Overview

The main website for Dock is http://dock.compbio.ucsf.edu

We have version 6.5 at the moment.

Install Directory

Executables are located at:

 
/sw/dock/6.5/gnu/bin 
/sw/dock/6.5/gnu.acml/bin   
/sw/dock/6.5/gnu.ompi/bin

gnu ==> compiled with gnu compiler
gnu.acml ==> compiled using gnu compilers and included acml libraries
gnu.ompi ==> compiled using openMPI

Usage

module load dock/6.6.gnu
OR
module load dock/6.5.gnu
module load dock/6.5.gnu.acml
module load dock/6.5.ompi

Dock 6.5 Compile Configuration

dock6.5-gnu

Installation Notes

http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Installation

 
mkdir  /sw/dock/6.5 
mkdir src
cd /sw/dock/6.5/src
cp /data1/dock.6.5_source.tar.gz  .
tar -zxvf dock.6.5_source.tar.gz
/sw/dock/6.5/src/dock6/install
make distclean

>>>>>>>>>>>>
 ./configure gnu
The requested configuration file was found.
The DOCK configuration file has been created.

more config.h
# DOCK configuration file for GNU compilers.
# This configuration file can be used on many platforms:
#  Linux, Macintosh OS X, Windows with Cygwin, etc.
# If g77 is not available then change FC below to gfortran or g95.

# CC is the C compiler
# CXX is the C++ compiler
# CFLAGS is the flags for the C and C++ compilers
# FC is the Fortran compiler
# FFLAGS is the flags for the Fortran compiler
# LIBS is the flags for the linker
# LINK_WITHOUT_FORTRAN_MAIN is the flag for linking without Fortran's main
# LOAD is the command to invoke the linker
# DOCK_SUFFIX is the suffix for the dock executable

CC=          gcc
CXX=         g++
CFLAGS=      -O2
FC=          gfortran   #Changed this from g77 to gfortran
FFLAGS=      -O2 -fno-automatic -fno-second-underscore
LIBS=        -lm -lpthread
LINK_WITHOUT_FORTRAN_MAIN=
LOAD=        g++
DOCK_SUFFIX=

# Macro definitions for NAB
# AR is the library archiver
# LEX is the lexical analyzer generator
# OCFLAGS is the flags for the C compilers with high optimization
# RANLIB is the library index generator
AR=          ar rv
LEX=         flex
OCFLAGS=     -O3 -D_ANSI_SOURCE
RANLIB=      ranlib
DOCKHOME=/sw/dock/6.5/gnu      #Changed this to /sw/dock/6.5/gnu
# Created at Thu Aug 11 13:44:42 EST 2011 via ./configure gnu

>>>>>>>>>>>


check: config.h
make all 2>&1 | tee log.configure.dock_gnu.txt

mv /sw/dock/6.5/src/dock6 /sw/dock/6.5/
cd /sw/dock/6.5/
mv dock6 gnu
cd /sw/dock/6.5/gnu/install
cd test; make test

Validation of
DOCK v6.5
is complete at Thu Aug 11 14:10:40 EST 2011.

dock6.5-gnu-acml

module list
Currently Loaded Modulefiles:
  1) library/acml/4.4.0-gnu   2) mpi/openMPI/1.4.3-gnu
/sw/dock/6.5/src
tar -zxvf dock.6.5_source.tar.gz
/sw/dock/6.5/src/dock6/install
make distclean
>>>>>>>>>>>>
 ./configure gnu.acml
The requested configuration file was found.
The DOCK configuration file has been created.
 REQUIREMENTS - define this environment variable:
 ACML_HOME is the root directory of the AMD Core Math Library

Edited the config.h :
DOCKHOME=/sw/dock/6.5/gnu-acml
ACML_HOME=      /sw/library/acml/4.4.0/gnu/gfortran64
make all 2>&1 | tee log.configure.dock_gnu-acml.txt
Installation of
DOCK v6.5
is complete at Thu Aug 11 14:33:07 EST 2011.

cd /sw/dock/6.5/src/
mv dock6 /sw/dock/6.5/gnu.acml
cd /sw/dock/6.5/gnu.acml/install/test
make test

dock6.5-intel

Not installed at the moment

dock6.5-intel-mkl

Not Installed at the moment

dock6.5-gnu-parallel

Modifications had to be made to the gnu.parallel file in order to point to the proper locations for MPI header files, etc.

module list
Currently Loaded Modulefiles:
1) mpi/openMPI/1.4.3-gnu


 ./configure gnu.parallel

The requested configuration file was found.
The DOCK configuration file has been created.
 REQUIREMENTS - define these environment variables:
 MPICH_HOME is the root directory of the MPICH2 MPI implementation

 vi config.h

>>>>>>>>>>>>>>>>>
MPICH_HOME=  /sw/openMPI/1.4.3-gnu
CC=          mpicc
CXX=         mpiCC
CFLAGS=      -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX -I$(MPICH_HOME)/include -O2
FC=          mpif77
FFLAGS=      -O2 -fno-automatic -fno-second-underscore
LIBS=        -lm
LINK_WITHOUT_FORTRAN_MAIN=
LOAD=        mpicxx
DOCK_SUFFIX= .mpi

AR=          ar rv
LEX=         flex
OCFLAGS=     -O3 -D_ANSI_SOURCE
RANLIB=      ranlib
DOCKHOME=/sw/dock/6.5/openmpi


>>>>>>>>>>>>>>>>>>>>>>>>>

make all
....
Installation of
DOCK v6.5
is complete at Thu Aug 11 14:57:34 EST 2011.

 cd /sw/dock/6.5/src
 mv dock6 /sw/dock/6.5/dock6-openmpi
cd /sw/dock/6.5/dock6-openmpi/install/test

Edit the "default_targets.h" and make sure the path for dock6 is correct (vi default_targets.h)

make test

Sample PBS script

#!/bin/bash
#
#PBS -r n
#PBS -m abe
#PBS -M YOUR_MAIL_ADDRESS_HERE
#
## Job settings
#PBS -N Test_DOCK_openMPI

## Job configuration

##Job resources
#PBS -l select=4:mem=4g
#PBS -l walltime=2:00:00

CPUS=`cat $PBS_NODEFILE | wc -l`
module load dock/6.5.ompi


EXE="/sw/dock/6.5/openmpi/bin/dock6.mpi"

# Execution directory
cd <YOUR_SCRATCH_DIR>/doc/my_dock_jobdir

which mpirun
echo Running $EXE
$MPIRUN $EXE -i dock_no_flex.in -o nci_1of3_100_noflex_auto.out

Ref

1. http://wiki.hpc.ufl.edu/index.php/Dock
2. http://www.cac.cornell.edu/Ranger/Environment/compiler_acml.aspx

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