SUBDOCK on C7: Difference between revisions
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Latest revision as of 21:15, 22 June 2026
SUBDOCK on C7
This page is for C7-specific notes on SUBDOCK. For the full SUBDOCK documentation, see SUBDOCK_DOCK3.8.
C7 setup
Load DOCK:
module load dock echo $DOCK_INSTALL_PATH echo $DOCKBASE
SUBDOCK is inside the DOCK install:
${DOCK_INSTALL_PATH}/SUBDOCK/subdock.bash
${DOCK_INSTALL_PATH}/SUBDOCK/rundock.bash
`subdock.bash` expects `rundock.bash` to be in the same directory.
Scheduler
C7 runs this workflow through SLURM (`sbatch`). Set the controller explicitly:
export USE_SLURM=true export USE_SGE=false export USE_PARALLEL=false export USE_CHARITY=false
If more than one controller is enabled, SUBDOCK exits with:
cannot select more than one job controller!
Required variables
SUBDOCK needs:
export EXPORT_DEST=/path/to/output
export INPUT_SOURCE=/path/to/split_database_index
export DOCKFILES=/path/to/dockfiles
export DOCKEXEC=${DOCK_INSTALL_PATH}/dock3/dock64
Use paths in your own workspace. Do not write output into the shared DOCK install, e.g. avoid:
${DOCK_INSTALL_PATH}/test/docking/output
Run
Example:
mkdir -p output
export EXPORT_DEST="$(pwd)/output"
export INPUT_SOURCE="$(pwd)/split_database_index"
export DOCKFILES="$(pwd)/dockfiles"
export DOCKEXEC="${DOCK_INSTALL_PATH}/dock3/dock64"
bash ${DOCK_INSTALL_PATH}/SUBDOCK/subdock.bash
Successful submission looks like:
submitting N out of N jobs Submitted batch job <jobid>
Check jobs
squeue -u $USER squeue -j <jobid>
`sacct` may not work on C7 if SLURM accounting is disabled. Check logs after completion:
ls output/logs less output/logs/1.out
Success usually includes:
starting DOCK vers=3.8 finished!