AMBER Archive (2004)

Subject: AMBER: amber8 parallel installation with mpich

From: cailliez (Fabien.Cailliez_at_ibpc.fr)
Date: Tue Nov 30 2004 - 06:24:41 CST

Dear all,

I am trying to install AMBER8 in parallel with mpich libraries.
The serail installation of AMBER8 worked fine.
mpich is already installed on my linux machine (knoppix distribution).
To do the parallel installation, I tried :

export AMBERHOME=/ibpc/matrix/opt/amber/amber8
export PATH=$PATH:$AMBERHOME/exe
export MPICH_HOME=/usr/lib/mpich
cd $AMBERHOME
source /ibpc/matrix/opt/intel_fc_80/bin/ifortvars.sh
./configure -mpich ifort
make parallel

The beginning of the compilation worked fine until this error message
arrived :
ifort -FR -o sander trace.o lmod.o decomp.o icosasurf.o egb.o
findmask.o pb_force.o sander.o cshf.o noecalc.o noeread.o caldis.o
calrate.o dinten.o drates.o indexn.o kmat.o pearsn.o plane.o remarc.o
nmrcal.o nmrred.o restal.o getnat.o nmrnrg.o modwt.o disnrg.o angnrg.o
tornrg.o nmrprt.o nmrgrp.o nmrcms.o nmrcmf.o impnum.o nmrsht.o at2res.o
chklin.o opnmrg.o printe.o runmin.o ndvprt.o force.o rdparm.o mdread.o
locmem.o runmd.o getcor.o r6ave.o r6drv.o aveint.o degcnt.o corf.o
threeb.o tripl.o nmrrad.o decnvh.o fastwt.o echoin.o parallel.o jnrg.o
shake.o ene.o mdwrit.o minrit.o set.o setmm.o dynlib.o mdfil.o nmlsrc.o
ew_force.o ew_setup.o ew_box.o ew_bspline.o ew_fft.o ew_direct.o
ew_recip.o pcshift.o align.o rstack.o istack.o rfree.o rgroup.o random.o
lsqfit.o amopen.o debug.o ew_recip_reg.o ew_handle_dips.o
ew_dipole_recip.o mexit.o new_time.o extra_pts.o thermo_int.o matinv.o
assert.o mmtsb.o mmtsb_client.o erfcfun.o veclib.o mdm.o pb_init.o
constantph.o prn_dipoles.o \
    ../lmod/lmod.a -L/image_rsh/lib -lmpich \
    ../lapack/lapack.a ../blas/blas.a ../lib/nxtsec.o ../lib/sys.a
/usr/bin/ld: cannot find -lmpich
make[1]: *** [sander] Error 1
make[1]: Leaving directory `/ibpc/matrix/opt/amber/amber8/src/sander'
make: *** [parallel] Error 2

Do you have any suggestion ?
Thank you in advance,
Fabien

Here is my file config.h after I make ./configure -mpich ifort

#==============================================================================
# AMBER Makefile configuration for compiler/architecture: ifort
# Generated via command: ./configure -mpich ifort
#
# Configuration script written mainly by Joe Krahn, Scott Brozell, and
# Dave Case, with contributions from lots of people.
#==============================================================================

#------------------------------------------------------------------------------
# Main AMBER source root directory
#------------------------------------------------------------------------------
AMBER_SRC=/ibpc/matrix/opt/amber/amber8/src

#------------------------------------------------------------------------------
# AMBERBUILDFLAGS provides a hook into the build process for installers;
# for example, to build debug versions of the amber programs
# make -e AMBERBUILDFLAGS="-DDEBUG -g"
#------------------------------------------------------------------------------
AMBERBUILDFLAGS=

#------------------------------------------------------------------------------
# LOCALFLAGS is intended for program specific modifications to the
# Fortran build process and may be modified by the program's local makefile
#------------------------------------------------------------------------------
LOCALFLAGS=

#------------------------------------------------------------------------------
# Availability and method of delivery of math and optional libraries
#------------------------------------------------------------------------------
USE_BLASLIB=$(SOURCE_COMPILED)
USE_LAPACKLIB=$(SOURCE_COMPILED)
USE_LMODLIB=$(LMOD_UNAVAILABLE)

#------------------------------------------------------------------------------
# C compiler
#------------------------------------------------------------------------------
CC= gcc
CPLUSPLUS=g++
ALTCC=gcc
CFLAGS=-O2 $(AMBERBUILDFLAGS)
ALTCFLAGS= $(AMBERBUILDFLAGS)
CPPFLAGS= $(AMBERBUILDFLAGS)

#------------------------------------------------------------------------------
# Fortran preprocessing and compiler.
# FPPFLAGS holds the main Fortran options, such as whether MPI is used.
#------------------------------------------------------------------------------
FPPFLAGS= -I/usr/lib/mpich/include -P -I$(AMBER_SRC)/include -DMPI
$(AMBERBUILDFLAGS)
FPP= cpp -traditional $(FPPFLAGS)
FC= ifort
FFLAGS= -w95 -mp1 -O0 $(LOCALFLAGS) $(AMBERBUILDFLAGS)
FOPTFLAGS= -w95 -mp1 -ip -O3 $(LOCALFLAGS) $(AMBERBUILDFLAGS)
FPP_PREFIX= _
FREEFORMAT_FLAG= -FR

#------------------------------------------------------------------------------
# Loader:
#------------------------------------------------------------------------------
LOAD= ifort $(LOCALFLAGS) $(AMBERBUILDFLAGS)
LOADCC= gcc $(LOCALFLAGS) $(AMBERBUILDFLAGS)
LOADLIB= -L/image_rsh/lib -lmpich
LOADPTRAJ= ifort -nofor_main $(LOCALFLAGS) $(AMBERBUILDFLAGS)
XHOME= /usr/X11R6

#------------------------------------------------------------------------------
# Other stuff:
#------------------------------------------------------------------------------
.SUFFIXES: .f90
SYSDIR=lib
AR=ar rv
M4=m4
RANLIB=ranlib
SFX=
MAKEDEPEND=$(AMBER_SRC)/../bin/amber_makedepend

# default rules for Fortran and C compilation:

.f.o: $<
        $(FPP) $< > $(FPP_PREFIX)$<
        $(FC) -c $(FFLAGS) -o $@ $(FPP_PREFIX)$<

.f90.o: $<
        $(FPP) $< > $(FPP_PREFIX)$<
        $(FC) -c $(FFLAGS) -o $@ $(FPP_PREFIX)$<

.c.o:
        $(CC) -c $(CFLAGS) $(CPPFLAGS) -o $@ $< 

-- 
__________________________________________________________________
Fabien Cailliez				Tel : 01 58 41 51 63				
Laboratoire de Biochimie Théorique	e-mail : cailliez_at_ibpc.fr
IBPC	13, rue Pierre et Marie Curie 		
75005 Paris					
__________________________________________________________________

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