Documentation
Commands
nonmem

bbi nonmem

Entry point for NONMEM-related subcommands

bbi nonmem [flags]

Examples 

  # Execute model run001
  bbi nonmem run (local|sge|slurm) run001.mod
  #  Run models run001.mod, run002.mod, and run003.mod
  bbi nonmem run (local|sge|slurm) 'run[001:003].mod'
  # Run all models in the current directory
  bbi nonmem run (local|sge|slurm) .

  # Summarize run001
  bbi nonmem summary run001/run001.lst
  # The extension may be omitted
  bbi nonmem summary run001/run001
  # Output JSON summary for run001 and run002
  bbi nonmem summary --json run001/run001 run002/run002

  # Display .cov/cor values from run001/run001.{cov,cor}
  bbi nonmem covcor run001/run001
  # Display the same values by specifying a full output file
  bbi nonmem covcor run001/run001.cov

Flags

  • --background: RAW NMFE OPTION - tell NONMEM not to scan stdin for control characters

  • -h, --help: help for nonmem

  • --licfile string: RAW NMFE OPTION - NONMEM license file to use

  • --maxlim int: RAW NMFE OPTION - set the maximum values for the buffers used by NONMEM (if 0, don't pass -maxlim to nmfe) (default 2)

  • --mpi_exec_path string: fully qualified path to mpiexec to use for NONMEM parallel operations (default "/usr/local/mpich3/bin/mpiexec")

  • --nm_version string: version of NONMEM from the configuration list to use

  • --nmqual: whether to execute with nmqual (autolog.pl)

  • --nobuild: RAW NMFE OPTION - do not build a new NONMEM executable

  • --parafile string: location of a user-provided parafile to use for parallel execution

  • --parallel: whether to run NONMEM in parallel mode

  • --parallel_timeout int: amount of time to wait for parallel operations in NONMEM before timing out (default 2147483647)

  • --prcompile: RAW NMFE OPTION - forces PREDPP compilation

  • --prdefault: RAW NMFE OPTION - do not recompile any routines other than FSUBS

  • --prsame: RAW NMFE OPTION - tell NONMEM to skip the PREDPP compilation step

  • --tprdefault: RAW NMFE OPTION - test if is okay to do -prdefault

Inherited

  • -d, --debug: debug mode

  • --json: show JSON output, if possible

  • -o, --output string: output file

  • -p, --preview: preview action, but don't actually run command

  • --threads int: number of threads to execute with locally or nodes to execute on in parallel (default 4)

  • -v, --verbose: verbose output

See also

initnonmem clean