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
>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sun Mar 28 2010 - 09:00:02 PDT
