Gibbs

From C3P
(Difference between revisions)
Jump to: navigation, search
 
(6 intermediate revisions by one user not shown)
Line 4: Line 4:
  
 
* '''6 nodes''' with 2 x CPU Intel Xeon Octa Core (''16 cores''), 128 GB of RAM, 2 x 300 GB HD SAS (10 krpm), OS Red Hat Enterprise Linux Server release 6.3
 
* '''6 nodes''' with 2 x CPU Intel Xeon Octa Core (''16 cores''), 128 GB of RAM, 2 x 300 GB HD SAS (10 krpm), OS Red Hat Enterprise Linux Server release 6.3
−
* '''4 nodes''' with 1 x CPU Intel Xeon 10 Core with hyperthreading (''20 cores''), 128 GB of RAM, 2 x 300 GB HD SAS (10 krpm), OS Scientific Linux release 6.6
+
* '''4 nodes''' with 2 x CPU Intel Xeon 10 Core (''20 cores''), 128 GB of RAM, 2 x 300 GB HD SAS (10 krpm), OS Scientific Linux release 6.6
−
for a total of 10 nodes, 176 cores.
+
* '''4 nodes''' with 1 x CPU Intel Xeon 24 Core, 256 GB of RAM, 2 x 300 GB HD SAS (10 krpm), OS Scientific Linux release 6.6
 +
for a total of 14 nodes, 272 cores.
  
  
 
== 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. Within the DiSC internet this can be simply done as:
  
−
: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 [[SLURM]] and the following queues are available:
 +
 
 +
* '''gibs''': max nodes 4, max walltime 336:00:00 (2 weeks)
  
−
* '''gibbs''': max nodes 4, max walltime 336:00:00 (2 weeks)
 
−
* '''gibbs-long''': max 1 node, 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 1 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 ==
+
== 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 gibbs
+
  <nowiki>#</nowiki>SBATCH --partition=gibbs
−
  <nowiki>#</nowiki>PBS -l nodes=''n''
+
  <nowiki>#</nowiki>SBATCH --account=gibbs
−
  <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 14:47, 5 February 2026

Contents

Description

Gibbs is equipped with the following software/hardware:

  • 6 nodes with 2 x CPU Intel Xeon Octa Core (16 cores), 128 GB of RAM, 2 x 300 GB HD SAS (10 krpm), OS Red Hat Enterprise Linux Server release 6.3
  • 4 nodes with 2 x CPU Intel Xeon 10 Core (20 cores), 128 GB of RAM, 2 x 300 GB HD SAS (10 krpm), OS Scientific Linux release 6.6
  • 4 nodes with 1 x CPU Intel Xeon 24 Core, 256 GB of RAM, 2 x 300 GB HD SAS (10 krpm), OS Scientific Linux release 6.6

for a total of 14 nodes, 272 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@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:

  • gibs: max nodes 4, 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=gibbs
#SBATCH --account=gibbs
#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=Gibbs&oldid=306"
Personal tools
Namespaces
Variants
Actions
Navigation
Events
Toolbox