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

Revision as of 00:45, 11 July 2007

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
Retrieved from "http://wiki.docking.org/index.php?title=SGE_Cluster_Docking&oldid=4300"