Log In

To log in, you have to type:  ssh ae-csmb@roc.csd.abdn.ac.uk

where ae-csmb is your login.

 

Submit a Job

To submit a job, you type:  qsub example.sh

where example.sh is a shell script where you specify the program that you want to run, and the queue to which you want to submit the job. An example can be found in this zip archive. Please see next section regarding the existing queues on the cluster.

Notice that programs should always be submitted to the queue system, and should NOT be started directly from any of the cluster nodes.

 

Queues on the Cluster

There are four different queues to which you can submit your job. They all have time limits (except the long-term one), so that if your job hits that time limit the system will terminate the job. Hence, make sure that you write the output of your program from time to time to avoid losing everything in case your job running time estimation was not correct and the system terminates it.

The queues are named as follows:

  1hr.q
1day.q
1week.q
long-term.q

with the names indicating the time limit of each queue. If your job is queued on 1hr.q, it will have priority overall queues below it. In the same way, the queue 1day.q has priority over the queues below it, and so on.

Each node has 12GB RAM and 16 slots. If the number of jobs exceeds the number of slots, jobs of a lower priority will still be shown as running but the system will nice them down to +20 (-20 is the highest priority in unix and +20 the lowest). If the number of jobs exceeds the number of slots and all jobs have the same priority, the last submitted ones will be queued.

 

How to Check Jobs Currently Running or Queued

If you type:   qstat

you will get a list of your jobs currently running or queued. Also you will be able to see the job identity number assigned by the queuing system to each job.

If you type:  qstat-all

you will get a list of all jobs, also those of other users, currently running and being queued.

 

How to Kill a Job

If after submitting a job you notice a mistake, you can kill the job by typing: qdel job_id

where job_id is the job identity number that you see in the list that you get when you type qstat. 

If you want to delete all of your jobs at once, type:  qdel  -u ae-csmb

where ae-csmb must be replaced by your username.

 

Example Codes

Download the more detailed instructions of how to write a shell script and your code to submit a job to the cluster. Moreover, the file example_codes.zip contains a folder with very simple example codes and bash shells that you can use as templates to submit your jobs to the cluster.