SGE Cluster Docking

SGE Cluster Information

• 'sgehead.compbio.ucsf.edu' is the submit machine for the Sun Grid Engine (SGE) cluster.
• 'sgemaster.compbio.ucsf.edu' is the admin machine for the SGE cluster.
• There are around 250 cluster nodes availabe as of July, 2007, named like 'node-1-1' through 'node-3-36'.

SGE Commands

• qsub: submit jobs
  
• qstat: check job status
  
• qdel: remove jobs
  
• qhost: check cluster status
  
• man sge_intro: start of manpage documentation
  

Typical Docking Workflow

ssh sgehead.compbio.ucsf.edu   # ssh to SGE submit machine
mkdir example                  # make docking directory
cd example                     # change to docking directory
cp <somedir>/rec.pdb .         # copy or create rec.pdb
cp <somedir>/xtal-lig.mol2 .   # copy or create xtal-lig.mol2 (or even xtal-lig.pdb)
touch .only_spheres            # stop after grid generation
startdockblaster4              # create spheres and grids
tail -f stdout                 # follow grid preparation as it happens (control-C to terminate)
cat stderr                     # check for any error messages during grid peparation
cp calibrate/INDOCK.1.A INDOCK # copy or create INDOCK
mksdir2.csh 2 50               # create directories for fragment-like in ~50 chunks
cd run.2                       # chdir into run directory
startdockbks3                  # submit database chunks to SGE cluster