Meta Workflow Builder - Job Settings Dialog Box

Meta Workflow Builder - Job Settings Dialog Box Features

• Output section
  • Incorporate option menu
• Job section
  • Name text box
  • n stages can use a CPU host text
  • n stages require a GPU host text
  • CPU Host option and controls
    • option menu
  • GPU Host option and controls
    • option menu
  • Run the meta workflow driver on options
  • For stages that run MD subtasks options
• Action buttons

Output section

Incorporate option menu

Choose the manner in which the structural and property results of the calculation are incorporated into the project. The options are:

Append new entries as a new group

Each structure in the output file is added to the project as a new entry, and the entries are grouped. The group name is set to the name of the file from which the entries were read, minus the extension. This is the default option.

Append new entries in place

Each new entry is added to the project immediately below its source entry, i.e. the entry that was used as input for the job. If there is no source entry, the new entry is added to the end of the entry list in the project as an individual entry.

Do not incorporate

No change is made to the project when the job is complete.

The choice that you make from this menu is persistent for a given job type: the next time you run a job of that type, the incorporation mode that you last used is the default mode. The incorporation mode is stored as a preference by Maestro, so the choice persists across Maestro sessions.

Job section

Name text box

Enter a name for the job. Job names cannot contain spaces or nonprinting characters.

When a job is started, a subdirectory of the working directory is created using the job name (depending on the application), for writing job files in. Job files are named with the job name as the first part (stem or prefix) of the file names.

The initial name shown is a standard name for the application, which might include calculation settings. A standard name that contains settings is updated when the settings change. You can modify a standard name; if you do and it still retains some settings, the name is updated if the settings change. You can also replace the entire job name.

When a standard name or modified standard name is used, the job name is made unique by appending an integer. This is done by checking for job directories or files in the current working directory. However, if you replace the job name to create a custom job name, the name might no longer be unique, and it is not automatically made unique. In that case, a warning is posted before any files are overwritten.

After a job is submitted, a new job name is automatically created for the next job from the current job name, by appending an integer or incrementing the integer. This is done for custom job names as well as standard or modified names.

n stages can use a CPU host text

Displays how many current stages can run on a CPU host. Only stages that do not require GPUs for either its driver or subjobs count toward this number. For example, stages whose driver can run on a CPU host but subjobs must run on a GPU host do not count as a stage that can use a CPU host. Stages which can run on either a CPU host or GPU host count as a stage that can use a CPU host.

n stages require a GPU host text

Displays how many current stages must run on a GPU host. Stages which contain a driver or subjobs that must run on a GPU host count toward this number. Stages which can run on either a CPU host or GPU do not count as a stage that requires a GPU host.

CPU Host option and controls

Select whether to use CPU hosts to run individual stages of the meta workflow. If a non-zero number is present in the n stages can use a CPU host text, this option can be selected. The total number of simultaneous subjobs is limited by the number of processors on the queue or host.

option menu

The CPU host option menu displays all the hosts defined in the $SCHRODINGER/schrodinger.hosts file. To run the selected job on a remote host, choose the host from this menu.

The host localhost means the host on which you are running Maestro. If you run a job locally, Maestro automatically reduces the priority of the job so that it does not compete with Maestro for resources. To change this behavior, set the SCHRODINGER_NICE environment variable (see Job Control Environment Variables (JOB CONTROL IS DEPRECATED)).

GPU Host option and controls

Select whether to use GPU hosts to run individual stages of the meta workflow. If a non-zero number is present in the n stages require a GPU host text, this option must be selected. The total number of simultaneous subjobs is limited by the number of processors on the queue or host.

option menu

The GPU host option menu displays all the hosts defined in the $SCHRODINGER/schrodinger.hosts file. To run the selected job on a remote host, choose the host from this menu.

The host localhost means the host on which you are running Maestro. If you run a job locally, Maestro automatically reduces the priority of the job so that it does not compete with Maestro for resources. To change this behavior, set the SCHRODINGER_NICE environment variable (see Job Control Environment Variables (JOB CONTROL IS DEPRECATED)).

If a host has more than one GPU, the GPUs are assigned automatically by the scheduler. You cannot assign individual GPUs to run a job.

Run the meta workflow driver on options

Specify what type of host the meta workflow driver should run on. If the workflow has mostly stages that will run on a CPU host, the driver should run on a CPU host. If the workflow has mostly stages that will run on a GPU host, the driver should run on a CPU host. If only one type of host is selected for running the individual workflow stages, the driver automatically runs on that type of host.

• The CPU host—The driver runs on a CPU host. Not available if only GPU host is selected

• The GPU host—The driver runs on a GPU host. Not available if only CPU host is selected

For stages that run MD subtasks options

For stages which have a driver that submits Desmond subjobs, you can choose to have the driver submit the subjobs to localhost rather than back through the queue. This is known as "umbrella mode", and is efficient because the Desmond subjobs do not have to wait in the queue, particular for stages which submit many Desmond subjobs in serial.

A -md_umbrella flag can be added to any driver that submits Desmond subjobs, and can be added to the command for any individual stage which submits Desmond subjobs. The options below control how to treat the stages which submit Desmond subjobs:

• Obey the command for that stage—The meta workflow driver follows the command set for each individual stage with regards to the umbrella mode. Stages that have the -md_umbrella flag run in umbrella mode while stages that do not have the -md_umbrella flag do not run in umbrella mode. Not available if the CPU host option is not selected.

• Never run in umbrella mode—The meta workflow driver removes any -md_umbrella flags set in the individual stages. The driver of the individual stage runs on a CPU host, and Desmond subjobs are submitted to the CPU queue. Not available if the CPU host option is not selected.

• Always run in umbrella mode—The meta workflow driver adds the -md_umbrella flag to all relevant stages. The driver of the individual stage runs on a GPU host, and Desmond subjobs are submitted locally to the stage driver node.

Action buttons

There are four actions you can take after making settings, by clicking one of these buttons:

• Run—Save the settings for this job type, and start the current job. If a job requires a GPU host but no GPU host is available in the hosts file, this button is disabled.
• OK—Save the settings for this job type, but do not start the job.
• Cancel—Discard the changes made to the settings.

Related Topics

• Meta Workflow Builder Panel