Implementation of a NONMEM cluster and add-ons within UCB
C. Castelain (1), A. Dalis (1), X. Deflorenne (1), M. Destrée (1), B. Lacroix (2), L. Sargentini-Maier (2)
(1)IT department, UCB, Belgium; (2)Global Exploratory Development, UCB, Belgium
Objectives: The goal of this project was to provide modelers with an efficient IT infrastructure to run the NONMEM software, together with better tools to improve models' diagnostics and validation. Another goal was to better fulfill regulatory requirements.
Methods: The NONMEM application has been installed on a Linux cluster gathering one head node and 4 compute nodes (2 dual cores processors each). The LSF [2] cluster program has been deployed. The Perl-speaks-NONMEM (PsN) [3] package has also been installed on the cluster. The NONMEM source code has been modified to include the user identification and the description of the cluster configuration in the modeling result file. Besides the cluster implementation, the R [4] using Xpose4 library [5] and Census [6] applications were installed on users laptops.
Results: The LSF cluster program allows the modelers to start several NONMEM runs in batch mode. PsN is used to automate some modeling tasks (bootstrap, model diagnostics...) and to start parallel execution of NONMEM jobs. The R/Xpose and Census packages are used for model diagnostics and results visualization. The source code versions are managed through Subversion [7].
Conclusions: The implemented system is now used by around 15 users located on 3 sites. Most of the computer intensive model validation procedures would not have been possible without the cluster implementation due to the time they require. Using this system, the modelers are able to answer questions from regulatory agencies reviewers in a more timely manner. The compliance to computerized systems regulations is greatly improved due to a central NONMEM installation and a version control system.
References:
[1] NONMEM software: Icon Development Solutions
[2] LSF: Platform computing
[3] PsN software: L. Lindbom, M. Karlsson, N. Jonsson and A. Hooker - Uppsala University - http://psn.sourceforge.net/
[4] R: R project - http://www.r-project.org/
[5] Xpose 4: A. Hooker, J. Wilkins, M. Karlsson and N. Jonsson http://xpose.sourceforge.net/
[6] Census: J. Wilkins - http://census.sourceforge.net/
[7]Subversion: source code management tool: http://subversion.tigris.org/
