Running NLME Engines in Command Line Mode

The Phoenix Modeling Language (PML) supports model building through a text-based modeling language that allows users to describe, fit, and simulate models.

The PML language supports specification of input and/or output data, trial related settings such as dosing and treatment sequence, as well as flexible model definitions for PK/PD and general Nonlinear Mixed Effects (NLME) modeling including survival analysis and modeling of categorical responses.

PML includes the necessary structures for seamless integration of modeling with trial simulation and related analyses. PML draws on established practices in S-PLUS and NONMEM to make PML user-friendly for people familiar with those software packages.

Users do not need to have Phoenix running in order to run PML models from the command line. When Phoenix is installed, the files necessary to run PML models from the command line are also installed.

This section covers the following topics, describing how to operate the NLME engine in Windows command line mode using batch scripts named RunNLME.bat and RunNLMEMPI.bat.

Requirements
PML and multi-processor or multi-core computers
Install the executables and examples
Basic command line syntax
Input files
Running QRPEM in command line mode

Requirements

Running PML models from the command line requires the following:

An NLME license and a PML license

Phoenix Platform/WinNonlin 8.3

MinGW (Minimalist GNU for Windows) C++ compiler
For more on MinGW, see the MinGW Web site. MinGW is installed during the Phoenix installation process. Only the version of MinGW that comes with the Phoenix installation package is guaranteed by Certara to be compatible with Certara software.

Two Ghz. Intel-compatible CPU

Four gigabyte RAM minimum, but eight gigabytes is recommended

300 megabytes free harddrive space

PML and multi-processor or multi-core computers

PML supports parallel processing through the use of the Message Passing Interface (MPI). Use the RunNLMEMPI.bat batch file to run models using multiple processors or processor cores.

Users with multiple processor or multiple-core computers can install MPICH2, a free and portable implementation of the Message Passing Interface. MPICH2 is also available for installation as part of the Phoenix installation process during Complete Installation or can be selected during Custom Installation. Or users can install MPICH2 themselves using the mpich2-1.4.1p1-win-x86-64.msi installer, which is included with the Phoenix installation package.

For more on MPICH2, visit the MPICH2 Web site.

Installing MPICH2 is optional, and is not necessary for computers with one processor or one processor core.