OLD DEPRECATED SGEBasics

Submitting your first job

To submit a job to run under SGE, we use the qsub command. qsub (queue submit) takes the commands you give it, and runs it through the scheduler, which finds the optimum place for your job to run. With over 150 nodes and 2500 cores to schedule, as well as differing priorities, hardware, and individual resources, the scheduler's job is not trivial.

There are a few things you'll need to know before running qsub.

• How many cores you need. Note that unless your program is created to use multiple cores (called "threading"), asking for more cores will not speed up your job. This is a common misperception. Beocat will not magically make your program use multiple cores! For this reason the default is 1 core.
• How much time you need. Many users when beginning to use Beocat neglect to specify a time requirement. The default is one hour, and we get asked why their job died after one hour. We usually point them to the FAQ.
• How much memory you need. The default is 1GB. If your job uses significantly more than you ask, your job will be placed on hold until you fix your request.
• Any advanced options. See the AdvancedSGE page for these requests. For our basic examples here, we will ignore these.

So let's now create a small script to test our ability to submit jobs. Create the following file (either by copying it to Beocat or by editing a text file and we'll name it myhost.sh. Both of these methods are documented on our LinuxBasics page.

#!/bin/sh
hostname

Be sure to make it executable

chmod u+x myhost.sh

Now, let's first run it on the headnode. As I write this, I'm logged into the headnode named 'minerva'. When I run it, it looks like this:

% ./myhost.sh
minerva

So, now lets submit it as a job and see what happens. Here I'm going to use three options

• -l mem= tells how much memory I need. In my example, I'm using our system minimum of 512 MB, which is more than enough. Note that your memory request is per core, which doesn't make much difference for this example, but will as you submit more complex jobs.
• -l h_rt= tells how much runtime I need. This can be in the form of seconds, or hours:minutes:seconds. This is a very short job, so 60 seconds should be plenty. Note that if you submit a job that needs to run for days or weeks, you'll need to translate that into hours. This can't be changed after the job is started please make sure you have requested a sufficient amount of time.
• -pe single 1 tells SGE that I need only a single core on one machine. The AdvancedSGE page has much more on the "Parallel Environment" switch.

% ls
myhost.sh
% qsub -l h_rt=60 -l mem=512M -pe single 1 ./myhost.sh
INFO: Requested resources for this job: pe=single cores=1 time(HH:MM:SS or SS)=60 mem(per-core)=512M
Your job 1483446 ("myhost.sh") has been submitted

Since this is such a small job, it is likely to be scheduled almost immediately, so a minute or so later, I now see

% ls
myhost.sh
myhost.sh.po1483446
myhost.sh.pe1483446
myhost.sh.e1483446
myhost.sh.o1483446

The four additional files that were created are in the form scriptname.XX.jjjjjjj - where scriptname is the script you submitted, XX is 'po' (parallel output), 'pe' (parallel error), 'e' (error), or 'o' (output), and jjjjjjj is the job number (which is given when you submitted your job, in this case 1483446).

If everything goes as planned, the po, pe, and e jobs will be blank...

% cat myhost.sh.po1483446
% cat myhost.sh.pe1483446
% cat myhost.sh.e1483446

...and the .o file will show the hostname of the node that ran the job...

% cat myhost.sh.o1483446
mage03

So we can see that this job ran on host 'mage03'.

Monitoring Your Job

TODO - qstat and status

Getting Help

TODO - self-diagnosis and asking for help