SGE Cluster Docking: Difference between revisions
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== SGE Cluster == | == SGE Cluster Information == | ||
* | *'sgehead.compbio.ucsf.edu' is the submit machine for the Sun Grid Engine (SGE) cluster. wilco is also authorized to submit jobs. | ||
'sgehead.compbio.ucsf.edu' is the submit | *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 == | |||
*sgestat: high level overview of cluster status | |||
*qsub: submit jobs<br> | |||
*qstat: check job status<br> | |||
*qdel: remove jobs<br> | |||
*qhost: check cluster status<br> | |||
*man sge_intro: start of manpage documentation<br> | |||
== 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) | |||
startdockblaster5 # create spheres and grids | |||
# Check output for WARNING messages, correct as needed | |||
* | * Setting up a docking run | ||
cp calibrate/INDOCK.1.A INDOCK # copy or create INDOCK | |||
md4db.csh bysubset 2 100 # create directories for docking run with 100 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 | |||
* Everything else | |||
See [[MUD - Michael's Utilities for Docking]] for how to submit, check, and analyse the docking run. | |||
For information on which ZINC | |||
[[Category:Internal]] | |||
[[Category:Tutorials]] | |||
[[Category:Cluster]] |
Latest revision as of 21:36, 27 February 2014
SGE Cluster Information
- 'sgehead.compbio.ucsf.edu' is the submit machine for the Sun Grid Engine (SGE) cluster. wilco is also authorized to submit jobs.
- 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
- sgestat: high level overview of cluster status
- 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) startdockblaster5 # create spheres and grids # Check output for WARNING messages, correct as needed
- Setting up a docking run
cp calibrate/INDOCK.1.A INDOCK # copy or create INDOCK md4db.csh bysubset 2 100 # create directories for docking run with 100 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
- Everything else
See MUD - Michael's Utilities for Docking for how to submit, check, and analyse the docking run.
For information on which ZINC