[Dock-fans] Parallel install

Francesco Pietra chiendarret at yahoo.com
Fri Sep 21 14:14:56 PDT 2007

On a shared memory computer with two dual-opterons, OS Linux Debian amd64 etch,
I have successfully installed


serial dock and accessory (DOCK 6.1) with g++ 4.1.2, gcc 3.4, g77 3.4.

On this computer, Amber9 is installed in /usr/local/amber9 with openmpi support


where openmpi is compiled with Intel.

I would be very grateful for suggesting me how to rearrange the config.h file
(please, see below) so that  MPICH_HOME points to openmpi:

# DOCK configuration file for GNU compilers with MPICH2 based parallelism.
# 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.

# REQUIREMENTS - define these environment variables:
# MPICH_HOME is the root directory of the MPICH2 MPI implementation

# 1. Linking problems, such as undefined references, cannot find -lbla_bla,
# and command not found errors:
# ensure that mpicxx exists;  ensure that the compiler invoked by mpicxx exists
# (for best results it should be g++); in the worst case try manual linking:
# change the LOAD definition below to g++, execute the command
# $MPICH_HOME/bin/mpicc -show
# and add to the LIBS definition below the output related to link flags, e.g
# LIBS= -lm -Lyada -Lyada_yada -lbla -lbla_bla ...
# 2. General advice: build a serial dock first then build a parallel
# dock using a validated MPI implementation.
# 3. Best practice advice:  the most straightforward route to successful
# parallel executable building is to use the same compilers for building
# the MPI implementation and dock.

# 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
# LOAD is the command to invoke the linker
#   http://www-unix.mcs.anl.gov/mpi/mpich2/faq.htm#cxxseek
# MPICH_SKIP_MPICXX  Dock does not use MPI C++ bindings; see
#   http://www-unix.mcs.anl.gov/mpi/mpi-standard/mpi-report-2.0/node226.htm
# SFX is the suffix for the executable

CC=          gcc
CXX=         g++
-I$(MPICH_HOME)/include -O2
FC=          g77
FFLAGS=      -O2 -fno-automatic -fno-second-underscore
LOAD=        $(MPICH_HOME)/bin/mpicxx
LIBS=        -lm
SFX=         .mpi

# 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
RANLIB=      ranlib
# Created at Fri Sep 21 18:36:29 CEST 2007 via ./configure gnu parallel

I plan to use Antechamber in Amber9.


francesco pietra

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