfgang Schreiner, Michael Buchberger, Thomas Kaltofen

In: Proceedings of ISPDC 2007, IEEE Computer Society (ed.), Proceedings of ISPDC 2007, 6th International Symposium on Parallel and Distributed Computing, pp. 151-158. 2007. 0. [url] [ps] [pdf]
[bib]
@inproceedings{RISC3092,
author = {Karoly Bosa and Wolfgang Schreiner and Michael Buchberger and Thomas Kaltofen},
title = {{A Grid Software for Virtual Eye Surgery Based on Globus 4 and gLite}},
booktitle = {{Proceedings of ISPDC 2007}},
language = {english},
abstract = {``Grid-Enabled SEE++'' is based on the SEE++ software system for the biomechanicalsimulation of the human eye. ``Grid-Enabled SEE++'' extends SEE++ inseveral steps in order to develop an efficient grid-based tool for``Evidence Based Medicine'', which supports surgeons in choosingoptimal surgery techniques for the treatment of certain eye motilitydisorders.Recently, we refined the design of ``Grid-Enabled SEE++'' and weworked on an extended version of the software, which is able to utilize the``Web Service Resource Framework'' architecture of theGlobus Toolkit 4.Since we met with some limitations of Globus 4, we also designed aversion of ``Grid-Enabled SEE++'' compatible with the gLitegrid middleware.In this paper, we report on our experience of porting a grid applicationto Globus 4 and gLite, describe the problems we encountered and discusspossible solution strategies. This may assist the porting of otherapplications to the grid using these middleware products.},
pages = {151--158},
isbn_issn = {0},
year = {2007},
editor = {IEEE Computer Society},
refereed = {yes},
keywords = {Grid Computing, SEE++},
length = {8},
conferencename = {ISPDC 2007, 6th International Symposium on Parallel and Distributed Computing},
url = {http://www.risc.uni-linz.ac.at/about/conferences/ispdc2007/}
}

2006

The Software Architecture of a Grid-Enabled Data Management System for SEE-GRID

Karoly Bosa, Wolfgang Schreiner, Michael Buchberger, Thomas Kaltofen

Research Institute for Symbolic Computation (RISC), Johannes Kepler University, Linz, Austria. Technical report no. AG-DA-1c-1-2006, March 2006. Austrian Grid Deliverable. [doc]
[bib]
@techreport{RISC2875,
author = {Karoly Bosa and Wolfgang Schreiner and Michael Buchberger and Thomas Kaltofen},
title = {{The Software Architecture of a Grid-Enabled Data Management System for SEE-GRID}},
language = {english},
abstract = {SEE-GRID is based on the SEE++ software system for the biomechanical simulation of the human eye. The goal of SEE-GRID is to extend SEE++ in several steps in order to develop an efficient grid-based tool for ``Evidence Based Medicine'', which supports surgeons in choosing optimal surgery techniques for the treatment of certain eye motility disorders.First, we have developed a grid-enabled version of the simulation of the Hess-Lancaster test, which is a medical examination by which the pathology of the patient can be estimated. Based on this, we work on a pathology fitting algorithm that attempts to give sufficiently close estimations for the pathological reasons of the disorder. Furthermore, we have started to develop a grid enabled distributed database where both real and simulated pathological cases can be collected, sorted and evaluated for improving both the later pathology fitting calculations and the future medical treatments.In this document, we present some new development on the “SEE++ to Grid Bridge”, by which among other things it is able to interact with the prototype version of the SEE-GRID database component. Then we give an overview on the future architecture of the SEE-GRID software system and outline its proposed components.},
number = {AG-DA-1c-1-2006},
year = {2006},
month = {March},
institution = {Research Institute for Symbolic Computation (RISC), Johannes Kepler University, Linz, Austria},
sponsor = {Austrian Grid Project},
length = {17},
type = {Austrian Grid Deliverable}
}

A Report on the First Prototype of a Grid-Enabled Data Management System for See-Grid

Karoly Bosa, Wolfgang Schreiner, Michael Buchberger, Thomas Kaltofen

Research Institute for Symbolic Computation (RISC), Johannes Kepler University, Linz, Austria. Technical report no. AG-DA-1c-4-2006, July 2006. Austrian Grid Deliverable. [doc]
[bib]
@techreport{RISC2939,
author = {Karoly Bosa and Wolfgang Schreiner and Michael Buchberger and Thomas Kaltofen},
title = {{A Report on the First Prototype of a Grid-Enabled Data Management System for See-Grid}},
language = {english},
abstract = {SEE-GRID is based on the SEE++ software system for the biomechanical simulation of the human eye. The goal of SEE-GRID is to extend SEE++ in several steps in order to develop an efficient grid-based tool for ``Evidence Based Medicine'', which supports surgeons in choosing optimal surgery techniques for the treatment of certain eye motility disorders.First, we have developed a grid-enabled version of the simulation of the Hess-Lancaster test, which is a medical examination by which the pathology of the patient can be estimated. Based on this, we work on a pathology fitting algorithm that attempts to give sufficiently close estimations for the pathological reasons of the disorder. Furthermore, we have developed a prototype version of a grid enabled medical database where both real and simulated pathological cases can be collected, sorted and evaluated for improving both the later pathology fitting calculations and the future medical treatments.In this document, we present a description of the elementary integration of the prototype database component into Globus 4. Then we give a short overview on a planned gLite (EGEE middleware) compatible architecture of the SEE-GRID software system and outline its proposed components.},
number = {AG-DA-1c-4-2006},
year = {2006},
month = {July},
institution = {Research Institute for Symbolic Computation (RISC), Johannes Kepler University, Linz, Austria},
length = {16},
type = {Austrian Grid Deliverable}
}

Investigations on Improving the SEE-GRID Optimization Algorithm by Parallelization

Johannes Watzl

Research Institute for Symbolic Computation (RISC), Johannes Kepler University, Linz, Austria. Technical report no. AG-DA-1c-3-2006, July 2006. Austrian Grid Deliverable. [pdf]
[bib]
@techreport{RISC2938,
author = {Johannes Watzl},
title = {{Investigations on Improving the SEE-GRID Optimization Algorithm by Parallelization}},
language = {english},
abstract = {This report deals with possible improvements of the current implementationof the optimization algorithm in the SEE-GRID project.First the present algorithm is analysed and benchmarked. Then weinitiate both sequential and parallel approaches for accelerating thecomputation. The sequential approach is done by the Broyden updatemethod; the parallel strategies work on the one hand with parallel Delaunaytriangulation for interpolating the function to minimize and onthe other hand with decoupling optimization from triangulation. Theinterpolation is chosen because the function we have to minimize hasto be evaluated thousands of times which takes more than half of thecomputation time.},
number = {AG-DA-1c-3-2006},
year = {2006},
month = {July},
institution = {Research Institute for Symbolic Computation (RISC), Johannes Kepler University, Linz, Austria},
length = {21},
type = {Austrian Grid Deliverable}
}

2005

The Initial Version of SEE-GRID

Karoly Bosa, Wolfgang Schreiner, Michael Buchberger, Thomas Kaltofen

Research Institute for Symbolic Computation (RISC). Technical report, Johannes Kepler University, Linz, Austria, Austrian Grid Deliverable AG-DA1c-1-2005_v1, March 2005. [pdf]
[bib]
@techreport{RISC2454,
author = {Karoly Bosa and Wolfgang Schreiner and Michael Buchberger and Thomas Kaltofen},
title = {{The Initial Version of SEE-GRID}},
language = {english},
abstract = {This document describes the functionality of the “SEE++ to Grid Bridge”, which is the initial component of SEE-GRID. SEE-GRID is based on the SEE++ software for the biomechanical simulation of the human eye. SEE++ was developed in the SEE-KID project by the Upper Austrian Research and the Upper Austria University of Applied Sciences. SEE++ consists of a client component for user interaction and of a server component that runs various computations. Via the “SEE++ to Grid Bridge”, normal SEE++ clients are able to access and exploit the computational power of the Austrian Grid. The bridge starts SEE++ servers on various grid sites and distributes to them computational tasks received from some SEE+ clients. This paper addresses the following issues:• How the initially proposed design of SEE-GRID was adapted to the current software infrastructure of the Austrian Grid. • How our environment was configured in order to access to the Austrian Grid. • How the “SEE++ to Grid Bridge” works together with SEE++ clients and the middleware software layer of the Austrian Grid.• How SEE++ server processes are started in the grid environment.• How computational tasks are distributed to the Austrian Grid resources.• How and with what kind of parameters the “SEE++ to Grid Bridge” can be used. At the end of this paper, we summarize our first experiences and benchmark results related to this initial version of SEE-GRID.},
address = {Johannes Kepler University, Linz, Austria},
year = {2005},
month = {March},
howpublished = {Austrian Grid Deliverable AG-DA1c-1-2005_v1},
institution = {Research Institute for Symbolic Computation (RISC)},
length = {18}
}

A Prototype of the SEE-GRID Pathology Fitter

Karoly Bosa, Wolfgang Schreiner, Michael Buchberger, Thomas Kaltofen

Research Institute for Symbolic Computation (RISC), Johannes Kepler University, Linz, Austria. Technical report, Austrian Grid Deliverable AG-DA1c-3-2005_v1.doc, July 2005. [pdf]
[bib]
@techreport{RISC2477,
author = {Karoly Bosa and Wolfgang Schreiner and Michael Buchberger and Thomas Kaltofen},
title = {{A Prototype of the SEE-GRID Pathology Fitter}},
language = {english},
abstract = {In the previous phase of the SEE-GRID project, we implemented the "SEE++ to Grid Bridge", via which normal SEE++ clients are able to access and exploit the computational power of the Austrian Grid.This document discusses the theory and the design of a new functionality of the SEE-GRID system called pathology fitting and described its two simple parallelized versions. SEE-GRID is based on the SEE++ software for the biomechanical simulation of the human eye. SEE++ was developed in the SEE-KID project by the Upper Austrian Research and the Upper Austria University of Applied Sciences. SEE++ consists of a client component for user interaction and of a server component that runs various computations. The pathology fitting algorithm in SEE-GRID uses the result data of the medical examination Hess-Lancastar Test as input and it is able to determine (approximately) the pathological cause of strabismus in case of a patient. This paper addresses the following issues:• How the sequential pathology fitting algorithm works.• How the sequential pathology fitting can be improved by using the results of the previous phase of the SEE-GRID project.• How the pathology fitter can be parallelized.At the end of this paper, we summarise our first experiences with the pathology fitting and make a plan for the further developments.},
year = {2005},
month = {July},
howpublished = {Austrian Grid Deliverable AG-DA1c-3-2005_v1.doc},
institution = {Research Institute for Symbolic Computation (RISC), Johannes Kepler University, Linz, Austria},
length = {18}
}

A REFINED DESIGN OF THE SEE-GRID DATABASE AND PATHOLOGY FITTER

Karoly Bosa, Wolfgang Schreiner, Michael Buchberger, Thomas Kaltofen

Research Institute for Symbolic Computation (RISC), Johannes Kepler University, Linz, Austria. Technical report, Austrian Grid Deliverable AG-DA1c-5-2005_v1.doc, November 2005. [pdf]
[bib]
@techreport{RISC2820,
author = {Karoly Bosa and Wolfgang Schreiner and Michael Buchberger and Thomas Kaltofen},
title = {{A REFINED DESIGN OF THE SEE-GRID DATABASE AND PATHOLOGY FITTER}},
language = {english},
abstract = {SEE-GRID is based on the SEE++ software for the biomechanical simulation of the human eye. The goal of SEE-GRID is to adapt and to extend SEE++ in several steps and to develop an efficient grid-based tool for “Evidence Based Medicine”, which supports the surgeons to choose the best/optimal surgery techniques in case of the treatments of different syndromes of strabismus. First, we developed the “SEE++ to Grid Bridge”, via which normal SEE++ clients are able to access and exploit the computational power of the Austrian Grid. We have implemented a distributed and grid-based version of the Hess-Lancaster test, which is a medical examination for the diagnosis of strabismus and whose original sequential simulation is time consuming in SEE++. Then, we also implemented a prototype version of the grid-enabled pathology fitting algorithm, which attempts to determine (approximately) the pathological reason of strabismus in case of a patient.In this document, we present some extended benchmark results of the parallel Hess Lancaster test, in which we used more grid resources and reached greater speedup values as before.Next, we describe the current state of the grid-enabled distributed medical database that we started to develop in the previous phases of the project for collecting, sorting and evaluating patient’s data and both real and simulated pathological cases. Then we outline the further development steps related to the SEE-GRID database. In the last section of this document, we discuss and evaluate the possible designs of grid-based Pathology Fitting and Surgery Fitting algorithms, which we plan to implement at a later phase of the project.},
year = {2005},
month = {November},
howpublished = {Austrian Grid Deliverable AG-DA1c-5-2005_v1.doc},
institution = {Research Institute for Symbolic Computation (RISC), Johannes Kepler University, Linz, Austria},
length = {17}
}

SEE-GRID, A Grid-Based Medical Decision Support System for Eye Muscle Surgery

Karoly Bosa, Wolfgang Schreiner, Michael Buchberger, Thomas Kaltofen

In: Proceedings of 1st Austrian Grid Symposium 2005, Jens Volkert et al. (ed.), pp. 61-74. December 1-2 2005. Austrian Computer Society (OCG), Austrian Grid, 3-85403-210-2. [pdf] [ps]
[bib]
@inproceedings{RISC3947,
author = {Karoly Bosa and Wolfgang Schreiner and Michael Buchberger and Thomas Kaltofen},
title = {{SEE-GRID, A Grid-Based Medical Decision Support System for Eye Muscle Surgery}},
booktitle = {{Proceedings of 1st Austrian Grid Symposium 2005}},
language = {english},
abstract = {SEE-GRID is based on the SEE++ software system for the biomechanical simulation of the human eye. The goal of SEE-GRID is to extend SEE++ in several steps in order to develop an efficient grid-based tool for “Evidence Based Medicine”, which supports surgeons in choosing optimal surgery techniques for the treatment of certain eye motility disorders. First, we have developed a grid-enabled version of the simulation of the Hess-Lancaster test, which is a medical examination by which the pathology of the patient can be estimated. Based on this, we work on a pathology fitting algorithm that attempts to give sufficiently close estimations for the pathological reasons of the disorder.Furthermore, we have started to develop a grid enabled distributed database where both realand simulated pathological cases can be collected, sorted and evaluated for improving both the laterpathology fitting calculations and the future medical treatments.},
pages = {61--74},
publisher = {Austrian Computer Society (OCG)},
isbn_issn = {3-85403-210-2},
year = {2005},
month = {December 1-2},
editor = {Jens Volkert et al.},
refereed = {yes},
organization = {Austrian Grid},
keywords = {Grid Computing, SEE-GRID, SEE++, Parallel Hess-Lancaster Test},
length = {14}
}

Grid Computing zur Simulation von Augenmuskeloperationen

Wolfgang Schreiner, Michael Buchberger

OCG Journal 5, pp. 23-24. December 2005. Austrian Computer Society (OCG), ISSN 1728-743X. [url]
[bib]
@article{RISC2790,
author = {Wolfgang Schreiner and Michael Buchberger},
title = {{Grid Computing zur Simulation von Augenmuskeloperationen}},
language = {german},
journal = {OCG Journal},
volume = {5},
pages = {23--24},
publisher = {Austrian Computer Society (OCG)},
isbn_issn = {ISSN 1728-743X},
year = {2005},
month = {December},
refereed = {no},
length = {2},
url = {http://www.ocg.at/publikationen/oj/index.html}
}

2004

SEE-GRID Design Overview

Karoly Bosa, Wolfgang Schreiner, Rebhi Baraka, Michael Buchberger, Thomas Kaltofen, Daniel Mitterdorfer

Research Institute for Symbolic Computation (RISC). Technical report no. A1c-1, Johannes Kepler University, Linz, Austria, Austrian Grid Deliverable, November 2004. Austrian Grid Deliverable. [pdf]
[bib]
@techreport{RISC431,
author = {Karoly Bosa and Wolfgang Schreiner and Rebhi Baraka and Michael Buchberger and Thomas Kaltofen and Daniel Mitterdorfer},
title = {{SEE-GRID Design Overview}},
language = {english},
abstract = {This document describes the initial design of the SEE-GRID software in the Austrian Grid.SEE-GRID is based on the SEE++ software for the biomechanical simulation of the humaneye. SEE++ was developed in the SEE-KID project by Upper Austrian Research and theUpper Austria University of Applied Sciences; it consists of a client component for userinteraction and of a server component that runs various computations (currently “HessDiagram Calculation” and “Pathology Fitting”, in the future also “Surgery Simulation”). Thegoal of SEE-GRID is to adapt and to extend SEE++ in several steps to make use of the grid:1. The simulation component is transformed to a grid service.2. “Hess Diagram Calculation” is parallelized and distributed over multiple grid nodes.3. “Pathology Fitting” is parallelized and distributed over multiple grid nodes.4. A grid database of “gaze patterns” is established with patterns derived frommeasurements and calculations. For querying this database for wanted patterns, manyinstances of the core problem of “pathology fitting” have to be performed; we willparallelize these queries and distribute them over multiple grid nodes.Based on above results, SEE++/SEE-GRID may be improved in order to provide a future“surgery simulation” component that gives the doctor recommendations for how to perform asurgery that corrects a particular impaired eye.},
number = {A1c-1},
address = {Johannes Kepler University, Linz, Austria},
year = {2004},
month = {November},
howpublished = {Austrian Grid Deliverable},
institution = {Research Institute for Symbolic Computation (RISC)},
length = {22},
type = {Austrian Grid Deliverable}
}

1995

Parallel Functional Programming for Computer Algebra

Wolfgang Schreiner

RISC, Johannes Kepler University Linz. PhD Thesis. 1995.
[bib]
@phdthesis{RISC4126,
author = {Wolfgang Schreiner},
title = {{Parallel Functional Programming for Computer Algebra}},
language = {english},
year = {1995},
translation = {0},
school = {RISC, Johannes Kepler University Linz},
length = {0}
}

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