To access ark cluster run the following command:

ssh ark10

Windows user: please read How can I SSH from Microsoft Windows?
When prompted for password use your TSRI password. Contact sargis@scripps.edu to request an account if needed.
If you are planning to use this often, consider setting up SSH without password. Here is how: run these commands from your local machine.

ssh-keygen -t rsa 
cp ~/.ssh/id_rsa.pub ~/.ssh/authorized_keys

Running Jobs Using PBS

There is plenty of documentation available on Portable Batch System so here we'll cover details relevant for ark cluster. First of all, pbs clients are running on all nodes but ark10, which runs pbs server. Second, /home folder from ark10 is mounted on all nodes under /home. /usr/local from ark10 is mounted on all nodes as /ark/local. Note that autofs does on-demand mounting so 'ls /ark' might not show local folders but, for instance, 'ls /ark/local' will.

Administrative Notes

Useful Links:

• PXE Server Setup
• Ganglia installation on Centos

Useful Commands:

for a in `cat hosts`; 
do echo $a; ssh $a "ssh-keygen; cd .ssh; wget www/~USER/authorized_keys"; done
for a in `cat hosts`; do echo $a; scp pbs_mom root@$a:/etc/init.d/pbs_mom; done
pdsh -w ssh:ark[01-120]
pdsh -w ssh:ark[01-100,102-107,109-120]

Further Readings:

• To Protect and Serve: Providing Data to Your Cluster and a link to Open Source Cluster Application Resources (OSCAR) in there. Since we already have PBS and Ganglia installed on ark, we don't need OSCAR yet. There is Cluster Command Control (C3) and System Installation Suite (SIS) distributed by OSCAR that seem very handy tools to have. Red Hat Global File System (GFS) seems interesting too.
• Preparing the TORQUE packages for the compute nodes.