SGE Cluster Docking: Difference between revisions

Revision as of 00:15, 4 July 2007

'sgehead.compbio.ucsf.edu' is the submit machines name.

qsub: submit jobs
qstat: check job status
qdel: remove jobs
qhost: check cluster status
man sge_intro: start of manpage documentation

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

@@ Line 23: / Line 23: @@
 <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>
-<tr><td>cat stderr</td><td>#check for any error messages</td></tr>
+<tr><td>cat stderr</td><td>#check for any error messages during grid peparation</td></tr>
 <tr><td>cp calibrate/INDOCK.1.A INDOCK</td><td>#copy or create INDOCK</td></tr>
 <tr><td>mksdir2.csh 2 50</td><td>#create directories for fragment-like in ~50 chunks</td></tr>