SUBDOCK on C7 - Revision history

Buyan: Buyan moved page SUBDOCK ON C7 to SUBDOCK on C7

2026-06-22T21:15:59Z

← Older revision

Revision as of 21:15, 22 June 2026

2026-06-22T21:15:04Z

← Older revision

Revision as of 21:15, 22 June 2026

2026-06-22T21:10:57Z

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-These are C7 specific notes for running [[SUBDOCK_DOCK3.8|SUBDOCK]] with [[DOCK 3.8]] on [[Cluster 7]].
+SUBDOCK on C7
-== What SUBDOCK does ==
+This page is for C7-specific notes on [[SUBDOCK_DOCK3.8|SUBDOCK]]. For the full SUBDOCK documentation, see [[SUBDOCK_DOCK3.8]].
-== Main C7 Rule ==
+== C7 setup ==
-C7 uses SLURM. Do not use SGE on C7.
 == Required variables ==
-# EXPORT_DEST is where results and logs go.
+SUBDOCK needs:
-On C7, after `module load dock`, the DOCK executable is usually:
+ export EXPORT_DEST=/path/to/output
-  ${DOCK_INSTALL_PATH}/dock3/dock64
+ export INPUT_SOURCE=/path/to/split_database_index
-== C7 path warning ==
+Use paths in your own workspace. Do not write output into the shared DOCK install, e.g. avoid:
-== Checking jobs ==
+ ${DOCK_INSTALL_PATH}/test/docking/output
-While jobs are running:
+== Run ==
-For one job:
+Example:
   squeue -j <jobid>
-After jobs finish, check the logs in the output directory.
 == Related pages ==
@@ Line 43: / Line 81: @@
 * [[DOCK 3.8]]
 [[Category:DOCK_3.8]]
 [[Category:Cluster 7]]

2026-06-22T20:16:43Z

← Older revision		Revision as of 20:16, 22 June 2026
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	C7 uses SLURM. Do not use SGE on C7.		C7 uses SLURM. Do not use SGE on C7.

	== ~~Load Dock on C7~~ ==		== Required variables ==
	~~module load dock~~		SUBDOCK needs four main paths:
	~~echo $DOCK_INSTALL_PATH~~		EXPORT_DEST
	~~echo $DOCKBASE~~		INPUT_SOURCE
			DOCKFILES
			DOCKEXEC

	~~The~~ DOCK executable is usually:		# EXPORT_DEST is where results and logs go.
			# INPUT_SOURCE is the file listing the ligand database files to dock.
			# DOCKFILES is the directory containing the prepared docking files.
			# DOCKEXEC is the DOCK executable.

			On C7, after `module load dock`, the DOCK executable is usually:
	${DOCK_INSTALL_PATH}/dock3/dock64		${DOCK_INSTALL_PATH}/dock3/dock64

	== ~~Required SUBDOCK variables~~ ==		== C7 path warning ==
	~~export EXPOST_DEST=/path/to/~~output		Do not write output into the shared DOCK installation.
	~~export INPUT_SOURCE~~=~~/path/to/split_database_index~~		Use a directory in your own workspace instead.
	~~export DOCKFILES~~=~~/path/to/dockfiles~~
	~~export DOCKEXEC=${DOCK_INSTALL_PATH}/dock3/dock64~~		== Checking jobs ==

			While jobs are running:
			squeue -u $USER

			For one job:
			squeue -j <jobid>
			After jobs finish, check the logs in the output directory.

			== Related pages ==

			* [[SUBDOCK_DOCK3.8]]
			* [[DOCK_3.8_testing_on_C7]]
			* [[DOCK 3.8]]

			[[Category:Buyan]]
			[[Category:DOCK_3.8]]
			[[Category:Cluster 7]]

2026-06-22T20:12:05Z

← Older revision		Revision as of 20:12, 22 June 2026
Line 1:		Line 1:
	notes for ~~c7 users:~~		These are C7 specific notes for running [[SUBDOCK_DOCK3.8\|SUBDOCK]] with [[DOCK 3.8]] on [[Cluster 7]].
	on [[Cluster 7]], use path /~~nfs~~/~~software~~/~~dock~~/~~versions~~/~~dock385~~/~~DOCK3.8~~/		For the full SUBDOCK reference, see [[SUBDOCK_DOCK3.8]].

			== What SUBDOCK does ==
			SUBDOCK submits many DOCK jobs to a scheduler.
			On C7, the scheduler is SLURM, so SUBDOCK submits jobs with sbatch.

			== Main C7 Rule ==
			C7 uses SLURM. Do not use SGE on C7.

			== Load Dock on C7 ==
			module load dock
			echo $DOCK_INSTALL_PATH
			echo $DOCKBASE

			The DOCK executable is usually:
			${DOCK_INSTALL_PATH}/dock3/dock64

			== Required SUBDOCK variables ==
			export EXPOST_DEST=/path/to/output
			export INPUT_SOURCE=/path/to/split_database_index
			export DOCKFILES=/path/to/dockfiles
			export DOCKEXEC=${DOCK_INSTALL_PATH}/dock3/dock64

2026-06-22T19:52:24Z

Created page with "notes for c7 users: on Cluster 7, use path /nfs/software/dock/versions/dock385/DOCK3.8/"

New page

notes for c7 users:
on [[Cluster 7]], use path /nfs/software/dock/versions/dock385/DOCK3.8/