SUBDOCK on C7: Difference between revisions

Revision as of 20:16, 22 June 2026

These are C7 specific notes for running SUBDOCK with DOCK 3.8 on Cluster 7. For the full SUBDOCK reference, see SUBDOCK_DOCK3.8.

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

C7 uses SLURM. Do not use SGE on C7.

SUBDOCK needs four main paths:

EXPORT_DEST
INPUT_SOURCE
DOCKFILES
DOCKEXEC

On C7, after `module load dock`, the DOCK executable is usually:

${DOCK_INSTALL_PATH}/dock3/dock64

Do not write output into the shared DOCK installation. Use a directory in your own workspace instead.

While jobs are running: squeue -u $USER

For one job:

squeue -j <jobid>

After jobs finish, check the logs in the output directory.

@@ Line 9: / Line 9: @@
 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:
   ${DOCK_INSTALL_PATH}/dock3/dock64
-== Required SUBDOCK variables ==
+== C7 path warning ==
- export EXPOST_DEST=/path/to/output
+Do not write output into the shared DOCK installation.
- export INPUT_SOURCE=/path/to/split_database_index
+Use a directory in your own workspace instead.
-  export DOCKFILES=/path/to/dockfiles
- export DOCKEXEC=${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]]