Cluster 3

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.

• obtain a general QB3 kerberos account from one of the QB3@UCSF WLAN account facilitators.
• once you have such an account, mail the information (user name, name of PI) to Joshua Baker-LePain (jlb at salilab dot org), the cluster administrator.

Setting up a run

Scripts from Peter Kolb 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.