SUBDOCK on C7: Difference between revisions

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C7 uses SLURM. Do not use SGE on C7.  
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
  ${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]]

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.

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
  1. EXPORT_DEST is where results and logs go.
  2. INPUT_SOURCE is the file listing the ligand database files to dock.
  3. DOCKFILES is the directory containing the prepared docking files.
  4. 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.

Related pages

Retrieved from "http://wiki.docking.org/index.php?title=SUBDOCK_on_C7&oldid=17332"