matsci_meta_workflow_driver.py Command Help

Command: $SCHRODINGER/run matsci_meta_workflow_gui_dir/matsci_meta_workflow_driver.py

usage: $SCHRODINGER/run matsci_meta_workflow_gui_dir/matsci_meta_workflow_driver.py
       [-h] -stages STAGES [-format] [-combine_input] [-cpu_host HOSTNAME:X]
       [-gpu_host HOSTNAME:X] [-md_umbrella]
       [-stage_umbrella {never,always,per_flag}] [-HOST <hostname>] [-D]
       [-VIEWNAME <viewname>] [-OPLSDIR OPLSDIR] [-JOBNAME JOBNAME]
       input_files [input_files ...]

steps of the workflow are capable multiple structures as input - i.e. ' 'steps
such as the Disordered System Builder or Polymer Builder.') A driver to run a
workflow of workflows Copyright Schrodinger, LLC. All rights reserved.

positional arguments:
  input_files           Input structure files. For most supported workflows,
                        these will be .mae, .maegz or .cms files. Other input
                        structure formats such as .smi, .pdb and .sdf are also
                        supported. If the file is a .mae, .maegz or .smi file
                        and contains multiple structures/SMILES strings, each
                        structure will be run in a separate workflow. Other
                        custom input such as .csv or .txt files are be
                        supported if the initial step in the workflow is a
                        custom script that handles such input. For workflows
                        that begin with a polymer builder step, the input
                        structure must be a multi-structure .mae/.maegz file
                        that contains all the required polymer components, and
                        only a single workflow will be run.

options:
  -h, -help             Show this help message and exit.
  -stages STAGES        The text file containing information for the workflow
                        stages (default: None)
  -format               Print extended information about the input format and
                        exit (default: None)
  -combine_input        Combine structures in the input file into a single
                        workflow rather than run one workflow per structure.
                        Only valid if the initial steps of the workflow are
                        capable of multiple structures as input - i.e. steps
                        such as the Disordered System Builder or Polymer
                        Builder or a custom script with input=other. Note that
                        having a root (first) stage that is a custom stage
                        that takes input=other will cause this behavior even
                        if -combine_input is not given on the command line.
                        (default: False)
  -cpu_host HOSTNAME:X  Specify the host, HOSTNAME, for CPU subjobs and the
                        number of allowed simultaneous CPU subjobs, X
                        (default: None)
  -gpu_host HOSTNAME:X  Specify the host, HOSTNAME, for GPU subjobs and the
                        number of allowed simultaneous GPU subjobs, X
                        (default: None)
  -md_umbrella          Allow some stages that run GPU (Desmond) tasks to run
                        locally on the driver machine, one at a time, rather
                        than resubmitting to the queue. The default behavior
                        is to allow only CPU tasks to run locally on the
                        driver machine. Use of this flag will request a
                        Desmond license from the queue to ensure that one is
                        available for local Desmond tasks. (default: False)
  -stage_umbrella {never,always,per_flag}
                        Stages that combine a Python driver with a GPU subjob
                        and implement the -md_umbrella flag can submit the
                        driver to the CPU queue and the subjob to the GPU
                        queue, or the driver to the GPU queue and then run the
                        subjob on that GPU without submitting the subjob back
                        to the queue. The latter is known as "umbrella" mode.
                        The value of the -stage_umbrella flag defines the
                        behavior for these stages. "per_flag" means that the
                        behavior for each stage is controlled by whether the
                        -md_umbrella flag is included in the command for that
                        stage. "always" means these stages will always use
                        umbrella mode, and "never" means these stages will
                        never use umbrella mode. "always" and "never" means
                        the presence or absence of the -md_umbrella flag in
                        the stage command will be ignored. Note that if
                        -cpu_host and -gpu_host are not given, the value of
                        this flag is ignored and the behavior of "always" is
                        used. (default: per_flag)

Job Control Options:
  -HOST <hostname>      Run job remotely on the indicated host entry.
                        (default: localhost)
  -D, -DEBUG            Show details of Job Control operation. (default:
                        False)
  -VIEWNAME <viewname>  Specifies viewname used in job filtering in maestro.
                        (default: False)
  -OPLSDIR OPLSDIR      Specifies directory for custom forcefield parameters.
                        (default: None)
  -JOBNAME JOBNAME      Provide an explicit name for the job. (default: None)