Nonmem and PsN


Versions of NONMEM

All versions of nonmem installed are available under the path /opt/NONMEM. For example, for nm74gf, the base path is `/opt/NONMEM/nm74gf`. No version of nonmem/nmfe is available by default on the user's system path.

For nonmem 74 and 73 both nmqual and normal installations are provided. Installations following the naming convention nm7<x>_gf correspond to the nmqual installed version (for backwards compatibily with prior versions of metworx). nm7<x>_nmfe are the standard install.

NOTE: For nonmem 7.5 nmqual has been deprecated. As a tool, its value around qualifying the possible heterogenous nonmem configurations is less relevant given user-defined custom modules are rare and the default configuration is suitable. In addition, as a tool, it did "everything" - handle installation, testing, running models. These have now been split out into separate stages and managed by independent tools and processes. Hence, for nonmem 75 it does not have a _gf designated install, and has been simplified to a single install under the path nm75

To maintain backwards compatibility, nonmem 7.4 and 7.3 installations will continue to be provided as both nmqual and regular installations.

Metworx 20.12 Series

NONMEM 7.5.0 compiled with gfortran is the default NONMEM installation for PsN. The following options are available:

  • nm75: 7.5 gfortran default
  • nm74_nmfe: 7.4 gfortran
  • nm74_gf: 7.4 gfortran + nmqual
  • nm73_nmfe: 7.3 gfortran
  • nm73_gf: 7.3 gfortran + nmqual

Metworx 20.03 20.04 and 20.06 Series

NONMEM 7.4.4 compiled with gfortran is the default NONMEM installation for PsN. The following options are available:

  • nm74_nmfe: 7.4 gfortran default
  • nm73_nmfe: 7.3 gfortran
  • nm73_gf: 7.3 gfortran + nmqual
  • nm74_gf: 7.4 gfortran + nmqual

Metworx 3.x Performance/Envision

NONMEM 7.4.3 compiled with gfortran is the default NONMEM installation for PsN. Your options are:

  • nm74: NONMEM 7.4, Intel fortran compiled
  • nm74_gf: NONMEM 7.4, gfortran compiled
  • nm74: NONMEM 7.4, Intel fortran compiled
  • nm72: NONMEM 7.2, gfortran
  • nm73: NONMEM 7.3, Intel
  • nm72_gf: NONMEM 7.2, gfortran
  • nm73_gf: NONMEM 7.3, gfortran

Usage

These can be specified with the argument -nm_version="nm74" passed to the execute command

Examples:

The nonmem_examples.zip file attached contains some example PsN/Pirana data and models. Upload through RStudio to your /data directory and it will automatically unzip. Some example command line PsN calls are shown below. These should be run put of the Hands_onA directory that is created when the zip file is uploaded via RStudio.

Default version execution on the master node

Using gfortran and 3.mod:

execute 1.mod

Default version execution on the compute node(s)

Using gfortran and 3.mod on one core run via nmqual

execute -nmqual -run_on_sge -sge_prepend_flags='-V' 3.mod

NONMEM 7.4.4 with nmqual execution on the compute node(s) in parallel mode

4 compute cores using gfortran

execute -nmqual -run_on_sge -nm_version='nm74gf' -parafile=3.pnm -sge_prepend_flags='-pe orte 4 -V' 3.mod

To use more or less cores for a parallel run you need to change both the pnm file and the PsN call. In the PsN call you should change the -pe orte 4 to the number of cores you would like to use (for example, for 8 cores it would be -pe orte 8). In the pnm file you should change Line 2 NODES=4 to NODES=8 (for 8 cores) and Line 26 -n 3 to one less than the number of cores you specified in Line 2 (for 8 cores this would be -n 7).

Bootstrap NONMEM jobs

Bootstrap of 3.mod utilizing 20 resamples and running 20 models simulaneously across compute nodes:

bootstrap -samples=20 -threads=20 -dir=bs_3 -run_on_sge -sge_prepend_flags='-V' 3.mod

nonmem_examples.zip