Difference between revisions of "Cluster 3"

Jump to: navigation, search
m (Setting up a run)
m (Setting up a run)
Line 9: Line 9:
==Setting up a run==
==Setting up a run==
Scripts can be obtained from [http://shoichetlab.compbio.ucsf.edu/~kolb Peter] in ~kolb/Scripts/Cluster.
Scripts can be obtained from [http://shoichetlab.compbio.ucsf.edu/~kolb Peter] and are located in ~kolb/Scripts/Cluster.
* copy files with <tt>transfer.data2chef.sh</tt>
* copy files with <tt>transfer.data2chef.sh</tt>
* unzip them with <tt>receive.datafromrage.sh</tt>
* unzip them with <tt>receive.datafromrage.sh</tt>

Revision as of 09:27, 7 August 2008

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 ibm32=true                   #-- 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.
  • currently (07/24/08) Pascal and Joshua are working to make ZINC visible on chef.