The SC Job Manager


The SC Job Manager is a simple queueing system that is included within GaussView. You can access its control dialog via the Calculate=>SC Job Manager menu path or the corresponding icon. This dialog is illustrated below:


The SC Job Manager
The dialog is initially open to its Long Jobs Queue panel.

Submitting Jobs from GaussView

When the SC Job Manager is specified to run Gaussian calculations, clicking on the Submit button in the Gaussian Calculation Setup dialog starts the process of submitting a job. First, you will be asked to save an input file (if necessary). Next, the following confirmation dialog will appear:

The dialog presents options for:

By default, the job is submitted immediately to the default SC Job Manager queue, and you will be notified when it completes.

If you select the upper checkbox in the preceding dialog, GaussView presents you with the dialog below:


The Submit Job Dialog when the SC Job Manager is in Use

When you click the Submit button at the bottom left of the dialog, the checked files in the file list will be submitted to specified SC Job Manager queue. You can use this dialog to modify the default job type and/or queue and to also select additional files for submission.

Adding Files to the File List

The Add Files button opens up a file viewer, whose form is specified in the UI Options panel, to choose files to add to the file list. Clicking the button will open the most recently used directory. By clicking on the down arrow to the right of the Add Files button, a menu opens allowing the user to select which directory to open.

The Add Recent File button creates a drop-down menu that allows the user to choose from files that were previously opened.

The Add Recent File List button will display a drop-down menu of prevoiusly opened groups of files (files opened in the same open operation).

The Actions button contains the following menu items:

Each of these menus contains the following items:

The Sorting checkbox controls whether the items in the file list can be sorted. When it is checked, then clicking on any column header will sort the items based upon the field. A caret character ^ (ascending order) or a “v” character (descending order) appears at the top of the current sort column:

The controls at the bottom of the dialog have the following uses:

Modfying the UI Options

The UI Options panel allows you to set the following options:

The SC Job Manager Dialog

The SC dialog has five panels:

The various panels in this control panel are discussed below in several separate sections.

The buttons at the bottom of the dialog have the following meanings:

Exiting from the SC Job Manager

When you select Exit, a prompt will appear, asking you if you wish to completly exit the SC Job Manager. Clicking Yes will result in a prompt to save the current SC Job Manager project. Choose any convenient directory location for this file. Selecting No will result discard all data about completed, running and pending jobs generated since the last opening the SC Job Manager.

When you restart the SC Job Manager after having saved the data, all previously pending jobs will be present in the queue(s). Queues that held jobs that were running when the SC Job Manager will be paused, and the previously-running jobs will be listed as pending.

The Long Jobs Queue, Short Jobs Queue, and Queueless Jobs Panels


The SC Job Manager
The panels corresponding to queued and queueless jobs all contain the same controls for and information about relevant jobs

The queue panels show current jobs controlled by the SC Job Manager. The fields in the various job lists contain the following information:

Double clicking on an item in the file list corresponding to a running job will stream the output for that job. Double clicking on a pending job will open the input file for the job.

Right clicking on an item in the job lists opens the context menu:

The items on the context menu have the following meanings:

The following items appear only on the context menus for queues:

The Running Jobs Panel

Selecting the Running Jobs panel results in the dialog below:


SC Job Manager: Running Jobs

The fields have the following meanings:

The Refresh button will update the job list to reflect all jobs’ current status.

The Only Show Known Job Types checkbox will limit the display to job types listed on the Job Types panel. If unchecked, all processes for the current user will be displayed.

Double clicking on an item in the file list will stream the output for that job. Right clicking on an item will allow you to remove it (i.e., kill the job).

The Finished Jobs Panel

Selecting the Finished Jobs panel brings up the dialog below:


SC Job Manager: List of Completed Jobs

The columns hold the following information:

Double clicking on an item in the file list will attempt to open the output file for that job.

Right clicking brings up a shortened version of the context menu used in the queue panels. It has these options:

The Job Types Panel

Selecting the Job Types tab will display the following dialog:

The columns in the table have the following meanings:


Right-clicking an item in the Job Types dialog displays the panel’s context menu, which is seen above:

Edit Job Type

This option is selected by clicking on Edit Selected Job Type from the context menu. It is displayed below:


Example Job Type: Cubegen Jobs

The dialog contains the following fields:

Note: This functionality should only be used by someone who has detailed knowledge running Gaussian and its utilities. If you are unsure of what these options are, it is recommended that you not use the Edit Job Type dialog.

Enabling Use of the SC Job Manager

Select Use SC Job Manager for one or more Applications in the Job Setup Preferences to enable this facility.


Enabling the SC Job Manager for Cubegen Jobs

The Job Setup Preferences dialog allows you to examine and customize how Gaussian and its utilities are launched from within GaussView. It is illustrated below. The Application field at the top of the panel specifies the program or utility whose execution method is currently displayed. Below this popup, there are launch choices, and the command line associated with the selected launch method is displayed in the Command Line area. The values of the GaussView internal variables used in the command line are displayed below the field for your convenience.

pref_gauss.tif
Job Setup Preferences
This example elects to run Gaussian directly on the local computer via the command line. The grey
box shows the command used to do so (which can be edited). The variables used in the command
line—in uppercase, starting with
@—are defined below the Command Line area.

For each job type, there are several launch choices:

The following figure illustrates the command line and other information displayed for running the Gaussian program using the second launch choice:


Running Gaussian via an External Script
This example is from a Windows system. Variable definitions differ on other system types.

Available Command Line Variables

The following table lists the variables used to access executables and scripts:

Item Direct Execution Script
Gaussian program @GXX (UNIX)
@GXXW (Windows)
@GXX_SCRIPT
CubeGen utility @CUBEGEN @CUBEGEN_SCRIPT
CubMan utility @CUBMAN @CUBMAN_SCRIPT
FormChk utility @FORMCHK @FORMCHK_SCRIPT
FreqChk utility @FREQCHK @FREQCHK_SCRIPT
GMMX facility @GMMX @GMMX_SCRIPT
Gaussian help @BROWSER @GAUSSIANHELP_SCRIPT
Text editor @SCFILEEDITOR @SCFILEEDITOR_SCRIPT

Some of the items have additional variables defined for their command lines. Their values are generated from controls within the GaussView interface. See the Gaussian User’s Reference for details on the parameters to the various utilities.

Item Variable(s)
all @INFILE: input file (multiple, numbered input file variables are used in some cases)
@OUTFILE: output file
most utilities

@MEMORY: amount of memory to use, specified via the field at the bottom of the dialog:

CubeGen @KIND: type of cube file
@NPTS: number of points per “side”
@HEADER: whether to include a header line
CubMan @KIND: type of cube file
@SCALE: scale factor
FreqChk @SAVE: whether to save normal modes
@NFD: whether to skip full matrix diagonalization
@SEL: whether normal modes will be specified (if applicable)
@TEMP, @PRESS, @SCALE: temperature, pressure, scale factor
@ISO: alternate isotope selection
@PROJ: whether to project out the gradient direction
@SELINPUT: list of normal modes to be included (if applicable)
Gaussian help @GAUSSIANHELP_URL: location of the Gaussian

GaussView-Provided Scripts

GaussView provides the following scripts in its bin subdirectory:

Menu Item Linux/UNIX/Mac OS X Windows
gv_gxx.sh gv_gxx.bat
gv_cubegen.sh gv_cubegen.bat
gv_cubman.sh gv_cubman.bat
gv_formchk.sh gv_formchk.bat
gv_freqchk.sh gv_freqchk.bat
gv_gmmx.sh gv_gmmx.bat
gv_gaussianhelp.sh
gv_gaussianhelp_mac.sh (Mac OS X)
gv_gaussianhelp.bat
gv_fileeditor.sh
gv_fileeditor_mac.sh (Mac OS X)
gv_fileeditor.bat

Each script’s usage is documented in comments at the beginning of the file. Prudence dictates making a backup copy of any script before modifying it in any way. Unless otherwise specified, all standard UNIX scripts are also provided on Mac OS X systems.