The example below (classical computation of pi using
numerical integration) shows steps you need to run a job in parallel
on the cluster. Please follow exactly. This example works as of
11/11/09.
You can also try to use documentation at
COS research computing website
amd
COE cluster website
for more information.
You need to have two Unix terminals open (Cygwin from Windows
will work). I will assume you have two terminals open: BLACK and RED.
Your username below will be your ONID username unless you already
have a cluster account.
- (BLACK) (ONE TIME ONLY FOR NEW USERS) Log in to the 64-submit node of the cluster
ssh username@submit64.eecs.oregonstate.edu
and change your password: use
htpasswd -n username
This will prompt for a new password (twice) and then print their user-name and a
password hash (ie msander:6c9orYURMJ2sk).
Copy that line and send an email to Clif Johnson cjohnson@science.oregonstate.edu so he can help to change it for you.
Log out. (Ctrl-D or exit)
- (BLACK) Log in to the 64-bit part of the cluster
ssh username@submit64.eecs.oregonstate.edu
username:ala0oFXfKSG/E
- (BLACK) Set-up environment
(You should include this line in your .cshrc file)
source /usr/local/apps/sge/settings.csh
Your .cshrc file is the one you should have in your home directory on the cluster.
Now either type the line above or just
source .cshrc
(I am assuming you created the file .cshrc before).
- (BLACK) Create a separate folder for this project: mydirpi
mkdir mydirpi
cd mydirpi
- (RED) Get the code and the
submission script, you can save them to a local directory you are working with.
- (RED) Copy the files to the cluster account and to that folder,
scp mypi.f username@submit64.eecs.oregonstate.edu:mydirpi
scp mypi_submit username@submit64.eecs.oregonstate.edu:mydirpi
- (BLACK) Compile (and link) your example:
mpif77 -o mypi mypi.f
- Understand your submission script ...
more mypi_submit
In particular, find the queue to which you are submiitting ... which
is em64t. Another one to try is amd64-low. Other queues are loaded with people
running big jobs so you will likely not get on.
- (BLACK) Submit your job
qsub mypi_submit
- (BLACK) Check your status:
qstat | grep yourname
- (BLACK) Check results: should be in the file ...
cat mypi_job.log
and they should look like those
If you want to find out more about how to submit, or delete jobs form the queue,
i.e. about qsub, qdel, you can type
man qsub
man qdel
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