SGE Cluster Docking: Difference between revisions
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== SGE Cluster Information == | == SGE Cluster Information == | ||
*'sgehead.compbio.ucsf.edu' is the submit machine for the Sun Grid Engine (SGE) cluster. | *'sgehead.compbio.ucsf.edu' is the submit machine for the Sun Grid Engine (SGE) cluster. wilco and bks148 are are also authorized to submit jobs. | ||
*'sgemaster.compbio.ucsf.edu' is the admin machine for the SGE cluster. | *'sgemaster.compbio.ucsf.edu' is the admin machine for the SGE cluster. | ||
*There are around 250 cluster nodes | *There are around 250 cluster nodes providing 600 total cores to run jobs in the sge queue as of May, 2009, named like 'node-1-1' through 'node-3-36' where the first number is the rack # and the second is the slot # in that rack. | ||
== SGE Commands == | == SGE Commands == |
Revision as of 19:44, 8 May 2009
SGE Cluster Information
- 'sgehead.compbio.ucsf.edu' is the submit machine for the Sun Grid Engine (SGE) cluster. wilco and bks148 are are also authorized to submit jobs.
- 'sgemaster.compbio.ucsf.edu' is the admin machine for the SGE cluster.
- There are around 250 cluster nodes providing 600 total cores to run jobs in the sge queue as of May, 2009, named like 'node-1-1' through 'node-3-36' where the first number is the rack # and the second is the slot # in that rack.
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
- Generate spheres and grids - See Using MakeDOCK for more information, including how to prepare the receptor and ligand
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) startdockblaster4 # create spheres and grids # Check output for WARNING messages, correct as needed
- Submit docking run
cp calibrate/INDOCK.1.A INDOCK # copy or create INDOCK mksdir2.csh 2 50 # create directories for docking run with 50 chunks # 2 indicates we want the fragment-like subset of ZINC (See http://zinc.docking.org/subset1) cd run.2 # chdir into run.2 directory startdockbks3 . # submit database chunks to SGE cluster
For information on which ZINC