Avogadro

Description

Avogadro is the largest, but oldest, cluster in the C3P facility. It is equipped with the following hardware/software:

• 71 nodes with 2 x CPU Intel Woodcrest Dual Core 2.6 GHz (4 cores), 2 x HD SAS 72 GB, 8 GB RAM, Infiniband, OS Red Hat Enterprise Linux WS release 4
• 9 nodes with 2 x CPU Intel Woodcrest Quad Core 2.6 GHz (8 cores), 2 x HD SAS 72 GB, 16 GB RAM, Infiniband, OS Red Hat Enterprise Linux WS release 4

for a total of 80 nodes, 356 cores.

Access

• Linux and Mac OS users can login within the DiSC internet connection using a terminal with the command:

ssh account@192.168.9.15

or from outside the Department using

ssh -p 50000 account@147.162.63.10

where "account" is the user's account.

• Windows users can use an interface program to the ssh service, e.g. Putty.

Queues

The queue manager is PBS and the following queues are available:

• avogadro: max nodes 40, max walltime 2 weeks (336 hours)
• avogadro-test: max nodes 1, max walltime 10 min
• avogadro-long: max 10 nodes, max walltime 1500:00:00 (ca. 2 months). This queue is to be used strictly to run jobs that do not allow checkpointing of the status of the calculation. This is considered an exceptional case, thus penalties are applied: i) a maximum of total 2 jobs can run at the same time on this queue, and ii) the initial priority is set to -1440 minutes, meaning that with respect to the normal queues, jobs on the avogadro-long queue shall wait for an additional day.

Example PBS file

A typical PBS input file script will be as follow (see the Support page for more help):

#!/bin/sh --login
#PBS -N jobname
#PBS -A account
#PBS -q queue
#PBS -l nodes=n
#PBS -w time in hh:mm:ss format

commands to execute

where the parts in italic should be changed as appropriate.