AMBER Archive (2002)

Subject: Parallel Amber on Solaris 2.6

From: Thomas A. Spraggins (tas_at_virginia.edu)
Date: Mon Jun 03 2002 - 09:49:45 CDT

I don't know whether this is an mpich gotcha or an amber gotcha, so I'm
writing to both.

I'm trying to build a parallel (mpich 1.2.4) Amber 7 for Solaris 2.6, using
a MACHINE file that looks like:

#! /bin/csh -f
########################################################################
# #
# Copyright (c) 1986, 1991, 1995 #
# Regents of the University of California #
# #
# All Rights Reserved #
# #
# Machine Dependency Handling System #
# #
# Bill Ross ross_at_cgl.ucsf.edu #
# 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. #
# #
# THE REGENTS OF THE UNIVERSITY OF CALIFORNIA DISCLAIM ALL #
# WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED #
# WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE #
# UNIVERSITY OF CALIFORNIA BE LIABLE FOR ANY SPECIAL, INDIRECT OR #
# CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM #
# LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, #
# NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN #
# CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. #
# #
########################################################################

#
# Machine dependencies written by George Seibel for Amber 3.0 Rev A
#
# Copy this file to amber5/src/MACHINE to install.
#
# This file is appropriate for: Sun SPARCstation using the f90 compiler.
#
# 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"
#
#
# IF PROGRAMS CRASH, try adding '-fast' to L0-L3
#

setenv MPI_HOME /solaris/mpich-1.2.4
setenv MPI_BIN $MPI_HOME/bin
setenv MPI_LIB $MPI_HOME/lib

setenv MACHINE "Sun SPARC"
setenv MACH SPARC
# Note - sparc has a fortran erfc routine, but it yields
# different results than others (different function)
# so -DHAS_FTN_ERFC is omitted
setenv MACHINEFLAGS "-DMEM_ALLOC -DMPI -I$MPI_HOME/include"

# CPP is the cpp for this machine
setenv CPP /usr/ccs/lib/cpp

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

# COMPILER ALIASES:

# LOADER/LINKER:
setenv LOAD "mpif90 -Bstatic -fast "
setenv LOADCC "/opt/SUNWspro/SC5.0/bin/cc "
setenv LOADLIB "-lm"

# little or no optimization:
setenv L0 "mpif90 -c -O1 "

# modest optimization (local scalar):
setenv L1 "mpif90 -c -fast -O2 "

# high scalar optimization (but not vectorization):
setenv L2 "mpif90 -c -fast -O3 "

# high optimization (may be vectorization, not parallelization):
setenv L3 "mpif90 -c -fast -O3 "

# ranlib, if it exists
setenv RANLIB ranlib

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

but I get messages like:

cd lib; make install
../Compile L2 -P new2oldparm.f
cat new2oldparm.f |
/usr/ccs/lib/cpp -P -DSPARC -DMEM_ALLOC -DMPI -I/solaris/mpich-1.2.4/incl
ude > _new2oldparm_.f
mpif90 -c -fast -O3 _new2oldparm_.f
../Compile L0 -P -DNEWPARM nxtsec.f
cat nxtsec.f |
/usr/ccs/lib/cpp -P -DNEWPARM -DSPARC -DMEM_ALLOC -DMPI -I/solaris/mpic
h-1.2.4/include > _nxtsec_.f
mpif90 -c -O1 _nxtsec_.f
../Compile LOAD -o new2oldparm new2oldparm.o nxtsec.o
mpif90 -Bstatic -fast -o new2oldparm new2oldparm.o nxtsec.o -lm
ld: fatal: library -laio: not found
ld: fatal: File processing errors. No output written to new2oldparm
*** Error code 1
make: Fatal error: Command failed for target `new2oldparm'
Current working directory /common/amber7/src/lib
*** Error code 1
make: Fatal error: Command failed for target `install'

Has anyone seen this before? There is a /usr/lib/libaio.so, but not
libaio.a, even though "mpif90 -link_info" gives:

f90 -L/solaris/mpich-1.2.4/lib -lmpichf90 -lmpich -lsocket -lnsl -lnsl -laio

Thanks for any ideas.

Tom Spraggins
tas_at_virginia.edu