Help:HPCC Torque: Difference between revisions
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=== Deleting a job === | === Deleting a job === | ||
If you want to delete a job that you already submitted, use the <tt>qdel</tt> command. This immediately removes your job from the queue and kills it if it is already running. To delete the job from the previous example (job number 45), | |||
and it | |||
<geshi> | <geshi> | ||
>qdel | >qdel 45 | ||
</geshi> | </geshi> | ||
Check the status of a job | === Check the status of a job === | ||
Use <tt>qstat</tt> to check the status of a job. This returns a brief status report of all your jobs that are either queued or running. For example, | |||
<geshi> | <geshi> | ||
>qstat | >qstat | ||
Job id Name User Time Use S Queue | Job id Name User Time Use S Queue | ||
------------------------- ---------------- --------------- -------- - ----- | ------------------------- ---------------- --------------- -------- - ----- | ||
45.beach.colorado.edu STDIN username 0 R workq | |||
46.beach.colorado.edu STDIN username 0 Q workq | |||
</geshi> | </geshi> | ||
In this case, job number 45 is running ('R'), and job number 46 is queued ('Q'). Both have been submitted to the workq. | |||
=== Advanced usage === | === Advanced usage === | ||
Revision as of 11:40, 13 May 2009
Submitting Jobs to the CSDMS HPCC
The CSDMS High Performance Computing Cluster uses Torque/Maui as a job scheduler. With Torque you can allocate resources, schedule and manage job execution, monitor and view the status of your jobs.
Torque uses instructions given on the command line and embedded within comments of the shell script that runs your program. This page describes basic Torque usage. Please visit the Torque website for a more complete guide.
The Torque Cheat Sheet
Frequently Used Commands
| Command | Description | Basic Usage | Example |
|---|---|---|---|
| qsub | Submit a pbs job | qsub [script] | > qsub job.pbs |
| qstat | Show status of pbs batch jobs | qstat [job_id] | > qstat 44 |
| qdel | Delete pbs batch job | qdel [job_id] | > qdel 44 |
| qhold | Hold pbs batch jobs | qhold [job_id] | > qhold 44 |
| qrls | Release hold on pbs batch jobs | qrls [job_id] | > qrls 44 |
Check Queue and Job Status
| Command | Description |
|---|---|
| qstat -q | List all queues |
| qstat -a | List all jobs |
| qstat -au <userid> | list jobs for userid |
| qstat -r | List running jobs |
| qstat -f <job_id> | List full information about job_id |
| qstat -Qf <queue> | List full information about queue |
| qstat -B | List summary status of the job server |
| pbsnodes | List status of all compute nodes |
Within-Script Torque Commands
| Command | Description |
|---|---|
| #PBS -N myjob | Set the job name |
| #PBS -m ae | Mail status when the job completes |
| #PBS -M your@email.address | Mail to this address |
| #PBS -l nodes=4 | Allocate specified number of nodes |
| #PBS -l walltime=1:00:00 | Inform the PBS scheduler of the expected runtime |
Basic Usage
Torque dynamically allocates resources for your job. All you need to do is submit it to the queue (with qsub) and it will find the resources for you. Note though that Torque is not aware of the details of the program that you are wanting to run and so may need to tell it what resources you require (memory, nodes, cpus, etc.).
Submitting a job
To submit a job to the queue you must write a shell script that torque will use to run your program. In its simplest form, a torque command file would look like the following: <geshi>
- !/bin/sh
my_prog </geshi> This shell script simply runs the program, my_prog. To submit this job to the queue, use the qsub command, <geshi> > qsub run_my_prog.sh </geshi> where the contents of the file run_my_prog.sh is code snippet above. Torque will respond with the job number and the server name, <geshi> 45.beach.colorado.edu </geshi> In this case Torque has identified your job with job number 45. You have now submitted your job to the default queue and will be run as soon as there are resources available for it. By default, the standard error and output of your script are redirected to files in your home directory. They will have the name <job_name>.o<job_no>, and <job_name>.e<job_no> for standard output and error, respectively. Thus, for our example, standard output will be written to run_my_prog.sh.o45, and standard error will be written to run_my_prog.sh.e.45.
Deleting a job
If you want to delete a job that you already submitted, use the qdel command. This immediately removes your job from the queue and kills it if it is already running. To delete the job from the previous example (job number 45), <geshi> >qdel 45 </geshi>
Check the status of a job
Use qstat to check the status of a job. This returns a brief status report of all your jobs that are either queued or running. For example, <geshi> >qstat
Job id Name User Time Use S Queue
------------------------- ---------------- --------------- -------- - -----
45.beach.colorado.edu STDIN username 0 R workq
46.beach.colorado.edu STDIN username 0 Q workq
</geshi> In this case, job number 45 is running ('R'), and job number 46 is queued ('Q'). Both have been submitted to the workq.
Advanced usage
Torque allows you to use advanced features and customizations when running jobs. The below sections are continuations of the sections above.
Job Submission: There are options in the shell script that can be used to customize your job.
A Basic script. <geshi> >cat test.sh
#!/bin/bash
#PBS -N testjob
cat $PBS_NODEFILE
sleep 30
</geshi>
$PBS_NODEFILE is the location of a file that contains a list of the nodes allocated for this job.
- PBS specifies an option to Torque. There are many listed below, but
more can be found in the man page for qsub.
<geshi>
- PBS -r n # The job is not rerunnable.
- PBS -r y # The job is rerunnable
- PBS -q testq # The queue to submit to
- PBS -N testjob # The name of the job
- PBS -o testjob.out # The file to print the output to
- PBS -e testjob.err # The file to print the error to
- Mail Directives
- PBS -m abe # The points durring the execution to send an email
- PBS -M me@colorado.edu # Who to Mail to
- PBS -l walltime=01:00:00 # Specify the walltime
- PBS -l pmem=100mb # Memory Allocation for the Job
- PBS -l nodes=4 # Number of nodes to Allocate
- PBS -l nodes=4:ppn=3 # Number of nodes and the number processors per node
</geshi>
You can use any of the above options in the script to customize your job. If all of the above options are used, the job will be named testjob and be put into the testq. It will only run for 1 hour and mail me@colorado.edu at the beginning and end of the job. It will use 4 nodes with 3 processors per node, with a total of 12 processors and 100 mb of memory.
Check the status of a job: Torque and Maui allow you to check the status of jobs and the queue status.
In Torque: Qstat has many options for checking a job status. The basic way is running the command with out any options which is showed above. Again the man pages are the best resources for information.
Other options include: -n, -f, -Q, -B, -u, -q
The -n option will show which nodes are running which jobs. <geshi> >qstat -n
server.colorado.edu:
Req'd Req'd Elap
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
-------------------- -------- -------- ---------------- ------ ----- --- ------ ----- - -----
78.server.colorado user workq STDIN 4811 -- -- -- -- R --
node34/0
79.server.colorado user workq STDIN 4830 -- -- -- -- R --
node34/1
80.server.colorado user workq STDIN 3867 -- -- -- -- R --
node33/0
81.server.colorado user workq STDIN 4821 -- -- -- -- R --
node32/0
82.server.colorado user workq STDIN 4840 -- -- -- -- R --
node32/1
83.server.colorado user workq STDIN 4859 -- -- -- -- R --
node32/2
</geshi>
The -f option will show the full details for a specified job. <geshi> >qstat -f 78 Job Id: 84.server.colorado.edu
Job_Name = STDIN
Job_Owner = username@server.colorado.edu
resources_used.cput = 00:00:00
resources_used.mem = 1704kb
resources_used.vmem = 8028kb
resources_used.walltime = 00:00:01
job_state = R
queue = workq
server = server.colorado.edu
Checkpoint = u
ctime = Fri Apr 24 16:21:51 2009
Error_Path = server.colorado.edu:/tmp/STDIN.e84
exec_host = node34/0
Hold_Types = n
Join_Path = n
Keep_Files = n
Mail_Points = a
mtime = Fri Apr 24 16:21:53 2009
Output_Path = server.colorado.edu:/tmp/STDIN.o84
Priority = 0
qtime = Fri Apr 24 16:21:51 2009
Rerunable = True
Resource_List.neednodes = node34
session_id = 4877
substate = 42
Variable_List = PBS_O_HOME=/tmp,PBS_O_LOGNAME=username,
PBS_O_PATH= /usr/local/bin:/usr/bin
PBS_O_SHELL=/bin/tcsh,PBS_SERVER=server.colorado.edu,
PBS_O_HOST=server.colorado.edu,PBS_O_WORKDIR=/tmp/
PBS_O_QUEUE=workq
euser = username
egroup = server
hashname = 84.server.colorado.edu
queue_rank = 83
queue_type = E
etime = Fri Apr 24 16:21:51 2009
start_time = Fri Apr 24 16:21:53 2009
start_count = 1
</geshi>
The -u option will show all jobs owned the specified user.
The -Q option will show the queue information. If a specific queue is specified it will only show the information from that queue.
<geshi> >qstat -Q
Queue Max Tot Ena Str Que Run Hld Wat Trn Ext T
---------------- --- --- --- --- --- --- --- --- --- --- -
testing 0 0 yes yes 0 0 0 0 0 0 E
normal 8 1 yes yes 0 1 0 0 0 0 E
short 0 0 yes yes 0 0 0 0 0 0 E
long 0 3 yes yes 0 3 0 0 0 0 E
special 0 0 yes yes 0 0 0 0 0 0 E
</geshi>
Maui
If maui is installed on your system, you will have access to another set of tools. One of these is showq. showq is a tool like qstat. It will show the queue information.
<geshi> >showq
ACTIVE JOBS--------------------
JOBNAME USERNAME STATE PROC REMAINING STARTTIME
624 user1 Running 4 21:00:01 Fri Apr 24 13:34:17
621 user2 Running 2 95:21:19:49 Mon Apr 20 13:54:06
622 user2 Running 2 95:21:23:06 Mon Apr 20 13:57:23
623 user2 Running 2 96:04:13:37 Mon Apr 20 20:47:54
4 Active Jobs 10 of 20 Processors Active (50.00%)
5 of 7 Nodes Active (71.43%)
IDLE JOBS----------------------
JOBNAME USERNAME STATE PROC WCLIMIT QUEUETIME
0 Idle Jobs
BLOCKED JOBS----------------
JOBNAME USERNAME STATE PROC WCLIMIT QUEUETIME
Total Jobs: 4 Active Jobs: 4 Idle Jobs: 0 Blocked Jobs: 0
</geshi>
