SGE Cluster Docking: Difference between revisions

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  cp <somedir>/rec.pdb .        # copy or create rec.pdb
  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)
  cp <somedir>/xtal-lig.mol2 .  # copy or create xtal-lig.mol2 (or even xtal-lig.pdb)
  touch .only_spheres            # stop after grid generation
  startdockblaster5             # create spheres and grids                 
startdockblaster4             # create spheres and grids
                                # Check output for WARNING messages, correct as needed
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
  cp calibrate/INDOCK.1.A INDOCK # copy or create INDOCK
  mksdir2.csh 2 50              # create directories for fragment-like in ~50 chunks
  mksdir2.csh 2 50              # create directories for a fragment-like(2) docking run with 50 chunks
  cd run.2                      # chdir into run directory
  cd run.2                      # chdir into run.2 directory
  startdockbks3                 # submit database chunks to SGE cluster
  startdockbks3 .                # submit database chunks to SGE cluster
 




Revision as of 21:27, 27 February 2008

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)
startdockblaster5              # create spheres and grids                 
                               # Check output for WARNING messages, correct as needed
cp calibrate/INDOCK.1.A INDOCK # copy or create INDOCK
mksdir2.csh 2 50               # create directories for a fragment-like(2) docking run with 50 chunks
cd run.2                       # chdir into run.2 directory
startdockbks3 .                # submit database chunks to SGE cluster
Retrieved from "http://wiki.docking.org/index.php?title=SGE_Cluster_Docking&oldid=4303"