Avogadro

From C3P
(Difference between revisions)
Jump to: navigation, search
 
(10 intermediate revisions by one user not shown)
Line 12: Line 12:
 
== Access ==
 
== Access ==
  
−
* Linux and Mac OS users can login within the DiSC internet connection using a terminal with the command:
+
* Linux and Mac OS users can login using a terminal. Windows 10 users can use the PowerShell.
  
−
ssh account@192.168.9.15
+
The first step si to open a tunnel:
  
−
:or from outside the Department using
+
  ssh -L 2000:192.168.16.253:22 account@147.162.63.10
−
 
+
−
  ssh -p 50000 account@147.162.63.10
+
  
 
:where "account" is the user's account.
 
:where "account" is the user's account.
  
−
* Windows users can use an interface program to the ssh service, e.g. [http://www.putty.org/ Putty].
+
 
 +
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 http://www.openssh.com/legacy.html for more information about this issue.
  
  
 
== Queues ==
 
== Queues ==
  
−
The queue manager is [[PBS]] and the following queues are available:
+
The queue manager is [[Support|SLURM]] and the following queues are available:
  
−
* '''avogadro''': max nodes 40, max walltime 2 weeks (336 hours)
+
* '''avogadro''': max nodes 40, max walltime 336:00:00 (2 weeks)
−
* '''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. Users will be warned if will make [[good behaviour|improper]] use of this queue, .
+
  
  
−
== Example PBS file ==
+
== Example SLURM file ==
  
−
A typical [[PBS]] input file script will be as follow (see the [[Support]] page for more help):
+
A typical SLURM script will be as follow (see the [[Support]] page for more help):
  
−
  <nowiki>#</nowiki>!/bin/sh --login
+
  <nowiki>#</nowiki>SBATCH --job-name=''name''
−
  <nowiki>#</nowiki>PBS -N ''jobname''
+
  <nowiki>#</nowiki>SBATCH --ntasks=''1''
−
  <nowiki>#</nowiki>PBS -A ''account''
+
  <nowiki>#</nowiki>SBATCH --cpus-per-task=''1''
−
  <nowiki>#</nowiki>PBS -q ''queue''
+
  <nowiki>#</nowiki>SBATCH --partition=avogadro
−
  <nowiki>#</nowiki>PBS -l nodes=''n''
+
  <nowiki>#</nowiki>SBATCH --account=avogadro
−
  <nowiki>#</nowiki>PBS -w ''time in hh:mm:ss format''
+
  <nowiki>#</nowiki>SBATCH --time=''100:00:00''
 
   
 
   
 
  ''commands to execute''
 
  ''commands to execute''
  
 
where the parts in ''italic'' should be changed as appropriate.
 
where the parts in ''italic'' should be changed as appropriate.

Latest revision as of 14:48, 5 February 2026

Contents

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
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 http://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.

Retrieved from "https://wwwdisc.chimica.unipd.it/c3p-wiki/index.php?title=Avogadro&oldid=307"
Personal tools
Namespaces
Variants
Actions
Navigation
Events
Toolbox