Using the serialjob command to submit jobs

On AVIDD, a script named serialjob provides a convenient method for submitting serial (single-processor) programs to the PBS batching and queuing system (a similar utility is available for the SP, that works with LoadLeveler). The script is designed so that programs can be submitted as jobs by prefixing the command-line with the word serialjob. The general form of the command is 


	serialjob program-name [ program-options ]  [ -wallhours n ] [ -- options-to-pbs ]

where program-name is the name of the program that you wish to be submitted as a job and program-options are command-line options that you would pass to the program. For example, suppose you've written a program called turtlecalc that runs for more than 20 minutes of processor time and that takes options that specify speed and the name of the file to be processed. You would enter the command 


	serialjob turtlecalc -speed slow mydata.dat

If the program that you wish to run is not on your default path, use the fully qualified path name of the program.

When your job runs, the current working directory of your program is the directory from which you ran the serialjob command.

The wallhours option is a convenient method of requesting more than the default amount of wall-clock time for a job. On AVIDD, jobs are allowed to run for two hours by default. If you need more time, specify the amount of time as an integer number of hours. For example, to run turtlecalc and allow it to run for 26 hours, the command would be 

	serialjob turtlecalc -speed slow mydata.dat -wallhours 26

Alternatively, you could request time using the PBS option. 

	serialjob turtlecalc -speed slow mydata.dat -- -l walltime=26:0:0

Serialjob should be on your path by default, and its manual page should be on your MANPATH by default. The best source of information about serial job is its Unix manual page.

Limits

Serialjob will not work for programs that make use of a -- (double-dash) argument because serialjob uses that argument to separate options to your program from options to PBS.

If you need to quote arguments, serial job handles only double-quotes. It cannot provide the protection that is usually afforded by single-quotes because the Bourne shell provides no mechanism for escaping characters within strings in single-quotes. Single-quotes are treated as double-quotes by serialjob.

Advanced Features

Output redirection is possible with serialjob. Output redirection symbols must be escaped to prevent them from being interpreted by the interactive shell. If a pipe is used, both programs in the pipe are run within the same serial job. It is not possible to pipe data from your interactive shell into a command that will be run from within serialjob.

The syntax for a pipe is 


	serialjob program1 [ options-to-program1 ] \| program2

The syntax for redirecting output to a file is 


	serialjob program [ options-to-program ] \> file

Pipes and redirection to a file can both be used in the same job.