Subject: Amber + MPI on Dec Alpha linux 5.2 cluster -- help please...

From: Verschelde Jean-Luc <[email-masked]>
Date: Fri, 4 Feb 2000 13:29:21 +0100

Dear all,

I installed and compiled AMBER5.0 and MPICH on a cluster od DEC alpha's with os Redhat linux 5.2.
When I start sander, I receiver following message:
# 0 - MPI_COMM_RANK : Null communicator
# [0] Aborting  program
# p0_1331: p4_error : 197

Is there someone who can help me.
Attached is the machine file I used for compiling.
Greetings,
Verschelde Jean-Luc
#! /bin/csh -f
########################################################################
#                                                                      #
#                Copyright (c) 1986, 1991, 1995                        #
#           Regents of the University of California                    #
#                                                                      #
#                    All Rights Reserved                               #
#                                                                      #
#             Machine Dependency Handling System                       #
#                                                                      #
#                Bill Ross [email-masked]                           #
#            An extension of work of George Seibel                     #
#                                                                      #
#           Dependencies written by various authors.                   #
#                                                                      #
#  Permission to use, copy, modify, and distribute this software and   #
#  its documentation for any purpose and without fee is hereby         #
#  granted, provided that the above copyright notice appear in all     #
#  copies and that both that copyright notice and this permission      #
#  notice appear in supporting documentation, and that the name of     #
#  the University of California not be used in advertising or          #
#  publicity pertaining to distribution of the software without        #
#  specific, written prior permission.                                 #
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#  THE REGENTS OF THE UNIVERSITY OF CALIFORNIA DISCLAIM ALL            #
#  WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED      #
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#  LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,     #
#  NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN           #
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#                                                                      #
########################################################################

#
# Machine dependencies adapted from f2c version of Thomas Huber.
#
#    When using g77 it is important to resize the COMMON blocks
#    if you are using ld version less than 2.6! The other option
#    is to download binutils-2.6 from GNU and the default sizes
#    works fine. I have done both and there is no problem.
#
#    Dr. R.R. Joshi, Bioinformatics Centre, University of Poona, India
#
# Copy this file to .../src/MACHINE to install.
#
# These aliases let us use the same command files for compilation
# on Unix systems with different names and/or flags for the fortran
# compiler.   Environment variables set here specify the location
# of system-specific source and control the use of Integer*2.
# See install.doc: "Setting Up the Configuration File"
#
#
setenv MACHINE "linux/FreeBSD PC"
setenv MACH F2C
setenv MACHINEFLAGS " -DSHARED_MEMORY_MAX_PROCESSOR=4 -DPROFILE -DREGNML 
* DEWALD -DHAS_FTN_ERFC -DMPI  -I/home/jeanluc/mpich-1.2.0/include "

# CPP is the cpp for this machine
setenv CPP "/lib/cpp -traditional  -DSECOND=secondx -Dsecond=secondx "

# SYSDIR is the name of the system-specific source directory relative to 
src/*/
setenv SYSDIR Machine/alpha

# COMPILER ALIASES:
# LOADER/LINKER:
setenv LOAD "/home/jeanluc/mpich-1.2.0/bin/mpif77  -O6"
setenv LOADLIB "-L/home/jeanluc/mpich-1.2.0/lib -lmpich  "
setenv LOCINCLUDE Machine/mpi
setenv G77_COMPAT "-fno-globals -Wno-globals -ff90 -funix-intrinsics-hide "
# little or no optimization:
setenv L0 "/home/jeanluc/mpich-1.2.0/bin/mpif77 -c -g"
# modest optimization (local scalar):
setenv L1 "/home/jeanluc/mpich-1.2.0/bin/mpif77 -c -O  -ffast-math 
* fomit-frame-pointer $G77_COMPAT"

# high scalar optimization (but not vectorization):
setenv L2 "/home/jeanluc/mpich-1.2.0/bin/mpif77 -c -O3 -ffast-math 
* fomit-frame-pointer $G77_COMPAT"

# high optimization (may be vectorization, not parallelization):
setenv L3 "/home/jeanluc/mpich-1.2.0/bin/mpif77  -c -O3 -ffast-math 
* fomit-frame-pointer $G77_COMPAT"

# ranlib, if it exists
setenv RANLIB ranlib

# spasms configuration
#SPASMS MACHINE.f2c_spasms_config
#SPASMS unix
#SPASMS n390
#SPASMS large