PBS/SCore(Open PBS/SCore) User's Guide

Index

1. Introduction
2. Commandline Usage
   1. Inspecting queue status
   2. Submitting a (not-SCore) job
   3. Submitting an SCore job
   4. sc_qsub
   5. Deletion of a submitted job
3. xpbs
   1. Inspecting queue status via xpbs
   2. Submitting a job via xpbs
   3. Submitting an SCore job via xpbs
   4. Job deletion via xpbs
   5. Terminating xpbs

Introduction

This ducument describes the fundamental usage of PBS/SCore. For further detail, please refer to PBS man pages.

PBS/SCore is supported only SCore-D single user mode, SCore-D multi user mode is not supported.

Commandline Usage

Inspecting queue status

For inspecting PBS queue status, use qstat command,

	qstat

and jobs in PBS are listed.

        Job id        Name           User         Time Use S Queue
	------------- ------------- ------------- -------- - -----
	95.user0      job1.sh       user0001      00:00:00 R default
	96.user0      job2.sh       user0001      00:00:00 R default
	97.user1      job3.sh       user0001             0 Q default

Submitting a (not-SCore) job

In PBS, submitted job must be a shell script file, not a binary file. The script is executed on compute host(s). Here is an example of the shell script.

	hostname
	date
	sleep 30

Let us assume that the file is saved as test.sh, and the file is submitted. To submit a job, use the qsub command.

	% qsub test.sh

If the job submission is succeeded, an allocated job ID is displaed.

	1.user0

Note that the value of the environment variable PATH depends on the login shell on the remote host. The current directory is set to /var/scored/pbs/mom_priv/jobs/<Job-ID> where is inside of the PBS spool directory.

If the qstat PBS command is executed just after submitting a job via qsub command, user can see the submitted job is in the PBS queue.

	qstat
	Job id	      Name	     User	  Time Use S Queue
	------------- ------------- ------------- -------- - -----
	1.user0	      test.sh	    user0001	  00:00:00 R default

Submitting an SCore job

Let's assume that a user want to submit the following SCore job via PBS.

	% scrun -nodes=4 ./cg.A.4

First of all, the user must prepare the following shell script file, so that the user program can be invoked via the scout -F ${PBS_NODEFILE} and scrun commands.

	scout -wait -F ${PBS_NODEFILE} -e scrun -nodes=4 /work/naspar/cg.A.4

When the script file is executed, the current directory is set to the PBS spool directory. The script file is copied onto a compute host, but program binary file is not copied by PBS. So, the program binary file must be executable by the compute hosts, and the path in the script file must be specified as an absoulte path which can be seen both user host and compute hosts.

Here it is assumed that the abvoe shell script is created as score.sh. To submit the job, execute the following qsub command.

	% qsub -l nodes=4:score score.sh

It should be noted that the number of nodes passed to the qsub command must be consistent with the number of nodes specified in the script file.

Also, user should specify score property when submitting an SCore job. This option is to distinguish between SCore jobs and not-SCore jobs in PBS/SCore.

Users can specify more proeprties. For example, if a user want to allocate hosts having the property "pcc", then both "score" and "pcc" properties must be specified like the following.

	qsub -l nodes=4:score:pcc score.sh

For more detail on the property, please refer to Section 6.2. Parallel Jobs of PBS Administrator Guide

sc_qsub

As described, users have to create a script file if they want to submit SCore jobs into PBS/SCore. The sc_qsub command, described in this section, automatically create the script file.

Let's assume that a user want to submit the following SCore job via PBS.

	% scrun -nodes=4 /work/naspar/cg.A.4

To submit the above program by using the sc_qsub command, do the following.

	% sc_qsub -nodes=4 /work/naspar/cg.A.4

Here, please note that nodes option. This option must be present always. qsub option(s), if any, must be in between sc_qsub and -nodes arguments. Note that you cannot specify nodes option via the "-l nodes=" option.

The following is an example sc_qsub command execution with a "-a" qsub option and SCore options.

	% sc_qsub -a 1000 -nodes=2x2,statistics /work/naspar/cg.A.4

Deletion of a submitted job

To delete a submitted job, use the qdel command. Let's assume the qstat command outputs the followings.

	qstat
	Job id	      Name	     User	  Time Use S Queue
	------------- ------------- ------------- -------- - -----
	1.user0       test.sh	    user0001	  00:00:00 R default
	2.user0       test.sh	    user0001	  00:00:00 R default

The qdel takes one argument to specify a job ID to delete.

	% qdel 1.user0

If the qstat command output the following, after the qdel command exection.

	qstat
	Job id	      Name	     User	  Time Use S Queue
	------------- ------------- ------------- -------- - -----
	2.user0       test.sh	    user0001	  00:00:00 R default

xpbs

PBS/SCore provides not only command line interface, such as qsub, but also GUI program, called xpbs running on X Window system.

xpbs is invoked from inside of Unix shell. In the following example, the DISPLAY environment variable must be set properly.

	% xpbs

xpbs will create a window on the specified X Window server.

Inspecting queue status via xpbs

To inspect queue status, firstly select a queue.

Then the queue status will be displayed in the JOB STATUS pane.

The displayed queue status is a snapshot. If the "Manual Update" button located in the upper left corner of the window is clicked, then the selected queue status is updated. If periodical update is desired, click the "Auto Update ..." button, then the following "Automatic Update of Data" dialog is popup.

Select an appropriate interval by clicking up-arrow or down-arrow button, and clock "start updating" button. Then the queue status is updated periodically. To stop the automatic update, click "stop updating" button.

Submitting a job via xpbs

To submit a (not-SCore) job via xpbs, click "Submit ..." button in the HOSTS pane. Eventually "Submit Job Dialog" window pos up.

Specify scirpt to submit in the SCRIPT pane of the "Submit Job Dialog" window.

There are two ways to select a script. One is to specify existing script file, and the other is to warite a script in a textbox. To specify a script file, click "File..." button, or enter a filename in the entry field located and then clock the "load" button.

Do not forget to click "confirm submit" button, when you finish to specify a script. Then the script is submitted. The "Submit Job Dialog" window is dismissed, and the submitted job is added to the JOBS pane of the main window.

Submitting an SCore job via xpbs

Basically, submitting an SCore job via xpbs is the same as submitting a not-SCore job. However, there are some restrictions.

To submit an SCore job to invoke the following parallel program,

	% scrun -nodes=4 ./cg.A.4

User has to prepare a script file in the same way described before, or write a script in the SCRIPT pane in the "Submit Job Dialog" window. In the script, scrun command must be invoke by scout -F ${PBS_NODEFILE} command.

	scout -wait -F ${PBS_NODEFILE} -e scrun -nodes=4 /work/naspar/cg.A.4

The "nodes" resource value in the "Resource List" pane of "Submit Job Dialog" window must be "<#node>:score."

Job deletion via xpbs

To delete a job via xpbs, select a job in the main window, and then click the "delete" button.

"Delete Job Dialog" window pops up, prompting to confirm the job to be deleted.

If the job is exactly you want delete, click the "delete" button, and the job will be deleted.

Terminating xpbs

If the xpbs command is invoked first time, a window pops up to ask if ~/.xpbsrc is creatde.

If click "yes", then xpbs terminates. Once ~/.pbscrc file is created, this confirmation window will never pop up again.

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