Faster Optimal Design Calculations for Practical Applications
Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
PopED is a software developed by the Pharmacometrics Research Group at the Department of Pharmaceutical Biosiences, Uppsala University written mainly in MATLAB. It uses pharmacometric population models to describe the pharmacokinetics and pharmacodynamics of a drug and then estimates an optimal design of a trial for that drug. With optimization calculations in average taking a very long time, it was desirable to increase the calculation speed of the software by parallelizing the serial calculation script. The goal of this project was to investigate different methods of parallelization and implement the method which seemed the best for the circumstances.The parallelization was implemented in C/C++ by using Open MPI and tested on the UPPMAX Kalkyl High-Performance Computation Cluster. Some alterations were made in the original MATLAB script to adapt PopED to the new parallel code. The methods which where parallelized included the Random Search and the Line Search algorithms. The testing showed a significant performance increase, with effectiveness per active core rangingfrom 55% to 89% depending on model and number of evaluated designs.
Place, publisher, year, edition, pages
2011. , 68 p.
UPTEC K, ISSN 1650-8297 ; 11011
Optimal Design, PopED, pharmacometrics, pharmacokinetics, pharmacodynamics, Fisher Information Matrix, parallelization
IdentifiersURN: urn:nbn:se:uu:diva-150802OAI: oai:DiVA.org:uu-150802DiVA: diva2:408845
Subject / course
Master Programme in Chemical Engineering
2011-02-25, BMC C2:305, Uppsala, 13:30 (English)
Nyberg, Joakim, MscUeckert, Sebastian, MscHooker, Andrew, PhD
Björkman, Sven, PhD