Installing DOCK

For the AMS 536 class, DOCK is already installed. This article is for users trying to install dock elsewhere. Please note that DOCK is licensed software; please contact UCSF for a license. DOCK licenses are free for academic users.

Generic Instructions

Untar the DOCK distribution.

cd dock6/install

Select the correct Makefile for your platform, and run the configure script.

./configure gnu
make install

Installing DOCK 6.3 on Ubuntu

These should also work for other versions of DOCK.

apt-get install build-essential flex bison gfortran
cd dock6/src/install

Edit the gnu profile to replace g77 with gfortran as directed

./configure gnu
make install

Configuration for Intel C Compiler with MPI

To compile DOCK with icc in parallel, add the file below as intel.parallel to your dock6/install directory.

CC=          icc
CXX=         $(MPICH_HOME)/bin/mpicxx
CFLAGS=      -O3 -ipo -fast -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX -I$(MPICH_HOME)/include
FC=          ifort
FFLAGS=      -O2
LIBS=        -L$(MKL_HOME)/lib/em64t -lvml -lmkl_lapack -lmkl -lguide -lpthread -lm
LINK_WITHOUT_FORTRAN_MAIN= -nofor_main
LOAD=        $(MPICH_HOME)/bin/mpicxx
DOCK_SUFFIX= .mpi

AR=          ar rv
LEX=         flex
OCFLAGS=     -O3 -D_ANSI_SOURCE
RANLIB=      ran lib

Compilation Blue Gene

For the front end node, gnu compilers work well. For the compute nodes, use the provided bluegenel and bluegenep files respectively. Note that energy grids have to be generated on the front end node in order to work on the compute nodes. Copying grids generated on a regular unix machine will not work due to different endian conventions.

Partial configuration file Makefile for BG/L

CC=          blrts_xlc
CXX=         blrts_xlC
BGL_SYS=     /bgl/BlueLight/ppcfloor/bglsys
CFLAGS=      -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK \
            -I$(BGL_SYS)/include -lmassv \
            -qarch=440d -qtune=440 -qinline -O5
FC=          blrts_xlf90
FFLAGS=      -qarch-440d -qtune=440 -O5
LOAD=        blrts_xlC
LIBS=        -lm -L$(BGL_SYS)/lib -lmpich.rts -lmsglayer.rts -lrts.rts -ldevices.rts

Partial configuration file for BG/P

CC=          mpixlc
CXX=         mpixlcxx
BGP_SYS=     /bgsys/drivers/ppcfloor
CFLAGS=      -qarch=450d -qtune=450 -O5  \
             -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK
FC=          mpixlf90
FFLAGS=      -qarch-450d -qtune=450 -O5
LOAD=        mpixlcxx
LIBS=         -lm
AR=          ar rv
LEX=         flex
OCFLAGS=     -D_ANSI_SOURCE
RANLIB=      ranlib