Avogadro

Revision as of 12:07, 19 November 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:

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 scp command.

Troubleshootng

In some Linux distributions, the first attempt to open the ssh tunnel may fail with the following message:

Unable to negotiate with 147.162.63.10 port 7000: no matching key exchange method found. Their offer: diffie-hellman-group1.sh1

to solve such an issue, open (or create) the file

~/.ssh/config

and then add to the file the following lines

Host 147.162.63.10
      KexAlgorithms +diffie-hellman-group1-sha1

Please, counsult www.openssh.com/legacy.html for more information about this issue.

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=name
#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.