Avogadro

Revision as of 14:26, 7 August 2021

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 using a terminal. Windows 10 users can use the PowerShell.

The first step si to open a tunnel. Within the DiSC internet this can be simply done as:

ssh -L 2000:192.168.16.253:22 account@192.168.9.15 -p 7000

or from outside the Department using

ssh -L 2000:192.168.16.253:22 account@147.162.63.10 -p 7000

where "account" is the user's account.

Then, in a different shell, login as:

ssh -p 2000 account@localhost

Through port 2000 users can also transfer files directly via the tunnel using the command scp.

Queues

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

• avogadro: max nodes 40, max walltime 336:00:00 (2 weeks)

Example SLURM file

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

#SBATCH --job-name=charmm
#SBATCH --ntasks 1
#SBATCH --cpus-per-task 1
#SBATCH --partition=avogadro
#SBATCH --account=avogadro
#SBATCH --time=100:00:00

commands to execute

where the parts in italic should be changed as appropriate.