SGE Cluster Docking: Difference between revisions
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<tr><td>touch .only_spheres</td><td>#stop after grid generation</td></tr> | <tr><td>touch .only_spheres</td><td>#stop after grid generation</td></tr> | ||
<tr><td>startdockblaster4</td><td>#create spheres and grids</td></tr> | <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>cp calibrate/INDOCK.1.A INDOCK</td><td>#copy or create INDOCK</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> | <tr><td>mksdir2.csh 2 50</td><td>#create directories for fragment-like in ~50 chunks</td></tr> |
Revision as of 23:28, 3 July 2007
SGE Cluster
- Head Node
'sgehead.compbio.ucsf.edu' is the submit machines name.
- SGE Commands
qsub: submit jobs
qstat: check job status
qdel: remove jobs
qhost: check cluster status
man sge_intro: start of manpage documentation
- 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 |
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 |