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autodock

About

AutoDock is a suite of automated docking tools, autogrid and autodock. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.

Version and Availability

▶ Display Softenv Keys for autodock all clusters
Machine Version Softenv Key
eric 4.2 +autodock-4.2-gcc-4.3.2
eric 4.3 +autodock-4.3-gcc-4.3.2
qb 4.2 +autodock-4.2-gcc-4.3.2
qb 4.3 +autodock-4.3-gcc-4.3.2
oliver 4.2 +autodock-4.2-gcc-4.3.2
oliver 4.3 +autodock-4.3-gcc-4.3.2
louie 4.2 +autodock-4.2-gcc-4.3.2
louie 4.3 +autodock-4.3-gcc-4.3.2
poseidon 4.2 +autodock-4.2-gcc-4.3.2
poseidon 4.3 +autodock-4.3-gcc-4.3.2
painter 4.2 +autodock-4.2-gcc-4.3.2
painter 4.3 +autodock-4.3-gcc-4.3.2
supermike2 4.2.3 +autodock-4.2.3-Intel-13.0.0
▶ Softenv FAQ?

The information here is applicable to LSU HPC and LONI systems.

Softenv

SoftEnv is a utility that is supposed to help users manage complex user environments with potentially conflicting application versions and libraries.

System Default Path

When a user logs in, the system /etc/profile or /etc/csh.cshrc (depending on login shell, and mirrored from csm:/cfmroot/etc/profile) calls /usr/local/packages/softenv-1.6.2/bin/use.softenv.sh to set up the default path via the SoftEnv database.

SoftEnv looks for a user's ~/.soft file and updates the variables and paths accordingly.

Viewing Available Packages

Using the softenv command, a user may view the list of available packages. Currently, it can not be ensured that the packages shown are actually available or working on the particular machine. Every attempt is made to present an identical environment on all of the LONI clusters, but sometimes this is not the case.

Example,

$ softenv
These are the macros available:
*   @default
These are the keywords explicitly available:
+amber-8                       Applications: 'Amber', version: 8 Amber is a
+apache-ant-1.6.5              Ant, Java based XML make system version: 1.6.
+charm-5.9                     Applications: 'Charm++', version: 5.9 Charm++
+default                       this is the default environment...nukes /etc/
+essl-4.2                      Libraries: 'ESSL', version: 4.2 ESSL is a sta
+gaussian-03                   Applications: 'Gaussian', version: 03 Gaussia
....
Listing of Available Packages

See Packages Available via SoftEnv on LSU HPC and LONI.

For a more accurate, up to date list, use the softenv command.

Caveats

Currently there are some caveats to using this tool.

  1. packages might be out of sync between what is listed and what is actually available
  2. resoft and soft utilities are not; to update the environment for now, log out and login after modifying the ~/.soft file.
Availability

softenv is available on all LSU HPC and LONI clusters to all users in both interactive login sessions (i.e., just logging into the machine) and the batch environment created by the PBS job scheduler on Linux clusters and by loadleveler on AIX clusters..

Packages Availability

This information can be viewed using the softenv command:

% softenv
Managing Environment with SoftEnv

The file ~/.soft in the user's home directory is where the different packages are managed. Add the +keyword into your .soft file. For instance, ff one wants to add the Amber Molecular Dynamics package into their environment, the end of the .soft file should look like this:

+amber-8

@default

To update the environment after modifying this file, one simply uses the resoft command:

% resoft

Usage

Please be aware that AutoDock and AutoGrid are a serial codes. It should be run in a single queue which will use one processor core. Running in any other queue will cause cores to be idle, but the job will be charged for all cores.

Running AutoDock Simulations

To successfully run a autodock simulation, you first need to run a autogrid simulation to generate a map around receptor atoms around which potentials are to be computed.

▶ Open Example?
 #!/bin/bash
 
#PBS -A your_allocation
#PBS -q single
#    Note: a single queue is not present on Queen Bee,
#    use workq or checkpt, but you will be charged for all cores.
#PBS -M your_email
# Change ppn to match cluster (4, 8 or 16) if no single queue.
#PBS -l nodes=1:ppn=1
#PBS -l walltime=06:00:00
#PBS -V
#PBS -o AutoGrid_test.out
#PBS -e AutoGrid_test.err
#PBS -N autogridtest
 
export EXEC=autogrid4 
export INPUT=hsg1.gpf
export OUTPUT=hsg1.glg
export WORK_DIR=$PBS_O_WORKDIR
 
cd $WORK_DIR
 
$EXEC -p $INPUT -l $OUTPUT

Submit your script using qsub.

▶ QSub FAQ?

Portable Batch System: qsub

qsub

All HPC@LSU clusters use the Portable Batch System (PBS) for production processing. Jobs are submitted to PBS using the qsub command. A PBS job file is basically a shell script which also contains directives for PBS.

Usage
$ qsub job_script

Where job_script is the name of the file containing the script.

PBS Directives

PBS directives take the form:

#PBS -X value

Where X is one of many single letter options, and value is the desired setting. All PBS directives must appear before any active shell statement.

Example Job Script
 #!/bin/bash
 #
 # Use "workq" as the job queue, and specify the allocation code.
 #
 #PBS -q workq
 #PBS -A your_allocation_code
 # 
 # Assuming you want to run 16 processes, and each node supports 4 processes, 
 # you need to ask for a total of 4 nodes. The number of processes per node 
 # will vary from machine to machine, so double-check that your have the right 
 # values before submitting the job.
 #
 #PBS -l nodes=4:ppn=4
 # 
 # Set the maximum wall-clock time. In this case, 10 minutes.
 #
 #PBS -l walltime=00:10:00
 # 
 # Specify the name of a file which will receive all standard output,
 # and merge standard error with standard output.
 #
 #PBS -o /scratch/myName/parallel/output
 #PBS -j oe
 # 
 # Give the job a name so it can be easily tracked with qstat.
 #
 #PBS -N MyParJob
 #
 # That is it for PBS instructions. The rest of the file is a shell script.
 # 
 # PLEASE ADOPT THE EXECUTION SCHEME USED HERE IN YOUR OWN PBS SCRIPTS:
 #
 #   1. Copy the necessary files from your home directory to your scratch directory.
 #   2. Execute in your scratch directory.
 #   3. Copy any necessary files back to your home directory.

 # Let's mark the time things get started.

 date

 # Set some handy environment variables.

 export HOME_DIR=/home/$USER/parallel
 export WORK_DIR=/scratch/myName/parallel
 
 # Set a variable that will be used to tell MPI how many processes will be run.
 # This makes sure MPI gets the same information provided to PBS above.

 export NPROCS=`wc -l $PBS_NODEFILE |gawk '//{print $1}'`

 # Copy the files, jump to WORK_DIR, and execute! The program is named "hydro".

 cp $HOME_DIR/hydro $WORK_DIR
 cd $WORK_DIR
 mpirun -machinefile $PBS_NODEFILE -np $NPROCS $WORK_DIR/hydro

 # Mark the time processing ends.

 date
 
 # And we're out'a here!

 exit 0

If you have successfully run the autogrid simulation to completion, you can run the autodock simulation

▶ Open Example?
 #!/bin/bash
 
#PBS -A your_allocation
#PBS -q single
#    Note: a single queue is not present on Queen Bee,
#    use workq or checkpt, but you will be charged for all cores.
#PBS -M your_email
# Change ppn to match cluster (4, 8 or 16) if no single queue.
#PBS -l nodes=1:ppn=1
#PBS -l walltime=06:00:00
#PBS -V
#PBS -o AutoDock_test.out
#PBS -e AutoDock_test.err
#PBS -N autogridtest
 
export EXEC=autodock4 
export INPUT=ind.dpf
export OUTPUT=ind.dlg
export WORK_DIR=$PBS_O_WORKDIR
 
cd $WORK_DIR
 
$EXEC -p $INPUT -l $OUTPUT

Submit your script using qsub.

▶ QSub FAQ?

Portable Batch System: qsub

qsub

All HPC@LSU clusters use the Portable Batch System (PBS) for production processing. Jobs are submitted to PBS using the qsub command. A PBS job file is basically a shell script which also contains directives for PBS.

Usage
$ qsub job_script

Where job_script is the name of the file containing the script.

PBS Directives

PBS directives take the form:

#PBS -X value

Where X is one of many single letter options, and value is the desired setting. All PBS directives must appear before any active shell statement.

Example Job Script
 #!/bin/bash
 #
 # Use "workq" as the job queue, and specify the allocation code.
 #
 #PBS -q workq
 #PBS -A your_allocation_code
 # 
 # Assuming you want to run 16 processes, and each node supports 4 processes, 
 # you need to ask for a total of 4 nodes. The number of processes per node 
 # will vary from machine to machine, so double-check that your have the right 
 # values before submitting the job.
 #
 #PBS -l nodes=4:ppn=4
 # 
 # Set the maximum wall-clock time. In this case, 10 minutes.
 #
 #PBS -l walltime=00:10:00
 # 
 # Specify the name of a file which will receive all standard output,
 # and merge standard error with standard output.
 #
 #PBS -o /scratch/myName/parallel/output
 #PBS -j oe
 # 
 # Give the job a name so it can be easily tracked with qstat.
 #
 #PBS -N MyParJob
 #
 # That is it for PBS instructions. The rest of the file is a shell script.
 # 
 # PLEASE ADOPT THE EXECUTION SCHEME USED HERE IN YOUR OWN PBS SCRIPTS:
 #
 #   1. Copy the necessary files from your home directory to your scratch directory.
 #   2. Execute in your scratch directory.
 #   3. Copy any necessary files back to your home directory.

 # Let's mark the time things get started.

 date

 # Set some handy environment variables.

 export HOME_DIR=/home/$USER/parallel
 export WORK_DIR=/scratch/myName/parallel
 
 # Set a variable that will be used to tell MPI how many processes will be run.
 # This makes sure MPI gets the same information provided to PBS above.

 export NPROCS=`wc -l $PBS_NODEFILE |gawk '//{print $1}'`

 # Copy the files, jump to WORK_DIR, and execute! The program is named "hydro".

 cp $HOME_DIR/hydro $WORK_DIR
 cd $WORK_DIR
 mpirun -machinefile $PBS_NODEFILE -np $NPROCS $WORK_DIR/hydro

 # Mark the time processing ends.

 date
 
 # And we're out'a here!

 exit 0

Note:To run a autodock calculations successfully, your autogrid job must complete without errors. If you are comfortable with submit scripts, you can use the following script to submit both the autogrid and autodock job using PBS Job Chains and Dependencies

▶ PBS Job Chains and Dependencies FAQ?

PBS Job Chains

Quite often, a single simulation requires multiple long runs which must be processed in sequence. One method for creating a sequence of batch jobs is to execute the qsub to submit its successor. We strongly discourage recursive, or "self-submitting," scripts since for some jobs, chaining isn't an option. When your job hits the time limit, the batch system kills them and the command to submit a subsequent job is not processed.

PBS allows users to move the logic for chaining from the script and into the scheduler. This is done with a command line option:

$ qsub -W depend=afterok:<jobid> <job_script>

This tells the job scheduler that the script being submitted should not start until jobid completes successfully. The following conditions are supported:

afterok:<jobid>
Job is scheduled if the job <jobid> exits without errors or is successfully completed.
afternotok:<jobid>
Job is scheduled if job <jobid> exited with errors.
afterany:<jobid>
Job is scheduled if the job <jobid> exits with or without errors.

One method to simplify this process is to write multiple batch scripts, job1.pbs, job2.pbs, job3.pbs etc and submit them using the following script:

#!/bin/bash
 
FIRST=$(qsub job1.pbs)
echo $FIRST
SECOND=$(qsub -W depend=afterany:$FIRST job2.pbs)
echo $SECOND
THIRD=$(qsub -W depend=afterany:$SECOND job3.pbs)
echo $THIRD

Modify the script according to number of job chained jobs required. The Job <$FIRST> will be placed in queue while the jobs <$SECOND> and <$THIRD> will be placed in queue with the "Not Queued" (NQ) flag in Batch Hold. When <$FIRST> is completed, the NQ flag will be replaced with the "Queued" (Q) flag and will be moved to the active queue.

A few words of caution: If you list the dependency as "afterok"/"afternotok" and your job exits with/without errors then your subsequent jobs will be killed due to "dependency not met".

Resources

Last modified: March 08 2013 11:13:46.