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
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:
- Customizing the job before submission (i.e., changing the queue): Confirm submission of Job at SCJobMan (default: unchecked).
- Requesting notification when the job completes: Notify when Job is finished (default: checked).
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:
- : Options
apply only to selected (highlighted) files.
- : Options apply
to all files in the list whether selected or not.
Each of these menus contains the following items:
- : This option
removes selected/all files.
- : This option
checks the box at the beginning of the line for selected/all items. Checking the box marks the items for submission.
- : This option
removes the check from the box for selected/all items, unselecting
them (excluding them from submission).
- : This option
switches the current state of the checkbox for selected/all 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:
- The Submit as: dropdown menu specifies
what type of job will be submitted. By default, is selected, and the job type is determined from the file extension. In
the above dialog, was selected.
- The Target: dropdown menu allows you to
specify which SC Job Manager queue the job is added to.
Modfying the UI Options
The UI Options panel allows you to set
the following options:
- Use Native File Browser:
When checked, GaussView will use the operating system’s native file
browser when adding items to the file list.
- Start with File Browser if
Initial File List is Empty: When checked, GaussView will
automatically open the file browser instead of the File
List panel when the file list is empty (i.e., you are opening a
new file).
- File List Detail: The
following options are available for displaying file information on the File List tab.
- : This shows only
basic amount of information about the file(s) being opened: molecule
group and structure (if any), filename, and directory.
- : This displays
more information about the file being opened: adds the file type.
- : This displays the
highest level of detail of a file that is being opened: adds the file
size and creation and modification dates.
- Allow Duplicate Files:
Checking this option allows GaussView to open the same file multiple
times. If it is unchecked, you will not be allowed to add the same file
to the file list more than once.
The SC Job Manager Dialog
The SC dialog has five panels:
- : The is where all of the files that have been targeted as
such in the Submit Jobs dialog will appear.
- : The is where all of the files that
have been targeted as such in the Submit Jobs dialog will appear.
- : The is where all of the files that have been targeted as
such in the Submit Jobs dialog will appear.
- : This panel provides
information on the jobs that are currently running or are queued to
run.
- : This panel provides
information on jobs that have finished running.
- : This panel provides
information on the type of jobs that can be run using the SC Job
Manager.
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:
- : This button will open the Submit Jobs dialog.
- : This button will hide the SC Job
Manager from your view, but it will not stop the jobs that are running,
and it will continue to run jobs that have been queued up.
- : This button will close the SC Job
Manager. Jobs that are currently running will continue, but no new jobs
will be started. If the SC Job Manager is not exited, it will remain
running as a seperate process even when GaussView is closed, continuing to process jobs.
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:
- : This is the ID given to the job. Jobs within the SC Job Manager are numbered sequentially
across queues starting from 1.
- : This is the name of the job file.
- : This field specifies whether
the job is running or it is queued to run in the future. Note that finished jobs do not appear in this list.
- : This field specifies the
type of job.
- : This field shows what
program is being used to run the job.
- : This field shows the
command line used to run the job.
- : This field gives you the
time and date when the job was submitted to the SC Job Manager.
- : This field gives you the time
and date when the job was started.
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:
- : Removes the selected job from
the queue. If the job is running, it stops the job (after a
confirmation prompt).
- : Displays the contents
of the input file for the selected job.
- : Streams the output
file as the job runs, allowing you to observe its progress.
- : Displays the
current standard output and standard error data from the operating
system. The data is not refreshed.
- : Streams the
standard output and standard error streams from the operating system.
- : Allows you to change the number of jobs which can be running in each queue at one time. By default, it is 1.
The following items appear only on the context menus for queues:
- : Specifies how many jobs
the SC Job Manager can be running at one time. By default, it is set to
1.
- : Pauses the current queue
of jobs, preventing any more from being started, but it will not end
the job this is currently running.
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:
- : This field displays the user who
is running the job.
- : This field displays the
OS process ID assigned to the job by the underlying operating system.
- : This field displays
the OS process ID of the parent process for the job.
- : This field displays the name
of the application that is being used to run the job.
- : This field displays the current
status of the job.
- : This field displays the path
to the application that is being used to run the job.
- : This field displays the
command line used to run the job.
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:
- : This is the ID given to the job
that is running. It is numbered sequentially, starting from 1. The Job
ID number will be reused once the job is cleared.
- : This is the name of the file that
is running, which includes its file extension.
- : This field specifies the
currrent job status. There are several different statuses that can appear here. Completed indicates that the job finished successfully, and an output file can be open. Failed indicates that the job had an issue, and stopped running, and it may or may not produce a partial output file. Crashed indicates that the job failed without output (often before computation had started). Killed indicates that the job was stopped by the user.
- : This field specifies the type
of job.
- : This field displays what queue
the job ran in.
- : This field shows what
program was used to run the job.
- : This field shows the full
command line used to run the job.
- : This field gives you the
time and date when the job was submitted to the SC Job Manager.
- : This field gives you the time
and date when the job was started.
- : This field gives you the time
and date when the job was finished.
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:
- : This button will remove the
file from the list.
- : This button displays
the input file used to run the job.
- : This button displays
the output file from the completed job.
- : This button
displays the standard output and standard error streams from the
operating system.
The Job Types Panel
Selecting the Job Types tab will display the following dialog:

The columns in the table have the following meanings:
- : This is the database ID for the
job type (separate numbering from the jobs themselves).
- : This is the display name of the
application used for running jobs.
- : This is the file
name of the application executable used for running jobs.
- : This displays the path
to the executable.
- : This displays which
queue this job type uses by default.
- : This specifies what
type of input file the job type uses.
- : This specifies what
type of output file this job type produces.
- : Relevant
environment variables for this job type.
- : Command line
template for launching this job type. This is defined in the Job Setup Preferences.

Right-clicking an item in the Job Types dialog displays the panel’s
context menu, which is seen above:
- : This allows you add a new
job type to the list.
- : This allows you
to edit the job type (see below).
- : This removes
the selected job type from the current list.
- : This removes
all of the job types in the current list.
- : This option adds all of the default job types that the SCJM begins with.
- : This
option adds default Ampac jobs.
- : This
option adds default Gaussian jobs.
- : This option
adds default GMMX jobs.
- : This
option adds default Cubegen jobs.
- : This
option adds default Formchk jobs.
- : This
option adds default Freqchk jobs.
- : This
option adds default Cubman jobs.
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:
- : This is the display name of the
application used for running jobs.
- : This displays which
queue this job type uses by default.
- : This is the program
name of the application used for running jobs.
- : This displays the path
where the application is.
- : Command line
template for launching this job type. This is defined in the Job Setup Preferences.
- : This specifies what
type of input file the job type uses.
- : This specifies what
type of output file this job type produces.
- : Relevant
environment variables for this job type.
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.

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:
- Execute directly using default
command line: The job will be started on the local system using
the command line specified in the lower area.
- Execute indirectly through
script using default command line: The job will be started on
the local system using a GaussView-provided script. These scripts are
located in the subdirectory of the
GaussView installation directory. Their names are listed below. The
associated command line appears in the lower area of the dialog. You
can customize the script if desired, using a text editor. To use a
different script, define a custom command line (see the next bullet).
- Execute using custom command line:
Use the command line specified in the box to start the job. You can
enter whatever command line is appropriate for your situation. The
GaussView-provided scripts may be called if desired. Successfully using
this feature depends on a clear understanding of the command line
invocation of Gaussian and its utilities under the current operating
system. Consult the Gaussian User’s Reference
for details.
- Use SC Job Manager: This
functionailty is described in this current document.
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
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.