SUBDOCK on C7

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!

Related pages

• SUBDOCK_DOCK3.8
• DOCK_3.8_testing_on_C7
• DOCK 3.8