Dear Amber users,
I encountered problems while compiling AmberTools on Ubuntu.
system:
OS: Ubuntu 9.10
CPU: Intel Core i7
installation steps:
Download AmberTools.tar.bz2
cp AmberTools.tar.bz2 /opt
cd /opt
mkdir amber11
tar xvf AmberTools.tar.bz2
cd amber11
download bugfix.all from
http://ambermd.org./bugfixesat.html
patch -p0 -N < bugfix.all
set $AMBERHOME and $PATH
./configure gnu
make -f Makefile_at
The compilation failed at the following step
.
.
.
(cd nss && make install )
make[1]: Entering directory `/opt/amber11/src/nss'
/opt/amber11/bin/nab -c symop.nab
symop.c: In function \u2018MAT_ico\u2019:
symop.c:219: warning: passing argument 2 of \u2018rot4p\u2019 from
incompatible pointer type
/opt/amber11/include/nabcode.h:186: note: expected \u2018REAL_T *\u2019
but argument is of type \u2018REAL_T (*)[3]\u2019
/opt/amber11/bin/nab -c matop.c
/opt/amber11/bin/nab -c tss.c
ar rv libsym.a symop.o matop.o tss.o
ar: creating libsym.a
a - symop.o
a - matop.o
a - tss.o
ranlib libsym.a
cp -p libsym.a /opt/amber11/lib
/opt/amber11/bin/nab -c matextract.nab
/opt/amber11/bin/nab -o matextract matextract.o libsym.a
/opt/amber11/bin/nab -c matgen.nab
/opt/amber11/bin/nab -o matgen matgen.o libsym.a
/opt/amber11/lib/libnab.a(sff.o): In function `mm_options':
sff.c:(.text+0x1f24): undefined reference to `mmolex'
collect2: ld returned 1 exit status
cc failed!
make[1]: *** [matgen] Error 1
make[1]: Leaving directory `/opt/amber11/src/nss'
Could you please help me to identify the problem.
Thanks
Thomas
###########
## my config.h
$> cat config.h
# Amber configuration file, created with: ./configure gnu
###############################################################################
# (1) Location of the installation
BINDIR=/opt/amber11/bin
LIBDIR=/opt/amber11/lib
INCDIR=/opt/amber11/include
DATDIR=/opt/amber11/dat
NABHOME=/opt/amber11/dat
###############################################################################
# (2) If you want to search additional libraries by default, add them
# to the FLIBS variable here. (External libraries can also be
linked into
# NAB programs simply by including them on the command line;
libraries
# included in FLIBS are always searched.)
FLIBS= $(LIBDIR)/libsym.a $(LIBDIR)/carpack.a $(LIBDIR)/clapack.a
$(LIBDIR)/cblas.a $(LIBDIR)/f2c.a
FLIBS_PTRAJ= $(LIBDIR)/carpack.a $(LIBDIR)/clapack.a $(LIBDIR)/cblas.a
$(LIBDIR)/f2c.a
FLIBSF= $(LIBDIR)/carpack.a $(LIBDIR)/lapack.a $(LIBDIR)/blas.a
$(LIBDIR)/f2c.a
FLIBS_FFTW2=
###############################################################################
# (3) Modify any of the following if you need to change, e.g. to use
gcc
# rather than cc, etc.
SHELL=/bin/sh
# Set the C compiler, etc.
# For GNU: CC-->gcc; LEX-->flex; YACC-->bison -y -t;
# Note: If your lexer is "really" flex, you need to set
# LEX=flex below. For example, on many linux distributions,
# /usr/bin/lex is really just a pointer to /usr/bin/flex,
# so LEX=flex is necessary. In general, gcc seems to need
# flex.
CC=gcc
CXX=g++
CPLUSPLUS=g++
CFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ
$(AMBERBUILDFLAGS)
OCFLAGS=-O3 -mtune=generic -msse -mfpmath=sse -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -DBINTRAJ $(AMBERBUILDFLAGS)
NABFLAGS=
LDFLAGS= $(AMBERBUILDFLAGS)
LEX= flex
YACC= $(BINDIR)/yacc
AR= ar rv
M4= m4
RANLIB=ranlib
MAKE=make
# Set the C-preprocessor. Code for a small preprocessor is in
# uccp-1.3; it gets installed as $(BINDIR)/ucpp;
# this can generally be used (maybe not on 64-bit machines like
altix).
CPP= $(BINDIR)/ucpp -l
# These variables control whether we will use compiled versions of BLAS
# and LAPACK (which are generally slower), or whether those libraries
are
# already available (presumably in an optimized form).
LAPACK=install
BLAS=install
F2C=install
# These variables determine whether builtin versions of certain
components
# can be used, or whether we need to compile our own versions.
UCPP=install
C9XCOMPLEX=skip
# For Windows/cygwin, set SFX to ".exe"; for Unix/Linux leave it empty:
SFX=
# Information about Fortran compilation:
FC=gfortran
FFLAGS= -O0 $(LOCALFLAGS) $(AMBERBUILDFLAGS)
FOPTFLAGS= -O3 -mtune=generic -msse -mfpmath=sse $(LOCALFLAGS)
$(AMBERBUILDFLAGS)
FREEFORMAT_FLAG= -ffree-form
LM=-lm
FPP=cpp -traditional -P -DNO_SANDER_DIVCON -DBINTRAJ
FPPFLAGS=-P -DNO_SANDER_DIVCON -DBINTRAJ
BUILD_SLEAP=install_sleap
XHOME= /usr/X11R6
XLIBS= -L/usr/X11R6/lib
MAKE_XLEAP=install_xleap
LIBDIVCON=
INCDIVCON=
MODULEDIR=-I
TESTSANDERDIVCON=skipsanderDIVCON
NETCDF=netcdf.mod
NETCDFLIB=../netcdf/lib/libnetcdf.a
PNETCDF=no
PNETCDFLIB=
HASFC=yes
MDGX=no
COMPILER=gnu
MKL=
MKL_PROCESSOR=
$>
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Received on Sun Mar 28 2010 - 07:00:03 PDT
