SUBDOCK on C7
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These are C7 specific notes for running SUBDOCK with DOCK 3.8 on Cluster 7. 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.
Required variables
SUBDOCK needs four main paths:
EXPORT_DEST INPUT_SOURCE DOCKFILES DOCKEXEC
- 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
C7 path warning
Do not write output into the shared DOCK installation. Use a directory in your own workspace instead.
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.