Initial Setup

Workshop training account on AVIDD

For the purpose of this workshop, we have already created a training account (hpctrnXX) for you on AVIDD. We request you use the training account, provided to you, through out this workshop.
Note: See To establish your own AVIDD account for more information on obtaining your own account.

SSH onto AVIDD

Use the ssh command on a Unix based workstation/laptop or an SSH Client on Microsoft Windows to login to the AVIDD cluster.

Exercise: Do this!

 $ ssh -x <your username>@avidd-b.iu.edu

 [agopu@peart agopu]$ ssh -x hpctrn01@avidd-b.iu.edu
 The authenticity of host 'avidd-b.uits.indiana.edu (129.79.228.232)' can't be established.
 RSA key fingerprint is 9c:63:4f:a0:90:95:5b:e3:76:c3:17:eb:96:9b:f3:87.
 Are you sure you want to continue connecting (yes/no)? yes
 hpctrn01@avidd-b.uits.indiana.edu's password:

 [hpctrn01@bh2 hpctrn01]$

Set email address in ~/.forward file if you have not done that yet. (Warning: You should use a valid email id! Failing to do so will result in inability to check status of your jobs.)

Exercise: Do this!
```
 [hpctrn01@bh2 hpctrn01]$ echo "myfavoriteemailid@hotmail.com" > ~/.forward 
```
Note: Detailed information about SSHing onto AVIDD from Microsoft Window/Unix machines is available in the Login to AVIDD using SSH section of the Working on AVIDD document. Use of the -x flag to disable X11 forwarding from the AVIDD head-node is also explained in that section. If you have not done so, we strongly recommend you go through that document before proceeding forward in this workshop.

Grab Interactive Compute Nodes using `qsub -I`

We will be using interactive nodes through out this workshop to run MPI jobs. Request two compute nodes (2 processors on each node) for 6 hours from PBS.
Exercise: Do this!
```
 [agopu@bh2 agopu]$ qsub -I -l nodes=2:ppn=2 -l walltime=6:00:00
```
You can expect to see a message like this:
```
 qsub: waiting for job 281988.aviss.avidd.iu.edu to start
 qsub: job 281988.aviss.avidd.iu.edu ready

 [agopu@bc56 agopu]$ 
```
If you want to know what nodes have been allocated to your job, then you can find that information in a file pointed to, by $PBS_NODEFILE.
```
 [agopu@bc81 agopu]$ cat $PBS_NODEFILE
 bc81
 bc53
 bc81
 bc53 
```
Note: Later in the workshop when you run example MPI code, you'll realize that each process' rank is determined by the order of the nodes in $PBS_NODEFILE. We will return to this later in the session.

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