Documentation
Commands
nonmem run

bbi nonmem run

Run models locally or on the grid

Synopsis

This is the entry point to subcommands for running NONMEM models. Each subcommand represents a different "mode" of execution (e.g., local).

bbi nonmem run [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) .

Flags

  • --additional_post_work_envs strings: additional values (as ENV KEY=VALUE) to provide for the post execution environment

  • --clean_lvl int: clean level used for output (default 1)

  • --config string: path to another bbi.yaml to load

  • --copy_lvl int: copy level used for output

  • --delay int: Selects a random number of seconds between 1 and this value to stagger / jitter job execution. Assists in dealing with large volumes of work dealing with the same data set. May avoid NMTRAN issues about not being able read / close files

  • --git: whether git is used

  • -h, --help: help for run

  • --log_file string: file into which to store the output / logging details from bbi

  • --output_dir string: Go template for the output directory to use for storing details of each executed model (default "{{ .Name }}")

  • --overwrite: whether to remove existing output directories

  • --post_work_executable string: script or binary to run when job execution completes or fails

  • --save_config: whether to save the existing configuration to the output directory (default true)

Inherited

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

  • -d, --debug: debug mode

  • --json: show JSON output, if possible

  • --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

  • -o, --output string: output file

  • --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

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

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

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

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

  • -v, --verbose: verbose output

See also

nonmem recleannonmem run local