Hello,
I am having difficulties with the installation of Amber V8 that we
purchased
just prior to the release of V9. Here is a description of the series
of steps that
lead up to the error during compilation: my objectives, the procedure
taken,
the error message during the serial make, my system configuration
(compilers, etc.),
and the config.h file.
Objective:
-Compile Amber V8.0 on Ubuntu 7.10 using Intel Compilers V10.1
Procedure:
-extracted amber8.tgz in home directory after copying from
installation media
-In .bashrc, added the following lines
export AMBERHOME=~/amber8
export PATH=$PATH:$AMBERHOME/exe
-Sourced .bashrc file
-The return values from echo $PATH and echo $AMBERHOME confirmed that
the values were correctly set
-ran the configuration script to specify compiler as ifort:
cd $AMBERHOME/src
./configure ifort
-Return value from ./configure was:
________________________
AMBERHOME is set to ~/Amber8
Setting up Amber configuration file for architecture: ifort
Using parallel communications library: none
The MKL_HOME environment variable is not defined.
The MKL is recommended for optimal performance.
The configuration file, config.h, was successfully created.
________________________
-Configuration file config.h is included at end of this message
-Ran make clean
-Removed $AMBERHOME/exe directory for fresh installation
-Ran make serial
-The following output resulted with the error message occurring
towards the end of the following output:
Starting installation of Amber8 (serial) at Tue Mar 11 19:44:46 PDT
2008.
mkdir ../exe
cd lib; make install
make[1]: Entering directory `/home/rangel/amber8/src/lib'
cpp -traditional -P -I/home/rangel/Amber8/src/include new2oldparm.f >
_new2oldparm.f
ifort -c -w95 -mp1 -O0 -o new2oldparm.o _new2oldparm.f
cpp -traditional -P -I/home/rangel/Amber8/src/include nxtsec.f >
_nxtsec.f
ifort -c -w95 -mp1 -O0 -o nxtsec.o _nxtsec.f
ifort -o new2oldparm new2oldparm.o nxtsec.o
mv new2oldparm ../../exe
/bin/rm _*.f
make[1]: Leaving directory `/home/rangel/amber8/src/lib'
cd addles; make install
make[1]: Entering directory `/home/rangel/amber8/src/addles'
cpp -traditional -P -I/home/rangel/Amber8/src/include lesmain.f >
_lesmain.f
ifort -c -w95 -mp1 -O0 -o lesmain.o _lesmain.f
cpp -traditional -P -I/home/rangel/Amber8/src/include addspace.f >
_addspace.f
ifort -c -w95 -mp1 -O0 -o addspace.o _addspace.f
cpp -traditional -P -I/home/rangel/Amber8/src/include readprm.f >
_readprm.f
ifort -c -w95 -mp1 -O0 -o readprm.o _readprm.f
cpp -traditional -P -I/home/rangel/Amber8/src/include writprm.f >
_writprm.f
ifort -c -w95 -mp1 -O0 -o writprm.o _writprm.f
cpp -traditional -P -I/home/rangel/Amber8/src/include readcrd.f >
_readcrd.f
ifort -c -w95 -mp1 -O0 -o readcrd.o _readcrd.f
cpp -traditional -P -I/home/rangel/Amber8/src/include writcrd.f >
_writcrd.f
ifort -c -w95 -mp1 -O0 -o writcrd.o _writcrd.f
cpp -traditional -P -I/home/rangel/Amber8/src/include pick.f > _pick.f
ifort -c -w95 -mp1 -O0 -o pick.o _pick.f
cpp -traditional -P -I/home/rangel/Amber8/src/include rline.f >
_rline.f
ifort -c -w95 -mp1 -O0 -o rline.o _rline.f
cpp -traditional -P -I/home/rangel/Amber8/src/include nxt.f > _nxt.f
ifort -c -w95 -mp1 -O0 -o nxt.o _nxt.f
cpp -traditional -P -I/home/rangel/Amber8/src/include intgr.f >
_intgr.f
ifort -c -w95 -mp1 -O0 -o intgr.o _intgr.f
cpp -traditional -P -I/home/rangel/Amber8/src/include find.f > _find.f
ifort -c -w95 -mp1 -O0 -o find.o _find.f
cpp -traditional -P -I/home/rangel/Amber8/src/include of.f > _of.f
ifort -c -w95 -mp1 -O0 -o of.o _of.f
cpp -traditional -P -I/home/rangel/Amber8/src/include geti.f > _geti.f
ifort -c -w95 -mp1 -O0 -o geti.o _geti.f
cpp -traditional -P -I/home/rangel/Amber8/src/include unit.f > _unit.f
ifort -c -w95 -mp1 -O0 -o unit.o _unit.f
cpp -traditional -P -I/home/rangel/Amber8/src/include getc.f > _getc.f
ifort -c -w95 -mp1 -O0 -o getc.o _getc.f
cpp -traditional -P -I/home/rangel/Amber8/src/include alert.f >
_alert.f
ifort -c -w95 -mp1 -O0 -o alert.o _alert.f
cpp -traditional -P -I/home/rangel/Amber8/src/include echo.f > _echo.f
ifort -c -w95 -mp1 -O0 -o echo.o _echo.f
cpp -traditional -P -I/home/rangel/Amber8/src/include get4c.f >
_get4c.f
ifort -c -w95 -mp1 -O0 -o get4c.o _get4c.f
cpp -traditional -P -I/home/rangel/Amber8/src/include getd.f > _getd.f
ifort -c -w95 -mp1 -O0 -o getd.o _getd.f
cpp -traditional -P -I/home/rangel/Amber8/src/include wlesprm.f >
_wlesprm.f
ifort -c -w95 -mp1 -O0 -o wlesprm.o _wlesprm.f
cpp -traditional -P -I/home/rangel/Amber8/src/include lesprm.f >
_lesprm.f
ifort -c -w95 -mp1 -O0 -o lesprm.o _lesprm.f
cpp -traditional -P -I/home/rangel/Amber8/src/include les2prm.f >
_les2prm.f
ifort -c -w95 -mp1 -O0 -o les2prm.o _les2prm.f
cpp -traditional -P -I/home/rangel/Amber8/src/include checksz.f >
_checksz.f
ifort -c -w95 -mp1 -O0 -o checksz.o _checksz.f
cd ../lib; ./Makelist ../lib/random.o ../lib/mexit.o ../lib/nxtsec.o
/bin/sh: ./Makelist: not found
make[1]: *** [libobj] Error 127
make[1]: Leaving directory `/home/rangel/amber8/src/addles'
make: *** [serial] Error 2
System configuration:
Amber version = 8
Machine = Intel MacBook
OS = Ubuntu 7.10, 2.6.22-14-generic #1 SMP Sun Oct 14 23:05:12 GMT
2007 i686 GNU/Linux
Compilers =
ifort v10.1
icc v10.1
gcc version 4.1.3 20070929
X11 Development Library
libx11-dev 2:1.1.1-1ubuntu4 X11 client-side library
Config.h File contents:
#=
=
=
=
=
=
========================================================================
# AMBER Makefile configuration for compiler/architecture: ifort
# Generated via command: ./configure 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=/home/rangel/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= $(AMBERBUILDFLAGS)
#------------------------------------------------------------------------------
# Fortran preprocessing and compiler.
# FPPFLAGS holds the main Fortran options, such as whether MPI is used.
#------------------------------------------------------------------------------
FPPFLAGS= -P -I$(AMBER_SRC)/include $(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=
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 $. $<
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Received on Wed Mar 12 2008 - 06:07:55 PDT
