FEP+ Protocol Builder - Job Settings Dialog Box

The Job Settings dialog box is used to specify settings that are used when starting jobs from Maestro. Settings are stored for each application (with a few exceptions).

To open this dialog box, click the Job Settings button in the Job Toolbar,

or click the arrow next to this button and choose Job Settings.

  • Features
  • Additional Resources

FEP+ Protocol Builder - Job Settings Dialog Box Features

Job section

This section provides options for controlling various aspects of the running of the job.

Job 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.

Hosts section

Choose the hosts to run the driver and subjobs on.

Driver host option menu

Choose a host to run the driver on. The menu displays all the hosts defined in the $SCHRODINGER/schrodinger.hosts file, with the number of CPUs or GPUs available on the host in parentheses.

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.

GPU subhost option menu

Choose the GPU host used to run the edge simulations. This option menu displays all the GPU hosts defined in the $SCHRODINGER/schrodinger.hosts file, with the number of GPUs available on the host in parentheses. You should choose a host that has enough GPUs to run all the simulations that can be run simultaneously.

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

CPU subhost option menu

Choose the host to run the protocols on. This option menu displays all the CPU hosts defined in the $SCHRODINGER/schrodinger.hosts file, with the number of CPUs available on the host in parentheses. Choose the host to run the CPU subjobs on 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.

Limit # simultaneous FEP protocols option and text box

Limit the number of protocols that can be run at the same time.

Limit # simultaneous FEP subjobs/protocol option and text box

Limit the number of subjobs that can be run at the same time for any protocol to the number specified in the text box. This places a limit on the number of GPUs that can be used for a given FEP protocol. The total number of GPUs used is this number times the maximum number of simultaneous protocols.

Action buttons

There are several 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.

The Help button is also in this set.

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