Memory-based scheduling of scientific computing clusters

This study looks at how increased memory utilisation affects throughput and energy consumption in scientific computing, especially in high-energy physics. Our aim is to minimise energy consumed by a set of jobs without increasing the processing time. The earlier tests indicated that, especially in data analysis, throughput can increase over 100% and energy consumption decrease 50% by processing multiple jobs in parallel per CPU core. Since jobs are heterogeneous, it is not possible to find an optimum value for the number of parallel jobs. A better solution is based on memory utilisation, but finding an optimum memory threshold is not straightforward. Therefore, a fuzzy logic-based algorithm was developed that can dynamically adapt the memory threshold based on the overall load. In this way, it is possible to keep memory consumption stable with different workloads while achieving significantly higher throughput and energy-efficiency than using a traditional fixed number of jobs or fixed memory threshold approaches.

FastEpistasis: a high performance computing solution for quantitative trait epistasis.

Motivation: Genome-wide association studies have become widely used tools to study effects of genetic variants on complex diseases. While it is of great interest to extend existing analysis methods by considering interaction effects between pairs of loci, the large number of possible tests presents a significant computational challenge. The number of computations is further multiplied in the study of gene expression quantitative trait mapping, in which tests are performed for thousands of gene phenotypes simultaneously. Results: We present FastEpistasis, an efficient parallel solution extending the PLINK epistasis module, designed to test for epistasis effects when analyzing continuous phenotypes. Our results show that the algorithm scales with the number of processors and offers a reduction in computation time when several phenotypes are analyzed simultaneously. FastEpistasis is capable of testing the association of a continuous trait with all single nucleotide polymorphism ( SNP) pairs from 500 000 SNPs, totaling 125 billion tests, in a population of 5000 individuals in 29, 4 or 0.5 days using 8, 64 or 512 processors.

Lomborg, Vanhanen ja Intelligent Design - kommentti Matti Kamppiselle

Kommentti Matti Kamppisen kirjoitukseen TT -lehdessä 1/2005

The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods.

The M-Coffee server is a web server that makes it possible to compute multiple sequence alignments (MSAs) by running several MSA methods and combining their output into one single model. This allows the user to simultaneously run all his methods of choice without having to arbitrarily choose one of them. The MSA is delivered along with a local estimation of its consistency with the individual MSAs it was derived from. The computation of the consensus multiple alignment is carried out using a special mode of the T-Coffee package [Notredame, Higgins and Heringa (T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 2000; 302: 205-217); Wallace, O'Sullivan, Higgins and Notredame (M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res. 2006; 34: 1692-1699)] Given a set of sequences (DNA or proteins) in FASTA format, M-Coffee delivers a multiple alignment in the most common formats. M-Coffee is a freeware open source package distributed under a GPL license and it is available either as a standalone package or as a web service from www.tcoffee.org.

Trust region versus line search for computing the optical flow

We consider the numerical treatment of the optical flow problem by evaluating the performance of the trust region method versus the line search method. To the best of our knowledge, the trust region method is studied here for the first time for variational optical flow computation. Four different optical flow models are used to test the performance of the proposed algorithm combining linear and nonlinear data terms with quadratic and TV regularization. We show that trust region often performs better than line search; especially in the presence of non-linearity and non-convexity in the model.

Report of the Workshop on Intelligent Construction for Earthworks: April 14-16, 2009

The objectives of this workshop were to update the strategies identified during the 2008 workshop; provide a collaborative exchange of ideas and experiences; share research results; increase participants' knowledge; develop research, education, and implementation initiatives for intelligent compaction (IC) and automated machine guidance (AMG) technologies; and develop strategies to move forward. The 2 1/2 day workshop was organized as follows: Day 1: Review of 2008 workshop proceedings, technical presentations on IC and AMG technologies, and participating state department of transportation (DOT) briefings. Day 2: Industry/equipment manufacturer presentations and breakout interactive sessions on three topic areas. Day 3: Breakout session summary reporting and panel discussion involving state DOT, contractor, and industry representatives. The results of the breakout sessions on day 2 were analyzed to identify the priorities for advancement in each of the three topic areas. Key issues for each topic were prioritized by reviewing the recorder's notes in detail, finding common topics among sessions, and summarizing the participant votes.

Effects of computing parameters and measurement locations on the estimation of 3D NPS in non-stationary MDCT images.

The goal of this study was to investigate the impact of computing parameters and the location of volumes of interest (VOI) on the calculation of 3D noise power spectrum (NPS) in order to determine an optimal set of computing parameters and propose a robust method for evaluating the noise properties of imaging systems. Noise stationarity in noise volumes acquired with a water phantom on a 128-MDCT and a 320-MDCT scanner were analyzed in the spatial domain in order to define locally stationary VOIs. The influence of the computing parameters in the 3D NPS measurement: the sampling distances bx,y,z and the VOI lengths Lx,y,z, the number of VOIs NVOI and the structured noise were investigated to minimize measurement errors. The effect of the VOI locations on the NPS was also investigated. Results showed that the noise (standard deviation) varies more in the r-direction (phantom radius) than z-direction plane. A 25 × 25 × 40 mm(3) VOI associated with DFOV = 200 mm (Lx,y,z = 64, bx,y = 0.391 mm with 512 × 512 matrix) and a first-order detrending method to reduce structured noise led to an accurate NPS estimation. NPS estimated from off centered small VOIs had a directional dependency contrary to NPS obtained from large VOIs located in the center of the volume or from small VOIs located on a concentric circle. This showed that the VOI size and location play a major role in the determination of NPS when images are not stationary. This study emphasizes the need for consistent measurement methods to assess and compare image quality in CT.

Report of the 4th Workshop for Technology Transfer for Intelligent Compaction Consortium, TPF-5(233), 2015

This document summarizes the discussion and findings of the 4th workshop held on October 27–28, 2015 in Frankfort, Kentucky as part of the Technology Transfer Intelligent Compaction Consortium (TTICC) Transportation Pooled Fund (TPF-5(233)) study. The TTICC project is led by the Iowa Department of Transportation (DOT) and partnered by the following state DOTs: California, Georgia, Iowa, Kentucky, Missouri, Ohio, Pennsylvania, Virginia, and Wisconsin. The workshop was hosted by the Kentucky Transportation Cabinet and was organized by the Center for Earthworks Engineering Research (CEER) at Iowa State University of Science and Technology. The objective of the workshop was to generate a focused discussion to identify the research, education, and implementation goals necessary for advancing intelligent compaction for earthworks and asphalt. The workshop consisted of a review of the TTICC goals, state DOT briefings on intelligent compaction implementation activities in their state, voting and brainstorming sessions on intelligent compaction road map research and implementation needs, and identification of action items for TTICC, industry, and Federal Highway Administration (FHWA) on each of the road map elements to help accelerate implementation of the technology. Twenty-three attendees representing the state DOTs participating in this pooled fund study, the FHWA, Iowa State University, University of Kentucky, and industry participated in this workshop.

Evaluation of performance analysis software for Linux computing cluster

Tietokonejärjestelmän osien ja ohjelmistojen suorituskykymittauksista saadaan tietoa,jota voidaan käyttää suorituskyvyn parantamiseen ja laitteistohankintojen päätöksen tukena. Tässä työssä tutustutaan suorituskyvyn mittaamiseen ja mittausohjelmiin eli ns. benchmark-ohjelmistoihin. Työssä etsittiin ja arvioitiin eri tyyppisiä vapaasti saatavilla olevia benchmark-ohjelmia, jotka soveltuvat Linux-laskentaklusterin suorituskyvynanalysointiin. Benchmarkit ryhmiteltiin ja arvioitiin testaamalla niiden ominaisuuksia Linux-klusterissa. Työssä käsitellään myös mittausten tekemisen ja rinnakkaislaskennan haasteita. Benchmarkkeja löytyi moneen tarkoitukseen ja ne osoittautuivat laadultaan ja laajuudeltaan vaihteleviksi. Niitä on myös koottu ohjelmistopaketeiksi, jotta laitteiston suorituskyvystä saisi laajemman kuvan kuin mitä yhdellä ohjelmalla on mahdollista saada. Olennaista on ymmärtää nopeus, jolla dataa saadaan siirretyä prosessorille keskusmuistista, levyjärjestelmistä ja toisista laskentasolmuista. Tyypillinen benchmark-ohjelma sisältää paljon laskentaa tarvitsevan matemaattisen algoritmin, jota käytetään tieteellisissä ohjelmistoissa. Benchmarkista riippuen tulosten ymmärtäminen ja hyödyntäminen voi olla haasteellista.

Utilisation of Statistics in Intelligent Web Applications

Web-portaalien aiheenmukaista luokittelua voidaan hyödyntää tunnistamaan käyttäjän kiinnostuksen kohteet keräämällä tilastotietoa hänen selaustottumuksistaan eri kategorioissa. Tämä diplomityö käsittelee web-sovelluksien osa-alueita, joissa kerättyä tilastotietoa voidaan hyödyntää personalisoinnissa. Yleisperiaatteet sisällön personalisoinnista, Internet-mainostamisesta ja tiedonhausta selitetään matemaattisia malleja käyttäen. Lisäksi työssä kuvaillaan yleisluontoiset ominaisuudet web-portaaleista sekä tilastotiedon keräämiseen liittyvät seikat.