2010 - Berlin - Germany

PAGE 2010: Methodology- Other topics
William Knebel

A Strategy for Efficient Implementation of NONMEM 7 and the Intel Fortran Compiler in a Distributed Computing Environment

W. Knebel*(1), T. Bergsma (1), C. Dagdigian (2), J. Hane (1), M. R. Gastonguay (1)

(1) Metrum Institute, Tariffville, CT, USA; (2) BioTeam, Middleton, MA, USA

Objectives: NONMEM 7 (NM7) [1], was developed and optimized for compilation with the commercial Intel fortran compiler (IFC)[2]. IFC licensing for a grid implementation is issued at the user-level and requires the use of the FlexLM license manager. In order to increase license utilization efficiency, a strategy building upon the existing MIfuns [3, 4] R package, was developed for the deployment of NM7 with IFC in a distributed computing environment.

Methods: The R package, MIfuns (R version 2.7.2 or above) runs on single workstation computers (Windows XP or Mac OSX)  and across computer grids (Mac OSx, NetBSD, linux) utilizing the Sun Grid Engine (SGE) [4] distributed computing software.  SGE has built in functionality allowing for the use of license-managed software. NM7 via NMqual-7.0.2, SGE v6.1u4, FlexLM license manager, and a five-seat IFC cluster license were deployed in their standard configurations across a grid computing environment with 4 nodes (8 CPU cores/node) running Mac OSX Leopard Server. SGE was configured with a consumable resource equal to the number of IFC cluster seats and a special compile only queue (in addition to the standard set of queues). MIfuns was adapted to make use of the existing compile and execute flags available with an NMQual [5] mediated NONMEM installation.

Results: NM7 runs submitted to the grid via MIfuns were compiled then executed utilizing SGE. If IFC license seats were not available, the NM7 job would wait in a queue until a license was available for compiling. Once compiled the NM7 runs were executed and distributed across the grid (one job per CPU) via SGE. This approach was implemented on top of an existing grid system for running NONMEM 6 (NM6) with the g77 fortran compiler.

Conclusions: The application of MIfuns and SGE allowed for the distribution of NM7 runs in a grid environment, while efficiently managing IFC licenses. This approach also allowed for the simultaneous deployment of NM6 and NM7 in a grid environment.

[1] NONMEM VI and 7, ICON Development Solutions, Ellicott City, MD, USA
[2] Intel Fortran Compiler, Intel Corporation, Santa Clara, CA, USA
[3] Facilitating the Pharmacometrics Work-Flow with the MItools R Package, ACOP 2009, Tuscon, AZ
[4] http://mifuns.googlecode.com/
[5] Sun Microsystems, http://gridengine.sunsource.net/
[6] NONMEM® Installation with NMQual, Metrum Institute, Tariffville, CT, USA 

Reference: PAGE 19 (2010) Abstr 1761 [www.page-meeting.org/?abstract=1761]
Poster: Methodology- Other topics
Click to open PDF poster/presentation (click to open)