Difference between revisions of "Cluster 3"

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m (Setting up a run)
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* major difference: more than one queue. The queue is selected based on the CPU time requirements.
 
* major difference: more than one queue. The queue is selected based on the CPU time requirements.
 
  #$ -l mem_free=1G                  #-- submits on nodes with enough free memory
 
  #$ -l mem_free=1G                  #-- submits on nodes with enough free memory
  #$ -l ibm32=true                  #-- SGE resources (CPU type)
+
  #$ -l arch=lx24-amd64            #-- SGE resources (CPU type)
 
  #$ -l panqb3=1G,scratch=1G        #-- SGE resources (home and scratch disks)
 
  #$ -l panqb3=1G,scratch=1G        #-- SGE resources (home and scratch disks)
 
  #$ -l h_rt=24:00:00                #-- runtime limit (see above; this requests 24 hours)
 
  #$ -l h_rt=24:00:00                #-- runtime limit (see above; this requests 24 hours)
 
* additionally one can make use of the /scratch partition which is available on most of the nodes.
 
* additionally one can make use of the /scratch partition which is available on most of the nodes.
* currently (07/24/08) Pascal and Joshua are working to make [http://zinc.docking.org ZINC] visible on chef.
+
* ZINC is visible through at /bks/raid6, so you don't have to copy db files over.

Revision as of 15:59, 19 August 2009

Information about the cluster (specs, queues, flags, ...) can be found in the QB3 cluster wiki. It is password-protected and will be accessible once you have obtained an account.

Obtaining an account

The individual steps are also described in this document.

Setting up a run

Scripts can be obtained from Peter and are located in ~kolb/Scripts/Cluster.

  • copy files with transfer.data2chef.sh
  • unzip them with receive.datafromrage.sh
  • it is possible to use the standard docking scripts (after copying them over).
  • major difference: more than one queue. The queue is selected based on the CPU time requirements.
#$ -l mem_free=1G                  #-- submits on nodes with enough free memory
#$ -l  arch=lx24-amd64             #-- SGE resources (CPU type)
#$ -l panqb3=1G,scratch=1G         #-- SGE resources (home and scratch disks)
#$ -l h_rt=24:00:00                #-- runtime limit (see above; this requests 24 hours)
  • additionally one can make use of the /scratch partition which is available on most of the nodes.
  • ZINC is visible through at /bks/raid6, so you don't have to copy db files over.