Kimik: Difference between revisions

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go back to [[Main_Page]], [[Computational Resources]], [[Clusters]], [[Local Clusters]]
go back to [[Main_Page]], [[Computational Resources]], [[Clusters]], [[Local Clusters]]


== Kimik Information ==
Kimik is a cluster (currently) containing 94 nodes.


It is of general use of the Institute (computational groups and some experimentalists too).


Kimik is a (by now) 137 nodes's cluster.[[Kimik's Quads]]
The disk is shared with [[Kimik2]]


* '''Queues/jobs:'''
* '''Queues/jobs:'''


Each user can use up to '''15''' slots for jobs. There are 4 types of queues in it.  
Each user has a quota of slots for jobs. The cluster is divided into three queues as follows...  


nanYar.short  
nanYar.short  
           queue with 2 nodes that allows you to run jobs for only 1 hour.
           Two single processor machines (nodes 001 and 002).
          Allows all job types, but has a 1 hour time limit.
 
nanYar     
nanYar     
           queue from node kimik003.iciq.es to kimik045.iciq.es. For running mostly adf jobs (adf has preferences       
           Older single processor machines from nodes 003 to 045.  
           because licenses are for kimik001 to kimik45 and kimik050) although you can run others one.
          Works with all job types.
           Currently disabled due to problems vs. the SIRIUS server.
 
nanYar.l   
nanYar.l   
           queue from node kimik046.iciq.es to kimik094.iciq.es. Send all kind of (installed) jobs, so for 
           Single processor machines from nodes 046 to 094.
          Gaussian or others please use these queue instead of nanYar (unless there are many free nodes on 
          Works with all jobs types.
          nanYar queue).
 


nanYar.quad
          For "Quad Core 2" nodes.
          Right now, mainly for running Gaussian jobs, as you cannot get a good perfomance with Jaguar jobs.
* '''Quota/file server space'''
* '''Quota/file server space'''


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== Kimik "How to ..." ==
== Kimik "How to ..." ==
* '''How to connect to kimik'''
From a linux PC:
    ssh -X kimik.iciq.es
from outside ICIQ look at [[Connecting from Outside]]


* '''How to submit calculations'''
* '''How to submit calculations'''
       Use the qs command. If you type the command “qs” you get a help menu that shows you how to use the  
       Use the qs command.
       command.
      If you type the command “qs” you get a help menu that shows you how to use the  
       The name of the job in the queue system is that of the input file starting from the end (up to 10
       command and some specific tips for submission of gaussian jobs.
      letters).
 
       With qs you choose from the four available queues in the cluster:
       qs numproc queue typejob nameinput.in
       short queue (s): two machines: “kimik 001” and “kimik 002” in which jobs can last up to one hour, after     
   
       which the system kills the jobs.
       With qs you specify the number of nodes you want, which one of the four available queues to access
       normal queue (n): nodes 003 to 045. No time restrictions. Currently disabled.
       (short queue (s),long-queue (l)), which program to use (adf,  
       long-queue (l): nodes 046 to 094. No time restrictions.
       gaussian, etc.), and then the input file name (usually with the *.in extension)
       quad-queue (q): nodes 095 to 140. No time restrictions.
 
* '''How to view the status of your jobs'''
       Use the command qstat to give a list of jobs running on the system.
       For more information on the jobs, use the -f key.
       For information on a specific user, use the key -u ''username''.


* '''How to kill jobs'''
* '''How to kill jobs'''
       Use the command qdel and the job identifier.
       Use the command qdel and the job identifier.
* '''How to check the state of a queue'''
      Use qstat command or go to the webpage: kimik.iciq.es/ganglia


* '''How to check the quota'''
* '''How to check the quota'''
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* '''How to print from kimik'''
* '''How to print from kimik'''
       Laserjet printer: command lpr. The queues are:
       You can run the next command from command line:
      bn1c: prints on one page (1 side, vertically)
             
      bn1c2: prints two pages on one side horizontally (booklet style)
                  lpr -PLEXMARK file_to_print
      bn1ch: prints one page on one side horizontally
      bn2c1: prints on two pages (both sides) vertically 
      bn2c2: prints two pages on both sides (horizontally, booklet style)
      bn2ch: prints one page on both sides horizontally
      Hp printer: command lpr. The queue is called “petita”
      Hp color printer: command lpr. The queue is called “color”

Latest revision as of 13:21, 15 September 2010

go back to Main_Page, Computational Resources, Clusters, Local Clusters


Kimik is a cluster (currently) containing 94 nodes.

It is of general use of the Institute (computational groups and some experimentalists too).

The disk is shared with Kimik2

  • Queues/jobs:

Each user has a quota of slots for jobs. The cluster is divided into three queues as follows...

nanYar.short 

         Two single processor machines (nodes 001 and 002).
         Allows all job types, but has a 1 hour time limit.

nanYar 

         Older single processor machines from nodes 003 to 045. 
         Works with all job types.
         Currently disabled due to problems vs. the SIRIUS server.

nanYar.l 

         Single processor machines from nodes 046 to 094.
         Works with all jobs types.


  • Quota/file server space

The $HOME of each user has a quota of 23 GB.

There is softquota, that will announce by a message that you are close to exceed the quota limit.

After reaching the maximum, the user will not be able to write in the $HOME until deleting/compressing some files. That also affects the calculations, if there is not enough space to write the output, they will unfortunately die.

Kimik "How to ..."[edit]

  • How to connect to kimik

From a linux PC: 

    ssh -X kimik.iciq.es

from outside ICIQ look at Connecting from Outside

  • How to submit calculations
     Use the qs command.
     If you type the command “qs” you get a help menu that shows you how to use the 
     command and some specific tips for submission of gaussian jobs.
 
     qs numproc queue typejob nameinput.in
   
     With qs you specify the number of nodes you want, which one of the four available queues to access 
     (short queue (s),long-queue (l)), which program to use (adf, 
     gaussian, etc.), and then the input file name (usually with the *.in extension)
  • How to view the status of your jobs
     Use the command qstat to give a list of jobs running on the system.
     For more information on the jobs, use the -f key.
     For information on a specific user, use the key -u username.
  • How to kill jobs
     Use the command qdel and the job identifier.
  • How to check the quota

You can check the disk space you are using by looking at how to check the disk space used

  • How to print from kimik
     You can run the next command from command line:
              
                  lpr -PLEXMARK file_to_print
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