SGE Cluster Docking: Difference between revisions

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== SGE Cluster ==
== SGE Cluster Information ==


* Head Node
*'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 machines name.
*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>


* SGE Commands
== Typical Docking Workflow ==
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>


*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


* Docking Workflow
* Setting up a docking run
<table>
cp calibrate/INDOCK.1.A INDOCK # copy or create INDOCK
<tr><td>ssh sgehead.compbio.ucsf.edu</td><td>#ssh to SGE submit machine</td></tr>
md4db.csh bysubset 2 100      # create directories for docking run with 100 chunks
<tr><td>mkdir example</td><td>#make docking directory</td></tr>
                                # 2 indicates we want the fragment-like subset of ZINC (See http://zinc.docking.org/subset1)
<tr><td>cd example</td><td>#change to docking directory</td></tr>
cd run.2                       # chdir into run.2 directory
<tr><td>cp <somedir>/rec.pdb .</td><td>#copy or create rec.pdb</td></tr>
 
<tr><td>cp <somedir>/xtal-lig.mol2 .</td><td>#copy or create xtal-lig.mol2 (or even xtal-lig.pdb)</td></tr>
* Everything else
<tr><td>touch .only_spheres</td><td>#stop after grid generation</td></tr>
See [[MUD - Michael's Utilities for Docking]] for how to submit, check, and analyse the docking run.
<tr><td>startdockblaster4</td><td>#create spheres and grids</td></tr>
 
<tr><td>tail -f stdout</td><td>#follow grid preparation as it happens (control-C to terminate)</td></tr>
For information on which ZINC
<tr><td>cat stderr</td><td>#check for any error messages</td></tr>
 
<tr><td>cp calibrate/INDOCK.1.A INDOCK</td><td>#copy or create INDOCK</td></tr>
[[Category:Internal]]
<tr><td>mksdir2.csh 2 50</td><td>#create directories for fragment-like in ~50 chunks</td></tr>
[[Category:Tutorials]]
<tr><td>cd run.2</td><td>#chdir into run directory</td></tr>
[[Category:Cluster]]
<tr><td>startdockbks3</td><td>#submit database chunks to SGE cluster</td></tr>
</table>

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

Retrieved from "http://wiki.docking.org/index.php?title=SGE_Cluster_Docking&oldid=6321"