Region Batch Processing Interface

Overview

Several Priism applications which use a command-line interface also have a graphical interface to specify the command-line arguments and some other aspects (priority, batch queue) of how the application will be run. The elements that these graphical interfaces have in common and the corresponding command-line arguments are described in this document; application specific elements are described elsewhere.

At the top of the interface are entries for the input and output files for the application. For each file there is a button which you can use to open a file selection dialog and a text field which shows the current file selection. You can change the selected file by changing the name shown in the field.

Below the file selection items, there are a series of controls to select a subset of the input to process. These controls are further described in the X Range, Y Range, Z Range, T Range, and Wave topics.

The remainder of the dialog, with the exception of the buttons at the bottom, contains items specific to the application. The functions of the buttons at the bottom are:

Exit: Closes the dialog.
Save: Saves the current dialog settings to a file in your home directory. You can reload these settings at a later time using the Restore button.
Restore: Loads the dialog entries that had been previously saved using the Save button.
Options: Opens a dialog which allows you to control how the application will be run including whether or not a batch queue should be used, what priority the job should have, names for the command and script files, and whether or not to chain multiple jobs together. For more information see the Priority, Chain, Queue, Logfile, and Comfile topics.
Do It: If the option to chain jobs is turned off (this is set from the dialog opened by the Options button), pressing this button causes the application to be run with the current settings. If the application is run on the current machine, the label on the button will be changed to Cancel while the job runs and pressing the button will terminate the job.
The first time the Do It button is pressed after the option to chain jobs is turned on, nothing will be executed though the commands that would have been executed will be written to the command file. The next time the "Do It" button is pressed, the commands to run the current job are written to a command file, a line is added to the previous command file to run the one with the commands for the current job, and the previous command file is executed. The label on the Do It button then changes to Cancel and the button can be used to cancel the combined jobs.

Topics

X Range

Next to the X Range label is a field which shows the full x size of the input data in the form

            <minimum x index>:<maximum x index>

Next to that field is another in which you can specify the x range to process. The first value in the field is the first x index to process and the second value is the last x index to process.

On the command-line, the x range to process is specified with an option of the form (optional parts are listed in brackets)

            -x=xstart[:xend]

If the option is not supplied, the entire x range of the input is processed. When the last x index to process, xend, is omitted, it is assumed to be the maximum x index in the input file.

Topics

Y Range

Next to the Y Range label is a field which shows the full y size of the input data in the form

            <minimum y index>:<maximum y index>

Next to that field is another in which you can specify the y range to process. The first value in the field is the first y index to process and the second value is the last y index to process.

On the command-line, the y range to process is specified with an option of the form (optional parts are listed in brackets)

            -y=ystart[:yend]

If the option is not supplied, the entire y range of the input is processed. When the last y index to process, yend, is omitted, it is assumed to be the maximum y index in the input file.

Z Range

Next to the Z Range label is a field which shows the full z size of the input data in the form

            <minimum z index>:<maximum z index>

Next to that field is another in which you can specify the z range to process. The first value in the field is the first z index to process and the second value is the last z index to process.

On the command-line, the z range to process is specified with an option of the form (optional parts are listed in brackets)

            -z=zstart[:zend]

If the option is not supplied, the entire z range of the input is processed. When the last z index to process, zend, is omitted, it is assumed to be the maximum z index in the input file.

T Range

Next to the T Range label is a field which shows the full time extent of the input data in the form

            <minimum time index>:<maximum time index>:1

Next to that field is another in which you can specify the time range to process. The first value in the field is the first time index to process, the second value is the last time index that could be processed, and the last value is the index step between times that are processed.

On the command-line, the time range to process is specified with an option of the form (optional parts are listed in brackets)

            -t=tstart[:tend[:tstep]]

If the option is not supplied, the entire time range of the input is processed. When the time index step, tstep is omitted, it is assumed to be one. When the last time to process, tend is omitted, it is assumed to be the maximum time index in the input file.

Wave

The wavelengths available in the input are shown next to the Wave label. Those wavelengths that will be included in the processing have the toggle button next to them in the on state.

On the command line, the wavelengths to be processed are specified with an option of the form (optional parts are listed in brackets)

            -w=wave1[:wave2[:wave3[:wave4[:wave5]]]]

When the option is not specified, all input wavelengths are processed. A wavelength can either be listed by its wavelength or by its index in the input file (a value between zero and the number of input wavelengths minus one).

Priority

When the Lower priority toggle is on, commands will be executed at a lower priority for access to the computer's resources. It is equivalent to using the Unix nice command with the default priority increment to decrease a command's priority.

Chain

When the Chain option toggle is off and the "Do It" button is pressed, the application is immediately sent to a batch queue or executed locally. When the toggle is on, the needed commands are written to the command file when the Do It button is pressed but are not submitted or run until the next time the Do It button is pressed. To use this effectively to chain two jobs together, do the following

Turn the chain option toggle on.
Set the parameters for the first job and press Do It.
Change the name of the command file; using the same name as was used for the first job will cause the first job to run in an infinite loop.
Set the parameters for the second job and press Do It.
Turn the chain option toggle off.

Because submitting the second job turns the Do It button into a button to cancel the currently running job, it is not generally possible to chain more than two jobs together.

Queue

There is the option to run the application in a batch queue. Use the pulldown menu next to "Submit to queue" to select the batch queue to use or use the run locally option to run jobs on the current machine without using a queue. If you just want to write the commands that would be executed to the script file, use the write script only option.

The names of the batch queues, if any, are set by the environment variables QUE1, QUE2, ..., QUE10. The command to submit a task to a queue are also set with environment variables. A command specific to a single queue can be set with the QUECOM1, ..., or QUECOM10 variables. The command combined with the name of the command file (for instance,

            $QUECOM1 script.com

) is what is used when submitting a task. The QCOMMAND environment variable is used for all queues that do not have a specific command set. When QCOMMAND is used,

            $QCOMMAND <name of queue> <name of script file>

is what is used when submitting a task.

Logfile

Anything that the application writes to standard output will be stored in the file listed in the LogFile field. If the LogFile field is blank, standard output is not redirected by the command file.

Comfile

The commands used to run the application are written to the file listed in the ComFile field. If you intend to run multiple jobs at once (for instance if you are submitting multiple jobs to batch queues), you should change the name of the command file for each one so that you don't overwrite the commands for a previous job that may not have completed. It would also be a good idea to change the name of the log file for each job as well.

Overview

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