Connecting to a HPC resource

If using SSH keys, once the keys are created and uploaded on the PDC interface, entering the cluster is as simple as:

$ ssh -Y <username>@dardel.pdc.kth.se

Which should get you into the PDC supercomputer. The -Y flag is used to be able to open graphical windows on the supercomputer, e.g. to visualise images. This will work only if you have a running local X server (if you are on Linux/WSL, you most likely do). Alternatively, you may choose to use Kerberos as an authentication method. To do that, you first need to ask for a Kerberos ticket:

$ kinit -f <username>@NADA.PDC.KTH.SE

After that, the SSH command looks like the following:

$ ssh -o GSSAPIAuthentication=yes -Y <username>@dardel.pdc.kth.se

More information about Kerberos can be found at this address.

Type-Along

Let us check on which node we ended up. The name of the machine can be checked with the hostname command:

$ hostname

We can get a sense of the size of Dardel by using the sinfo command:

$ sinfo -s
PARTITION AVAIL  TIMELIMIT   NODES(A/I/O/T) NODELIST
gpu          up 1-00:00:00        49/9/4/62 nid[002792-002853]
main         up 1-00:00:00  604/256/112/972 nid[001012-001531,001756-001816,001818-001819,001821-001896,001898-002007,002009-002023,002552-002567,002588-002759]
scania       up 4-00:00:00    22/187/15/224 nid[001532-001755]
scania-hf    up 4-00:00:00          0/3/1/4 nid[000011-000014]
memory       up 7-00:00:00        34/8/0/42 nid[000101-000118,001772-001779,002552-002567]
shared       up 7-00:00:00        27/5/0/32 nid[001000-001011,002568-002587]
long         up 7-00:00:00        76/4/0/80 nid[001800-001819,002588-002647]
eggnog       up 7-00:00:00          4/0/0/4 nid[002536-002539]
supernova    up 14-00:00:0         5/6/5/16 nid[001817,001820,001897,002008,002540-002551]

E.g. the main partition has 972 nodes, each containing 128 cores.

A general sense of the amount of work load can be gained with the squeue command, which shows all the jobs (running, queued):

$ squeue