Conformational Search - Job Settings Dialog Box

Conformational Search - Job Settings Dialog Box Features

• Output section
  • Incorporate option menu
• Job section
• Job text box
• Separate into N subjobs text box
• Host list table
• Action buttons

Output section

This section provides options for handling the output of the job.

Incorporate option menu

Choose the manner in which the structural and property results of the calculation are incorporated into the project. The menu can have one or more of the following options:

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. This option is always present on the menu.

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

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

Job 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.

Separate into N subjobs text box

For jobs that can be distributed over multiple CPUs (and multiple hosts), specify the number of subjobs to split the job into. Some job drivers optimize the number of subjobs, so the number actually used might not be exactly the number given.

Host list table

The Host list table is available for applications that can distribute jobs over multiple hosts. The table displays all the hosts defined in the $SCHRODINGER/schrodinger.hosts file, with the number of processors available on the host in the Processors column. The Use column specifies the number of processors to use from the given host. The default number is the number available, or * if it is a queue host. You can edit this column to set the number of processors, and you can reset the values to the default by clicking Reset All.

To specify the hosts, select the host rows in the table. To set the number of processors on the host, edit the values in the Use column as needed. The total number of processors for the job is reported in the Total to use text box (which is noneditable).

When you select hosts for the job, you can only select one queue host, and you cannot select both queue and non-queue hosts. If you select a queue host, all other table rows are deselected.

To reset the Host list table to the default values (use all processors on the local host), click Reset All.

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.