Submitting jobs

You can submit jobs to the batch queue for later proccessing with qsub. Batch queueing can get pretty fancy, so qsub comes with lots of options (see man qsub). For the most part, you can trust your sysadmin to have set up some good defaults, and not worry about setting any options explicitly. As you get used to the batch queue system, you'll want tighter control of how your jobs execute by invoking more sophisticated options yourself, but don't let that scare you off at the beginning. They are, after all, only options. This paper will give you a good start on the options I find myself using most often.

Simple submission

The simplest example of a job submission is:

$ echo "sleep 30 && echo 'Running a job...'" | qsub
2705.n0.physics.drexel.edu

Which submits a job executing sleep 30 && echo 'Running a job...' to the queue. The job gets an identifying ID in the queue, which qsub prints to stdout.

You can check the status of your job in the queue with qstat.

$ qstat
Job id            Name             User            Time Use S Queue
----------------- ---------------- --------------- -------- - -----
2705.n0           STDIN            sysadmin               0 Q batch

There is more information on qstat in the qstat section.

If your job is too complicated to fit on a single line, you can save it in a script:

#!/bin/bash
# file: echo_script.sh
sleep 30
echo "a really,"
echo "really,"
echo "complicated"
echo "script"

and submit the script:

$ qsub echo_script.sh
2706.n0.physics.drexel.edu

All the arguments discussed in later sections for the command line should have comment-style analogs that you can enter in your script if you use the script-submission approach with qsub.

Note that you cannot run executibles directly with qsub. For example

$ cat script.py
#!/usr/bin/python
print("hello world!")
$ qsub python script.py

will fail because python is an executible. Either use

$ echo python script.py | qsub

wrap your Python script in a Bash script

$ cat wrapper.sh
#!/bin/bash
python script.py
$ qsub wrapper.sh

or run your Python script directly (relying on the sha-bang)

$ qsub script.py

IO: Job names and working directories

You will often be interested in the stdout and stderr output from your jobs. The batch queue system saves this information for you (to the directory from which you called qsub) in two files <jobname>.o<jobID-number> and <jobname>.e<jobID-number>. Job IDs we have seen before, they're just the numeric part of qsub output (or the first field in the qstat output). Job IDs are assigned by the batch queue server, and are unique to each job. Job names are assigned by the job submitter (that's you) and need not be unique. They give you a method for keeping track of what job is doing what task, since you have no control over the job ID. The combined <jobname>.<jobID-number> pair is both unique (for the server) and recognizable (for the user), which is why it's used to label the output data from a given job. You control the job name by passing the -N <jobname> argument to qsub.

$ echo "sleep 30 && echo 'Running a job...'" | qsub -N myjob
2707.n0.physics.drexel.edu
$ qstat
Job id            Name             User            Time Use S Queue
----------------- ---------------- --------------- -------- - -----
2707.n0           myjob            sysadmin               0 Q batch

Perhaps you are fine with stdin and stdout, but the default naming scheme, even with the job name flexibility, is too restrictive. No worries, qsub lets you specify exactly which files you'd like to use with the unsurprisingly named -o and -e options.

$ echo "echo 'ABC' && echo 'DEF' > /dev/stderr" | qsub -o my_out -e my_err
2708.n0.physics.drexel.edu
 … time passes …
$ cat my_out
ABC
$ cat my_err
DEF

A time will come when you are no longer satified with stdin and stdout and you want to open your own files or worse, run a program! Because no sane person uses absolute paths all the time, we need to know what directory we're in so we can construct our relative paths. You might expect that your job will execute from the same directory that you called qsub from, but that is not the case. I think the reason is that that directory is not garaunteed to exist on the host that eventually runs your program. In any case, your job will begin executing in your home directory. Writing relative paths from your home directory is about as annoying as writing absolute paths, so qsub gives your script a nifty environment variable PBS_O_WORKDIR, which is set to the directory you called qsub from. Since you know that this directory exists on the hosts (since the home directories are NFS mounted on all of our cluster nodes), you can move to that directory yourself, using something like

$ echo 'pwd && cd $PBS_O_WORKDIR && pwd' | qsub
2709.n0.physics.drexel.edu
 … time passes …
$ cat STDIN.o2709
/home/sysadmin
/home/sysadmin/howto/cluster/pbs_queues

Note that if we had enclosed the echo argument in double quotes ("), we would have to escape the $ symbol in our echo argument so that it survives the shell expansion and makes it safely into qsub's input.

Long jobs

If you have jobs that may take longer than the default wall time (currently 1 hour), you will need to tell the job manager. Walltimes may seem annoying, since you don't really know how long a job will run for, but they protect the cluster from people running broken programs that waste nodes looping around forever without accomplishing anything. Therefor, your walltime doesn't have to be exactly, or even close to, your actual job execution time. Before submitting millions of long jobs, it is a good idea to submit a timing job to see how long your jobs should run for. Then set the walltime a factor of 10 or so higher. For example

$ echo "time (sleep 30 && echo 'Running a job...')" | qsub -j oe
2710.n0.physics.drexel.edu
 … time passes …
$ cat STDIN.o2710
Running a job...

real  0m30.013s
user  0m0.000s
sys  0m0.000s
$ echo "sleep 30 && echo 'Running a job...'" | qsub -l walltime=15:00
2711.n0.physics.drexel.edu
$ qstat -f | grep '[.]walltime'

You can set walltimes in [[H:]M:]S format, where the number of hours, minutes, and seconds are positive integers. I passed the -j oe combines both sdtout and stdin streams on stdin because time prints to stderr. Walltimes are only accurate on the order of minutes and above, but you probably shouldn't be batch queueing jobs that take less time anyway.

Job dependencies

You will often find yourself in a situation where the execution of one job depends on the output of another job. For example, jobA and jobB generate some data, and jobC performs some analysis on that data. It wouldn't do for jobC to go firing off as soon as there was a free node, if there was no data available yet to analyze. We can deal with dependencies like these by passing a -W depend=<dependency-list> option to qsub. The dependency list can get pretty fancy (see man qsub), but for the case outlined above, we'll only need afterany dependencies (because jobC should execute after jobs A and B).

Looking at the man page, the proper format for our dependency list is afterany:jobid[:jobid...], so we need to catch the job IDs output by qsub. We'll use Bash's command substitution ($(command)) for this.

$ AID=$(echo "cd \$PBS_O_WORKDIR && sleep 30 && echo \"we're in\" > A_out" | qsub)
$ BID=$(echo "cd \$PBS_O_WORKDIR && sleep 30 && pwd > B_out" | qsub)
$ COND="depend=afterany:$AID:$BID -o C_out -W depend=afterany:$AID:$BID"
$ CID=$(echo "cd \$PBS_O_WORKDIR && cat A_out B_out" | qsub -W depend=afterany:$AID:$BID -o C_out)
$ echo -e "A: $AID\nB: $BID\nC: $CID"
A: 2712.n0.physics.drexel.edu
B: 2713.n0.physics.drexel.edu
C: 2714.n0.physics.drexel.edu
$ qstat
Job id                    Name             User            Time Use S Queue
------------------------- ---------------- --------------- -------- - -----
2712.n0                   STDIN            sysadmin               0 R batch
2713.n0                   STDIN            sysadmin               0 R batch
2714.n0                   STDIN            sysadmin               0 H batch
 … time passes …
$ cat C_out
we're in
/home/sysadmin/howto/cluster/pbs_queues

Note that we have to escape the PBS_O_WORKDIR expansion so that the variable substitution occurs when the job runs, and not when the echo command runs.

Job arrays

If you have lots of jobs you'd like to submit at once, it is tempting try

$ for i in $(seq 1 5); do JOBID=`echo "echo 'Running a job...'" | qsub`; done

This does work, but it puts quite a load on the server as the number of jobs gets large. In order to allow the execution of such repeated commands the batch server provides job arrays. You simply pass qsub the -t array_request option, listing the range or list of IDs for which you'd like to run your command.

$ echo "sleep 30 && echo 'Running job \$PBS_ARRAYID...'" | qsub -t 1-5
2721.n0.physics.drexel.edu
$ qstat
Job id            Name             User            Time Use S Queue
----------------- ---------------- --------------- -------- - -----
2721-1.n0         STDIN-1          sysadmin               0 R batch
2721-2.n0         STDIN-2          sysadmin               0 R batch
2721-3.n0         STDIN-3          sysadmin               0 R batch
2721-4.n0         STDIN-4          sysadmin               0 R batch
2721-5.n0         STDIN-5          sysadmin               0 R batch

One possibly tricky issue is depending on a job array. If you have an analysis job that you need to run to compile the results of your whole array, try

$ JOBID=$(echo "cd \$PBS_O_WORKDIR && sleep 30 && pwd && echo 1 > val\${PBS_ARRAYID}_out" | qsub -t 1-5)
$ sleep 2  # give the job a second to load in...
$ JOBNUM=$(echo $JOBID | cut -d. -f1)
$ COND="depend=afterany"
$ for i in $(seq 1 5); do COND="$COND:$JOBNUM-$i"; done
$ echo "cd \$PBS_O_WORKDIR && awk 'START{s=0}{s+=\$0}END{print s}' val*_out" | \
      qsub -o sum_out -W $COND
2723.n0.physics.drexel.edu

$ qstat
Job id            Name             User            Time Use S Queue
----------------- ---------------- --------------- -------- - -----
2722-1.n0         STDIN-1          sysadmin               0 R batch
2722-2.n0         STDIN-2          sysadmin               0 R batch
2722-3.n0         STDIN-3          sysadmin               0 R batch
2722-4.n0         STDIN-4          sysadmin               0 R batch
2722-5.n0         STDIN-5          sysadmin               0 R batch
2723.n0           STDIN            sysadmin               0 H batch
$ cat sum_out
5

Note that you must create any files needed by the dependent jobs during the early jobs. The dependent job may start as soon as the early jobs finish, before the stdin and stdout files for some early jobs have been written. Sadly, depending on either the returned job ID or just its numeric portion doesn't seem to work.

It is important that the jobs on which you depend are loaded into the server before your depending job is submitted. To ensure this, you may need to add a reasonable sleep time between submitting your job array and submitting your dependency. However, your depending job will also hang if some early jobs have already finished by the time you get around to submitting it. In practice, this is not much of a problem, because your jobs will likely be running for at least a few minutes, giving you a large window during which you can submit your dependent job.

See the examples sections and man qsub for more details.

Querying

You can get information about currently running and queued jobs with qstat. In the examples in the other sections, we've been using bare qstats to get information about the status of jobs in the queue. You get information about a particular command with

$ JOBID=`echo "sleep 30 && echo 'Running a job...'" | qsub`
$ sleep 2 && qstat $JOBID
Job id            Name             User            Time Use S Queue
----------------- ---------------- --------------- -------- - -----
2724.n0           STDIN            sysadmin               0 R batch

and you can get detailed information on a every command (or a particular one, see previous example) with the -f (full) option.

$ JOBID=$(echo "sleep 30 && echo 'Running a job...'" | qsub)
$ sleep 2
$ qstat -f
Job Id: 2725.n0.physics.drexel.edu
    Job_Name = STDIN
    Job_Owner = sysadmin@n0.physics.drexel.edu
    job_state = R
    queue = batch
    server = n0.physics.drexel.edu
    Checkpoint = u
    ctime = Thu Jun 26 13:58:54 2008
    Error_Path = n0.physics.drexel.edu:/home/sysadmin/STDIN.e2725
    exec_host = n8/0
    Hold_Types = n
    Join_Path = n
    Keep_Files = n
    Mail_Points = a
    mtime = Thu Jun 26 13:58:55 2008
    Output_Path = n0.physics.drexel.edu:/home/sysadmin/STDIN.o2725
    Priority = 0
    qtime = Thu Jun 26 13:58:54 2008
    Rerunable = True
    Resource_List.nodect = 1
    Resource_List.nodes = 1
    Resource_List.walltime = 01:00:00
    session_id = 18020
    Variable_List = PBS_O_HOME=/home/sysadmin,PBS_O_LANG=en_US.UTF-8,
  PBS_O_LOGNAME=sysadmin,
  PBS_O_PATH=/home/sysadmin/bin:/usr/local/bin:/usr/local/sbin:/usr/bin
  :/usr/sbin:/bin:/sbin:/usr/X11R6/bin:/usr/local/maui/bin:/home/sysadmi
  n/script:/home/sysadmin/bin:.,PBS_O_MAIL=/var/mail/sysadmin,
  PBS_O_SHELL=/bin/bash,PBS_SERVER=n0.physics.drexel.edu,
  PBS_O_HOST=n0.physics.drexel.edu,
  PBS_O_WORKDIR=/home/sysadmin/,
  PBS_O_QUEUE=batch
    etime = Thu Jun 26 13:58:54 2008
    start_time = Thu Jun 26 13:58:55 2008
    start_count = 1

The qstat command gives you lots of information about the current state of a job, but to get a history you should use the tracejob command.

$ JOBID=$(echo "sleep 30 && echo 'Running a job...'" | qsub)
$ sleep 2 && tracejob $JOBID

Job: 2726.n0.physics.drexel.edu

06/26/2008 13:58:57  S    enqueuing into batch, state 1 hop 1
06/26/2008 13:58:57  S    Job Queued at request of sysadmin@n0.physics.drexel.edu, owner = sysadmin@n0.physics.drexel.edu, job name = STDIN, queue = batch
06/26/2008 13:58:58  S    Job Modified at request of root@n0.physics.drexel.edu
06/26/2008 13:58:58  S    Job Run at request of root@n0.physics.drexel.edu
06/26/2008 13:58:58  S    Job Modified at request of root@n0.physics.drexel.edu

You can also get the status of the queue itself by passing -q option to qstat

$ qstat -q

server: n0

Queue            Memory CPU Time Walltime Node  Run Que Lm  State
---------------- ------ -------- -------- ----  --- --- --  -----
batch              --      --       --      --    2   0 --   E R
                                               ----- -----
                                                   2     0

or the status of the server with the -B option.

$ qstat -B
Server             Max   Tot   Que   Run   Hld   Wat   Trn   Ext Status
----------------   ---   ---   ---   ---   ---   ---   ---   --- ----------
n0.physics.drexe     0     2     0     2     0     0     0     0 Active

You can get information on the status of the various nodes with qnodes (a symlink to pbsnodes). The output of qnodes is bulky and not of public interest, so we will not reproduce it here. For more details on flags you can pass to qnodes/pbsnodes see man pbsnodes, but I haven't had any need for fancyness yet.

Altering and deleting jobs

Minor glitches in submitted jobs can be fixed by altering the job with qalter. For example, incorrect dependencies may be causing a job to hold in the queue forever. We can remove these invalid holds with

$ JOBID=$(echo "sleep 30 && echo 'Running a job...'" | qsub -W depend=afterok:3)
$ qstat
Job id            Name             User            Time Use S Queue
----------------- ---------------- --------------- -------- - -----
2725.n0           STDIN            sysadmin               0 R batch
2726.n0           STDIN            sysadmin               0 R batch
2727.n0           STDIN            sysadmin               0 H batch
$ qalter -h n $JOBID
$ qstat
Job id            Name             User            Time Use S Queue
----------------- ---------------- --------------- -------- - -----
2725.n0           STDIN            sysadmin               0 R batch
2726.n0           STDIN            sysadmin               0 R batch
2727.n0           STDIN            sysadmin               0 Q batch

qalter is a Swiss-army-knife command, since it can change many aspects of a job. The specific hold-release case above could also have been handled with the qrls command. There are a number of other q* commands which provide detailed control over jobs and queues, but I haven't had to use them yet.

If you decide a job is beyond repair, you can kill it with qdel. For obvious reasons, you can only kill your own jobs, unless your an administrator.

$ JOBID=$(echo "sleep 30 && echo 'Running a job...'" | qsub)
$ qdel $JOBID
$ echo "deleted $JOBID"
deleted 2728.n0.physics.drexel.edu
$ qstat
Job id            Name             User            Time Use S Queue
----------------- ---------------- --------------- -------- - -----
2725.n0           STDIN            sysadmin               0 R batch
2726.n0           STDIN            sysadmin               0 R batch
2727.n0           STDIN            sysadmin               0 R batch