Hi Jason,
many thanks for the hint. Installing flex solved the problem.
Cheers
Thomas
On Sun, 2010-03-28 at 11:43 -0400, Jason Swails wrote:
> Hello,
>
> I, too, run Ubuntu 9.10 and use the gnu compilers. A quick grep in
> the sff directory leads me to believe that this is a flex issue. I
> know configure looks for flex, but I think I recall an issue with it
> "finding" flex when it's not really present earlier in the list (can't
> nail it down too much, so I don't want to go looking for it). My only
> suggestion would be to install flex from aptitude and see if it works
> then... Unless of course you've already installed flex (but it must
> be done manaully, it does not come with the distro).
>
> Good luck!
> Jason
>
> On Sun, Mar 28, 2010 at 9:39 AM, Thomas Stockner
> <thomas.stockner.meduniwien.ac.at> wrote:
> > 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=
> > $>
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
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Received on Sun Mar 28 2010 - 11:30:02 PDT
