DOCK 3.8 testing on C7

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These are instructions to run the DOCK 3.8 test on Cluster 7. This is only a C7 quick test, not a full DOCK tutorial. For general DOCK 3.8 usage, see DOCK 3.8 and SUBDOCK_DOCK3.8.

1. Log in and start screen

Log in to Cluster 7 first. The exact SSH command may depend on whether you are onsite, on VPN, or going through a portal/jump host. Once you are on C7, start a screen or tmux session so the job keeps running if your SSH disconnects. Start a screen or tmux session so the job keeps running if your SSH disconnects: Screen: 

screen -S dock_test

Tmux alternative: 

tmux new -s dock_test

2. Make a working folder

Use your own writable space, not the shared DOCK install directory.

Example: 

cd /nfs/home/xyz/hdd02
mkdir -p docking
cd docking

3. Load DOCK

module load dock

Check the DOCK paths: 

echo $DOCK_INSTALL_PATH
echo $DOCKBASE

4. Copy the test files

cp -r ${DOCK_INSTALL_PATH}/test/docking test
cd test

Remove old copied output. The shared test folder may already contain someone else's old results: 

rm -rf output
rm -f split_database_index

5. Edit test_subdock.sh

The copied test_subdock.sh may still point back to the shared DOCK install. Edit it so it writes to your local test folder.

Change: 

find test_ligs -name '*.db2.tgz' -exec realpath {} \; > ${DOCK_INSTALL_PATH}/test/docking/split_database_index

to: 

find test_ligs -name '*.db2.tgz' -exec realpath {} \; > split_database_index

Change: 

export EXPORT_DEST="${DOCK_INSTALL_PATH}/test/docking/output"
export INPUT_SOURCE="${DOCK_INSTALL_PATH}/test/docking/split_database_index"
export DOCKFILES="${DOCK_INSTALL_PATH}/test/docking/dockfiles"

to: 

export EXPORT_DEST="$(pwd)/output"
export INPUT_SOURCE="$(pwd)/split_database_index"
export DOCKFILES="$(pwd)/dockfiles"

Keep: 

export DOCKEXEC="${DOCK_INSTALL_PATH}/dock3/dock64"


6. Run with SLURM

C7 uses SLURM, not SGE. 

export USE_SLURM=true
export USE_SGE=false
mkdir -p output
./test_subdock.sh

Successful submission looks like: 

submitting 4 out of 4 jobs
Submitted batch job <jobid>

7. Check the job

squeue -u $USER

Check logs: 

ls output/logs
less output/logs/1.out

Success looks like: 

user=<your_username>
starting DOCK vers=3.8
finished!

If the log shows another user or paths under /nfs/software/dock/..., you are looking at old copied output, not your run.

Retrieved from "http://wiki.docking.org/index.php?title=DOCK_3.8_testing_on_C7&oldid=17329"