Navigating Viking

When you log in, you will be directed to one of several login nodes. These allow Linux command line access to the system, which is necessary for the editing programs, compiling and running the code. Usage of the login nodes is shared amongst all who are logged in. These systems should not be used for running your code, other than for development and very short test runs.   

Access to the job/batch submission system is through the login nodes. When a submitted job executes, processors on the compute nodes are exclusively made available for the purposes of running the job.   

For this exercise lets look at Viking and what is available and setup an area to run our jobs on Viking.

Exercise: Navigating Viking.

List the directories within your home area on Viking.  What do you see?

[abc123@login1(viking) ~] ls
bin  Chemistry  Desktop  examples  Experiments  intel  jobs  logs  tmp
[abc123@login1(viking) ~] ls -l
total 296
drwxr-xr-x 2 abs4 csrv        4096 Jun 24 09:39 bin
drwxr-xr-x 3 abs4 csrv        4096 Jun  6 09:23 Chemistry
drwxr-sr-x 2 abs4 elecclust   4096 Mar 11 10:53 Desktop
drwxr-xr-x 3 abs4 csrv        4096 Jun 30 12:21 examples
drwxr-xr-x 5 abs4 csrv        4096 May 23 11:34 Experiments
drwxr-xr-x 3 abs4 csrv        4096 Aug 14 12:26 intel
drwxr-sr-x 3 abs4 elecclust   4096 Aug 15 12:49 jobs
drwxr-xr-x 2 abs4 csrv      266240 Aug 15 13:48 logs
drwxr-xr-x 3 abs4 csrv        4096 Aug 14 14:50 tmp
-bash-4.1$ 

Your home directory is backed up, but there are strict file and size limits in this area.

To see what space you have available run the myquota command

[abc123@login1(viking) ~]$ /opt/site/york/bin/myquota 
Scratch quota:
Disk quotas for usr abc123 (uid 10506):
     Filesystem    used   quota   limit   grace   files   quota   limit   grace
    /mnt/lustre  268.6G      3T    3.1T       - 2157882       0       0       -

Home quota:
Disk quotas for user abc123 (uid 10506): 
     Filesystem  blocks   quota   limit   grace   files   quota   limit   grace
storage:/export/users
                2155420  52428800 78643200            1654  100000  150000        

Here two are are displayed.  Your home area and your scratch area.

Home Directory

This is the directory you start off in after logging on to one of the login nodes. It is NOT usable for large data-sets or frequent access files and no should jobs be run from here.

Lustre Fast Filesystem

This is the scratch directory in your home directory, and potentially any group data stores that you have access to. It is available to the compute nodes, and is the recommended place for your jobs to read and store data.

Here is a breakdown on the different areas and what they provide.

Any data you need to keep long term should be moved to a backed up storage area. Further details on storage options can be found here.

Let us now navigate to the scratch area and create a new directory to run workloads from.

[abc123@login1(viking) ~]$ pwd
/home/userfs/e/ejb573
[abc123@login1(viking) ~]$ cd scratch
[abc123@login1(viking) ~]$ pwd
/mnt/lustre/users/abc123/scratch
[abc123@login1(viking) ~]$ mkdir hpcintro
[abc123@login1(viking) ~]$ cd test
[abc123@login1(viking) ~]$ pwd
/mnt/lustre/users/abc123/scratch/hpcintro

We now have a new directory in scratch.