Publications

Articles in journals 12

Sten, Johan and Lilja, Harri and Hyväluoma, Jari and Westerholm, Jan and Aspnäs, Mats, Parallel Flow Accumulation Algorithms for Graphical Processing Units with Application to RUSLE Model. In: Computers & Geosciences . Elsevier, 2016

Mattila, Keijo and Puurtinen, Tuomas and Hyväluoma, Jari and Surmas, Rodrigo and Myllys, Markko and Turpeinen, Tuomas and Robertsén, Fredrik and Westerholm, Jan and Timonen, Jussi, A Prospect for Computing in Porous Materials Research: Very Large Fluid Flow Simulations. In: Journal of Computational Science. 2016 1

Eränen, David and Oksanen, Juha and Westerholm, Jan and Sarjakoski, Tapani, A Full Graphics Processing Unit Implementation of Uncertainty-Aware Drainage Basin Delineation. In: Computers and Geosciences. Elsevier, 2014 2

Timonen, Ville and Westerholm, Jan, Scalable Height Field Self-Shadowing. In: Computer Graphics Forum. 2010 1

Aspnäs, Mats and Mattila, Kimmo and Osowski, Kristoffer and Westerholm, Jan, Code Optimization of the Subroutine to Remove Near Identical Matches in the Sequence Database Homology Search Tool PSI-BLAST. In: Journal of Computational Biology. 2010 2

Signell, Artur and Schöring, Johan and Aspnäs, Mats and Westerholm, Jan, Parallelization, Spatial Decomposition and Load Balancing of a Single Tree Level Forest Dynamics Simulator. In: Mathematical and Computational Forestry and Natural Resource Sciences. 2010 1

Signell, Artur and Ogando, Francisco and Aspnäs, Mats and Westerholm, Jan, Scalable plasma simulation with ELMFIRE using efficient data structures for process communication.. In: Computer Physics Communications. 2008 1

Mattila, Keijo and Hyväluoma, Jari and Rossi, Tuomo and Aspnäs, Mats and Westerholm, Jan, An Efficient Swap Algorithm for the Lattice Boltzmann Method. In: Computer Physics Communications. Elsevier, 2007 1

Byholm, Thomas and Toivakka, Martti and Westerholm, Jan, The Application of Morphological Algorithms on 3-Dimensional Porous Structures for Identifying Pores and Gathering Statistical Data. In: WSEAS Transactions on Information Science and Applications. WSEAS Press, 2006

Arvo, Jukka and Westerholm, Jan, Hardware-Accelerated Soft Shadows Using Penumbra Quads. In: Journal of WSCG. 2004

Rosengren, Arsi and Salmi, Jussi and Aittokallio, Tero and Westerholm, Jan and Lahesmaa, Riitta and Nyman, Tuula and Nevalainen, Olli, Comparison of PDQuest and Progenesis Software Packages in the Analysis of Two-Dimensional Electrophoresis Gels. In: PROTEOMICS. 2003 2

Salmi, Jussi and Aittokallio, Tero and Westerholm, Jan and Griese, Matias and Rosengren, Arsi and Nyman, Tuula and Lahesmaa, Riitta and Nevalainen, Olli, Hierarchical Grid Transformation for Image Warping in the Analysis of Two-Dimensional Electrophoresis Gels. In: Proteomics. 2002 2

Articles in proceedings 11

Ersfolk, Johan and Boström, Pontus and Timonen, Ville and Westerholm, Jan and Wiik, Jonatan and Karhu, Otso and Linjama, Matti and Waldén, Marina, Optimal Digital Valve Control Using Embedded GPU. In: Preceedings of the Eight Workshop on Digital Fluid Power. Uusi-Heikkilä, Janne and Linjama, Matti (Eds.). Tampere University of Technology, 2016

Carabaño, Jesús and Sarjakoski, Tapani and Westerholm, Jan, Efficient Implementation of a Fast Viewshed Algorithm on SIMD Architectures. In: 23rd Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP). Daneshtalab, Masoud and Aldinucci, Marco and Leppänen, Ville and Lilius, Johan and Brorsson, Mats (Eds.). IEEE, 2015

Robertsén, Fredrik and Westerholm, Jan and Mattila, Keijo, Lattice Boltzmann Simulations at Petascale on Multi-GPU Systems with Asynchronous Data Transfer and Strictly Enforced Memory Read Alignment. In: 23rd Euromicro International Conference on Parallel, Distributed, and Network-Based Processing, {PDP} 2015, Turku, Finland, March 4-6, 2015. Daneshtalab, Masoud and Aldinucci, Marco and Leppänen, Ville and Lilius, Johan and Brorsson, Mats (Eds.). IEEE, 2015

Yurtesen, Evren and Ropo, Matti and Aspnäs, Mats and Westerholm, Jan, SSE Vectorized and GPU Implementations of Arakawa's Formula for Numerical Integration of Equations of Fluid Motion. In: Euromicro International Conference on Parallel, Distributed and Network-Based Computing. Cotronis, Yiannis Danuletto, Marco Papadopoullos, George (Eds.). IEEE Computer Society, 2011 1

Jackson, Adrian and Reid, Fiona and Booth, Stephen and Hein, Joachim and Westerholm, Jan and Aspnäs, Mats and Català, Miquel and Soba, Alejandro, Parallel Optimisation Strategies for Fusion Codes. In: Proceedings of the 19th International Euromicro Conference on Parallel, Distributed and Network-Based Computing. Cotronis, Yiannis and Danuletto, Marco and Papadopoullos, George (Eds.). IEEE Computer Society, 2011 1

Jackson, Adrian and Carter, Adam and Hein, Joachim and Westerholm, Jan and Aspnäs, Mats and Ropo, Matti and Soba, Alejandro, EUFORIA HPC: Massive Parallelization for Fusion Community. In: Proceedings of the 18th Euromicro Conference on Parallel, Distributed and Network-Based Processing. Danelutto, Marco Bourgeois, Julien Gross, Tom (Eds.). IEEE Computer Society, 2010 1

Signell, Artur and Schöring, Johan and Aspnäs, Mats and Westerholm, Jan, An Individual Tree Simulator for Assessment of Forest Management Methods. In: Cray User Group 2008 Proceedings (CD-ROM). 2008

Aspnäs, Mats and Signell, Artur and Westerholm, Jan, Efficient Assembly of Sparse Matrices Using Hashing. In: Proceedings of PARA 2006, Applied Parallel Computing, State of the Art in Scientific Computing. Kågström Bo and Elmroth, Erik and Dongarra, Jack and Wasniewski, Jerzy (Eds.). Lecture Notes in Computer Science Springer-Verlag, 2007 1

Byholm, Thomas and Westerholm, Jan and Toivakka, Martti, The Use of Morphological Algorithms on 3-Dimensional Paper Coating Structures for Identifying Pores, Gathering Statistical Data and Physical Constants. In: The 6th WSEAS International Conference on Simulation, Modelling and Optimization (SMO'06). 2006

Byholm, Thomas and Alam, Parvez and Westerholm, Jan and Toivakka, Martti, The Use Of Morphological Algorithms And Finite Difference Methods on 3-Dimensional Paper Coating Structures For Identifying Pores, Gathering Statistical Data And Physical Constants. In: 13th International Coating Science and Technology proceedings, 2006. 2006

Back, Ralph-Johan and Cerschi Seceleanu, Cristina and Westerholm, Jan, Symbolic Simulation of Hybrid Systems. In: Proceedings of the 9th Asia-Pacific Software Engineering Conference (APSEC 2002). Paul Strooper and Pornsiri Muenchaisri (Eds.). IEEE Computer Society, 2002

Technical reports 3

Timonen, Ville and Westerholm, Jan, Scalable Height Field Self-Shadowing. TUCS Technical Report 957. Turku Centre for Computer Science, 2009

Osowski, Kristoffer and Westerholm, Jan and Aspnäs, Mats, Two Cases of Data Overflow in the Protein Sequencing Program BLASTPGP. TUCS Technical Report 813. Turku Centre for Computer Science, 2007

Back, Ralph-Johan and Cerschi Seceleanu, Cristina and Westerholm, Jan, Symbolic Simulation of Hybrid Systems. TUCS Technical Report 503. Turku Centre for Computer Science, 2003

Supervised master's theses 45

Sten, Johan, Erosion prediction using graphical processing units. Supervisor(s): Westerholm, Jan and Aspnäs, Mats. 2014

Åkesson, Andreas, Win probabilities and conditional strength distributions in stochastic combat simulation models. Supervisor(s): Lappi, Esa and Åkesson, Bernt and Westerholm, Jan and Aspnäs, Mats. 2013

Robertsén, Fredrik, Implementing a high performance lattice Boltzmann solver on multi GPU systems. Supervisor(s): Westerholm, Jan. 2013

Eränen, David, Uncertainty-aware drainage basin delineation from digital elevation models using graphical processing units. Supervisor(s): Oksanen, Juha and Westerholm, Jan. 2012

Hinders, Marcus, GPU computations in heterogeneous grid environments. Supervisor(s): Westerholm, Jan. 2010

Ismark, Sture, Groupware calendar system : a prototype for non-profit organisations. Supervisor(s): Westerholm, Jan. 2010

Paro, Kristoffer, Implementing computational statistical methods in a scalable individual-tree simulator. Supervisor(s): Westerholm, Jan. 2010

Stenlund, Jonathan, Optimering av GPAW, ett program för beräkningar inom densitetsfunktionalteori. Supervisor(s): Westerholm, Jan and Aspnäs, Mats. 2010

Strand, Sebastian, Optimering av transportlogistik med heterogen bilpark och varudistribution. Supervisor(s): Carlsson, Christer and Westerholm, Jan. 2010

Sundell, Fredrik, Code optimization and parallelization improvements of the fusion simulation program TYR. Supervisor(s): Westerholm, Jan. 2009

Brunberg, Márius, Trådlöst Dolby surround system. Supervisor(s): Westerholm, Jan and Gyllenberg, Robert. 2008

Julin, Joakim, Funktionalitets- och kompatibilitetsundersökning för ett antal beställvideoservrar och -klienter. Supervisor(s): Björkqvist, Jerker and Westerholm, Jan. 2008

Kokkala, Susanna, Security and risks in radio frequency identification RFID. Supervisor(s): Westerholm, Jan. 2008

Lindgård, Jonas, Software emulation of electric guitar amplifiers and effects. Supervisor(s): Westerholm, Jan. 2008

Schöring, Johan, Design and implementation of a scalable forest simulator. Supervisor(s): Westerholm, Jan. 2008

Södergård, Magnus, Development of an object-oriented tree-level forest simulator. Supervisor(s): Westerholm, Jan. 2008

Söderlund, Andreas, Användning av SVG inom modern webbutveckling. Supervisor(s): Gustavson, Åke and Westerholm, Jan. 2008

Storsjö, Martin, Efficient triangle reordering for improved vertex cache utilisation in realtime rendering. Supervisor(s): Aarnio, Tomi and Nordström, Tero and Westerholm, Jan. 2008

Tigerstedt, Ulf, Mjukvarutelefonväxlar för samtal över Internet : protokoll och användningserfarenheter. Supervisor(s): Westerholm, Jan. 2008

Yurtesen, Evren, Code optimization of the biosequence analysis program HMMER. Supervisor(s): Westerholm, Jan and Aspnäs, Hans. 2008

Aaltokari, Marika, An overview of open source software : licensing, software engineering and future concerns. Supervisor(s): Westerholm, Jan. 2007

Ånäs, Johan, Optimering av datorprogrammet POY : ett kladistiskt verktyg inom fylogenin. Supervisor(s): Aspnäs, Mats and Westerholm, Jan. 2007

Mitts, Peter, The virtual instrument : constructing a real-time 3D graphics component for instrument software. Supervisor(s): Westerholm, Jan. 2007

Nylund, Niklas, Bildanalys för pappers- och tryckkvalitet. Supervisor(s): Toivakka, Martti and Sand, Anders and Westerholm, Jan. 2007

Osowski, Kristoffer, Code optimization of the sequence database homology search tool blastpgp. Supervisor(s): Aspnäs, Mats and Westerholm, Jan. 2007

Bertell, Carl-Petter, Automatisering av installationspaketsgenerering och dess integrering i mjukvaruutveckling. Supervisor(s): Westerholm, Jan. 2006

Signell, Artur, Optimering av datastrukturer och minnesanvändning i fusionsreaktorsimulatorn ELMFIRE. Supervisor(s): Westerholm, Jan and Aspnäs, Mats. 2006

Staffans, Johannes, Online occlusion culling. Supervisor(s): Westerholm, Jan and Arvo, Jukka. 2006

Wärnå, Matias, IT-etik i arbetslivet : en fallstudie. Supervisor(s): Westerholm, Jan and Soini, Annamari. 2006

Bäckström, Kristian, Säkra datorsystem med hjälp av objektförmågor. Supervisor(s): Westerholm, Jan. 2005

Granholm, Henry, Stokastisk optimering av syntetiska spektra. Supervisor(s): Westerholm, Jan. 2005

Gustafsson, Anders, Kodoptimering i högeffektiva datorberäkningar för Lattice-Boltzmann-metoden. Supervisor(s): Westerholm, Jan. 2005

Sandell, Thomas, VALO 2 : en systemlösning för fordonslogistik. Supervisor(s): Westerholm, Jan and Eklund, Patrik. 2005

Brunberg, Christoffer, Specifikation av system för uppföljning av studier vid Åbo Akademi. Supervisor(s): Westerholm, Jan. 2004

Sandström, Tommy, En algoritm för jämförelse av korta dokument. Supervisor(s): Westerholm, Jan. 2004

Enroth, Matias, Lokala färgsättningsmodeller i en minnes- och prestandabegränsad datoromgivning. Supervisor(s): Westerholm, Jan. 2003

Lindroos, Johan, Prototyping i programutvecklingsprocessen. Supervisor(s): Westerholm, Jan. 2003

Signell, Oskar, Scalable computer cluster for thin client environments. Supervisor(s): Westerholm, Jan. 2003

Granholm, Staffan, Tredimensionell grafik för minnes- och prestationsbegränsande system. Supervisor(s): Westerholm, Jan. 2002

Jakobsson, Tom, Kulörhantering i heterogen omgivning. Supervisor(s): Westerholm, Jan. 2002

Nygård, Magnus, Synkronisering av data i handdatorer : hur dataöverföringen kan tillämpas inom hemvården. Supervisor(s): Westerholm, Jan. 2002

Baafi, Kofi,, 3-dimensional localization using time difference of arrival. Supervisor(s): Westerholm, Jan and Björkqvist, Jerker.

Grönroos, Johan,, A multi-GPU approach to soil erosion modeling using digital elevation models. Supervisor(s): Westerholm, Jan and Aspnäs, Mats.

Kondareva, Ekaterina,, Parameter estimation of two conditionally correlated Gaussian variables. Supervisor(s): Westerholm, Jan and Lafond, Sebastien.

Wärnå, Daniel,, Design and implementation of a web based study planning tool a case study in usability. Supervisor(s): Soini, Annamari and Westerholm, Jan.