SGE Cluster Docking - Revision history

Frodo at 21:36, 27 February 2014

2014-02-27T21:36:55Z

← Older revision		Revision as of 21:36, 27 February 2014
Line 37:		Line 37:
	[[Category:Tutorials]]		[[Category:Tutorials]]
	[[Category:Cluster]]		[[Category:Cluster]]
	~~[[Category:Unix]]~~

Therese: 16 revisions

2012-10-08T20:32:23Z

16 revisions

← Older revision	Revision as of 20:32, 8 October 2012
(No difference)

Mysinger at 01:58, 5 December 2009

2009-12-05T01:58:23Z

← Older revision		Revision as of 01:58, 5 December 2009
Line 35:		Line 35:

	[[Category:Internal]]		[[Category:Internal]]
			[[Category:Tutorials]]
	[[Category:Cluster]]		[[Category:Cluster]]
	[[Category:Unix]]		[[Category:Unix]]

Mysinger: Update to modern workflow

2009-12-05T01:54:22Z

Update to modern workflow

← Older revision		Revision as of 01:54, 5 December 2009
Line 2:		Line 2:

	*'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 machine for the Sun Grid Engine (SGE) cluster. wilco is also authorized to submit jobs.
	*'sgemaster.compbio.ucsf.edu' is the admin machine for the SGE cluster.
	*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.		*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 ==		== SGE Commands ==
			*sgestat: high level overview of cluster status
	*qsub: submit jobs<br>		*qsub: submit jobs<br>
	*qstat: check job status<br>		*qstat: check job status<br>
Line 20:		Line 20:
	cp <somedir>/rec.pdb . # copy or create rec.pdb		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)		cp <somedir>/xtal-lig.mol2 . # copy or create xtal-lig.mol2 (or even xtal-lig.pdb)
	~~startdockblaster4~~ # create spheres and grids		startdockblaster5 # create spheres and grids
	# Check output for WARNING messages, correct as needed		# Check output for WARNING messages, correct as needed

	* ~~Submit~~ docking run		* Setting up a docking run
	cp calibrate/INDOCK.1.A INDOCK # copy or create INDOCK		cp calibrate/INDOCK.1.A INDOCK # copy or create INDOCK
	md4db.csh bysubset 2 50 # create directories for docking run with 50 chunks		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)		# 2 indicates we want the fragment-like subset of ZINC (See http://zinc.docking.org/subset1)
	cd run.2 # chdir into run.2 directory		cd run.2 # chdir into run.2 directory
	~~startdockbks3 . # submit database chunks to SGE cluster~~

			* Everything else
			See [[MUD - Michael's Utilities for Docking]] for how to submit, check, and analyse the docking run.

	For information on which ZINC		For information on which ZINC

Mysinger: /* Typical Docking Workflow */

2009-09-25T21:15:23Z

Typical Docking Workflow

← Older revision		Revision as of 21:15, 25 September 2009
Line 25:		Line 25:
	* Submit docking run		* Submit docking run
	cp calibrate/INDOCK.1.A INDOCK # copy or create INDOCK		cp calibrate/INDOCK.1.A INDOCK # copy or create INDOCK
	md4db.csh 2 50 # create directories for docking run with 50 chunks		md4db.csh bysubset 2 50 # create directories for docking run with 50 chunks
	# 2 indicates we want the fragment-like subset of ZINC (See http://zinc.docking.org/subset1)		# 2 indicates we want the fragment-like subset of ZINC (See http://zinc.docking.org/subset1)
	cd run.2 # chdir into run.2 directory		cd run.2 # chdir into run.2 directory

Frodo: /* SGE Cluster Information */

2009-08-06T20:10:09Z

SGE Cluster Information

← Older revision		Revision as of 20:10, 6 August 2009
Line 1:		Line 1:
	== SGE Cluster Information ==		== SGE Cluster Information ==

	*'sgehead.compbio.ucsf.edu' is the submit machine for the Sun Grid Engine (SGE) cluster. wilco ~~and bks148 are are~~ also authorized to submit jobs.		*'sgehead.compbio.ucsf.edu' is the submit machine for the Sun Grid Engine (SGE) cluster. wilco is also authorized to submit jobs.
	*'sgemaster.compbio.ucsf.edu' is the admin machine for the SGE cluster.		*'sgemaster.compbio.ucsf.edu' is the admin machine for the SGE cluster.
	*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.		*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.

Mysinger: /* Typical Docking Workflow */

2009-06-22T19:01:34Z

Typical Docking Workflow

← Older revision		Revision as of 19:01, 22 June 2009
Line 25:		Line 25:
	* Submit docking run		* Submit docking run
	cp calibrate/INDOCK.1.A INDOCK # copy or create INDOCK		cp calibrate/INDOCK.1.A INDOCK # copy or create INDOCK
	~~mksdir2~~.csh 2 50 # create directories for docking run with 50 chunks		md4db.csh 2 50 # create directories for docking run with 50 chunks
	# 2 indicates we want the fragment-like subset of ZINC (See http://zinc.docking.org/subset1)		# 2 indicates we want the fragment-like subset of ZINC (See http://zinc.docking.org/subset1)
	cd run.2 # chdir into run.2 directory		cd run.2 # chdir into run.2 directory

Frodo: /* SGE Cluster Information */

2009-05-08T19:44:48Z

SGE Cluster Information

← Older revision		Revision as of 19:44, 8 May 2009
Line 1:		Line 1:
	== SGE Cluster Information ==		== SGE Cluster Information ==

	*'sgehead.compbio.ucsf.edu' is the submit machine for the Sun Grid Engine (SGE) cluster.		*'sgehead.compbio.ucsf.edu' is the submit machine for the Sun Grid Engine (SGE) cluster. wilco and bks148 are are also authorized to submit jobs.
	*'sgemaster.compbio.ucsf.edu' is the admin machine for the 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'.		*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 ==		== SGE Commands ==

Mysinger: /* Typical Docking Workflow */

2009-03-13T20:45:57Z

Typical Docking Workflow

← Older revision		Revision as of 20:45, 13 March 2009
Line 20:		Line 20:
	cp <somedir>/rec.pdb . # copy or create rec.pdb		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)		cp <somedir>/xtal-lig.mol2 . # copy or create xtal-lig.mol2 (or even xtal-lig.pdb)
	~~startdockblaster5~~ # create spheres and grids		startdockblaster4 # create spheres and grids
	# Check output for WARNING messages, correct as needed		# Check output for WARNING messages, correct as needed

Mysinger at 21:42, 27 February 2008

2008-02-27T21:42:16Z

← Older revision		Revision as of 21:42, 27 February 2008
Line 25:		Line 25:
	* Submit docking run		* Submit docking run
	cp calibrate/INDOCK.1.A INDOCK # copy or create INDOCK		cp calibrate/INDOCK.1.A INDOCK # copy or create INDOCK
	mksdir2.csh 2 50 # create directories for a fragment-like(2) ~~docking run with 50 chunks~~		mksdir2.csh 2 50 # create directories for docking run with 50 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		cd run.2 # chdir into run.2 directory
	startdockbks3 . # submit database chunks to SGE cluster		startdockbks3 . # submit database chunks to SGE cluster


			For information on which ZINC

	[[Category:Internal]]		[[Category:Internal]]
	[[Category:Cluster]]		[[Category:Cluster]]
	[[Category:Unix]]		[[Category:Unix]]