[Dock-fans] Parallel install

Sudipto Mukherjee sudmukh at yahoo.com
Mon Sep 24 08:01:36 PDT 2007


Dear Francesco,

MPICH_HOME needs to be set as an environment variable. 
You should not have to make any modifications to config.h
For example, if your login shell is csh, add the following to your .cshrc
setenv MPICH_HOME      /path/to/openmpi

Please also note that MPICH_HOME needs to be the root of the MPI installation folder.
In your case, this is most likely /usr/local/openmpi or similar.
 
Regards
Sudipto Mukherjee
Graduate Student, Robert C. Rizzo Lab
Dept. of Applied Math & Statistics, Stony Brook University
Lab: 631-632-8519, Mobile: 631-220-5744


----- Original Message ----
From: Francesco Pietra <chiendarret at yahoo.com>
To: dock-fans <dock-fans at docking.org>
Sent: Friday, September 21, 2007 5:14:56 PM
Subject: [Dock-fans] Parallel install

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

/usr/local/dock6

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

MPI_HOME=/usr/local

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
# END REQUIREMENTS

# TROUBLESHOOTING
# 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.
# END TROUBLESHOOTING

# 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
# MPICH_IGNORE_CXX_SEEK  see
#   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++
CFLAGS=      -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX
-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
OCFLAGS=     -O3 -D_ANSI_SOURCE
RANLIB=      ranlib
DOCKHOME=/usr/local/dock6
# Created at Fri Sep 21 18:36:29 CEST 2007 via ./configure gnu parallel


I plan to use Antechamber in Amber9.

Thanks

francesco pietra



       
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