DOCK 3.8 testing on C7 - Revision history

Buyan at 19:34, 22 June 2026

2026-06-22T19:34:57Z

← Older revision		Revision as of 19:34, 22 June 2026
Line 1:		Line 1:
	These are instructions to run the [[DOCK 3.8]] test on [[Cluster 7]].		These are instructions to run the [[DOCK 3.8]] test on [[Cluster 7]]. This is only a C7 quick test, not a full DOCK tutorial. For general DOCK 3.8 usage, see [[DOCK 3.8]] and [[SUBDOCK_DOCK3.8]].

	== 1. Log in and start screen ==		== 1. Log in and start screen ==
	Log in to [[Cluster 7]] first. The exact SSH command may depend on whether you are onsite, on VPN, or going through a portal/jump host. Once you are on C7, start a screen or tmux session so the job keeps running if your SSH disconnects.		Log in to [[Cluster 7]] first. The exact SSH command may depend on whether you are onsite, on VPN, or going through a portal/jump host. Once you are on C7, start a screen or tmux session so the job keeps running if your SSH disconnects.

Buyan: Buyan moved page DOCK 3.8 C7 to DOCK 3.8 testing on C7: testing page

2026-06-22T19:33:28Z

Buyan moved page DOCK 3.8 C7 to DOCK 3.8 testing on C7: testing page

← Older revision

Revision as of 19:33, 22 June 2026

Buyan at 18:48, 22 June 2026

2026-06-22T18:48:40Z

← Older revision		Revision as of 18:48, 22 June 2026
Line 65:		Line 65:

	export DOCKEXEC="${DOCK_INSTALL_PATH}/dock3/dock64"		export DOCKEXEC="${DOCK_INSTALL_PATH}/dock3/dock64"


			== 6. Run with SLURM ==

			C7 uses SLURM, not SGE.

			export USE_SLURM=true
			export USE_SGE=false
			mkdir -p output
			./test_subdock.sh

			Successful submission looks like:

			submitting 4 out of 4 jobs
			Submitted batch job <jobid>

			== 7. Check the job ==

			squeue -u $USER

			Check logs:

			ls output/logs
			less output/logs/1.out

			Success looks like:

			user=<your_username>
			starting DOCK vers=3.8
			finished!

			If the log shows another user or paths under /nfs/software/dock/..., you are looking at old copied output, not your run.

	[[Category:Buyan]]		[[Category:Buyan]]

Buyan at 18:48, 22 June 2026

2026-06-22T18:48:09Z

← Older revision		Revision as of 18:48, 22 June 2026
Line 2:		Line 2:

	== 1. Log in and start screen ==		== 1. Log in and start screen ==
			Log in to [[Cluster 7]] first. The exact SSH command may depend on whether you are onsite, on VPN, or going through a portal/jump host. Once you are on C7, start a screen or tmux session so the job keeps running if your SSH disconnects.
	Start a screen session so the job keeps running if your SSH disconnects:		Start a screen or tmux session so the job keeps running if your SSH disconnects:
			Screen:
	screen -S dock_test		screen -S dock_test
			Tmux alternative:
	~~Detach: Ctrl-a, then d~~		tmux new -s dock_test

	~~Reattach~~:

	~~screen~~ -r dock_test

	== 2. Make a working folder ==		== 2. Make a working folder ==

Buyan at 18:44, 22 June 2026

2026-06-22T18:44:43Z

@@ Line 1: / Line 1: @@
-These are instructions to follow on [[Cluster 7]] to run [[DOCK 3.8]].
+These are instructions to run the [[DOCK 3.8]] test on [[Cluster 7]].
   module load dock
   echo $DOCK_INSTALL_PATH
   echo $DOCKBASE
-# copy test data to my account
+== 4. Copy the test files ==
-  cp -r ${DOCK_INSTALL_PATH}/test/docking  test
   cd test
-After copying the test directory into your own workspace, edit test_subdock.sh so it uses the local copied directory.
+Remove old copied output. The shared test folder may already contain someone else's old results:
-Change this line:
   find test_ligs -name '*.db2.tgz' -exec realpath {} \; > ${DOCK_INSTALL_PATH}/test/docking/split_database_index
 to:
   find test_ligs -name '*.db2.tgz' -exec realpath {} \; > split_database_index
-Change these:
   export EXPORT_DEST="${DOCK_INSTALL_PATH}/test/docking/output"
   export INPUT_SOURCE="${DOCK_INSTALL_PATH}/test/docking/split_database_index"
   export DOCKFILES="${DOCK_INSTALL_PATH}/test/docking/dockfiles"
 to:
   export EXPORT_DEST="$(pwd)/output"
   export INPUT_SOURCE="$(pwd)/split_database_index"
   export DOCKFILES="$(pwd)/dockfiles"
 [[Category:Buyan]]

Buyan at 18:00, 22 June 2026

2026-06-22T18:00:17Z

← Older revision		Revision as of 18:00, 22 June 2026
Line 19:		Line 19:
	./test_subdock.sh		./test_subdock.sh

			After copying the test directory into your own workspace, edit test_subdock.sh so it uses the local copied directory.
			Change this line:
			find test_ligs -name '*.db2.tgz' -exec realpath {} \; > ${DOCK_INSTALL_PATH}/test/docking/split_database_index
			to:
			find test_ligs -name '*.db2.tgz' -exec realpath {} \; > split_database_index
			Change these:
			export EXPORT_DEST="${DOCK_INSTALL_PATH}/test/docking/output"
			export INPUT_SOURCE="${DOCK_INSTALL_PATH}/test/docking/split_database_index"
			export DOCKFILES="${DOCK_INSTALL_PATH}/test/docking/dockfiles"
			to:
			export EXPORT_DEST="$(pwd)/output"
			export INPUT_SOURCE="$(pwd)/split_database_index"
			export DOCKFILES="$(pwd)/dockfiles"

	[[Category:Buyan]]		[[Category:Buyan]]

Frodo: asdf

2026-06-16T21:40:53Z

asdf

← Older revision		Revision as of 21:40, 16 June 2026
Line 21:		Line 21:

	[[Category:Buyan]]		[[Category:Buyan]]
	~~[[Category:Work in progress 2026]]~~
	~~[[Category:John told me to do this but it is crazy]]~~

Frodo: asdf

2026-06-16T21:33:51Z

asdf

← Older revision		Revision as of 21:33, 16 June 2026
Line 18:		Line 18:
	# edit file to point to my own copy		# edit file to point to my own copy
	./test_subdock.sh		./test_subdock.sh


			[[Category:Buyan]]
			[[Category:Work in progress 2026]]
			[[Category:John told me to do this but it is crazy]]

Frodo: asdf

2026-06-16T21:19:18Z

asdf

← Older revision		Revision as of 21:19, 16 June 2026
Line 12:		Line 12:
	echo $DOCK_INSTALL_PATH		echo $DOCK_INSTALL_PATH
	echo $DOCKBASE		echo $DOCKBASE

			# copy test data to my account
			cp -r ${DOCK_INSTALL_PATH}/test/docking test
			cd test
			# edit file to point to my own copy
			./test_subdock.sh

Frodo: asdf

2026-06-16T21:08:32Z

asdf

New page

These are instructions to follow on [[Cluster 7]] to run [[DOCK 3.8]].

* step 1. log in to C7
* cd hdd02 # find a place to work
* mkdir docking # create an area for docking
* cd docking
* pwd
/nfs/home/xyz/hdd02/docking
* screen -S john # could also be tmux
# set up a docking environment on C7
module load dock
echo $DOCK_INSTALL_PATH
echo $DOCKBASE