Dear Jason,
Thanks you. I think so. However, when do all these steps and I do the test. all the sleap jobs were failed. Error message said that the sleap cannot be found.
I also found the X11R6 is missing in my computer. Do I need to install additional library?
Best regards,
Cat
> Date: Tue, 8 Jun 2010 07:23:56 -0400
> Subject: Re: [AMBER] How to modify config.h if I cannot get g77 running? Pls kindly help.
> From: jason.swails.gmail.com
> To: amber.ambermd.org
>
> Hello,
>
> It is fine, it's using gfortran instead of g77, which will work just as
> well.
>
> Good luck!
> Jason
>
> 2010/6/8 Catein Catherine <askamber23.hotmail.com>
>
> >
> > Dear Sir/madam,
> >
> > I have type the followings lines in ubuntu 9.1.
> >
> > > sudo apt-get install bison csh flex gfortran g++ xorg-dev
> >
> > > sudo apt-get install build-essential byacc
> >
> > > g++ -v, it is what I got.
> >
> >
> > ======================================================================================================
> > Using built-in specs.
> > Target: i486-linux-gnu
> > Configured with: ../src/configure -v --with-pkgversion='Ubuntu
> > 4.4.1-4ubuntu9' --with-bugurl=file:///usr/share/doc/gcc-4.4/README.Bugs
> > --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr --enable-shared
> > --enable-multiarch --enable-linker-build-id --with-system-zlib
> > --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix
> > --with-gxx-include-dir=/usr/include/c++/4.4 --program-suffix=-4.4
> > --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-objc-gc
> > --enable-targets=all --disable-werror --with-arch-32=i486
> > --with-tune=generic --enable-checking=release --build=i486-linux-gnu
> > --host=i486-linux-gnu --target=i486-linux-gnu
> > Thread model: posix
> > gcc version 4.4.1 (Ubuntu 4.4.1-4ubuntu9)
> >
> > =======================================================================================================
> >
> > Then I type ./configure_at gcc to create the config.h file, here is the
> > error message that I saw for g77 compiler and the config.h file created. I
> > found g77 is not working (see error message below), but I think we can use
> > gfortran instead to install ambertools 1.2 and amber10. Do I need to
> > modifiy the config.h file below? Could you mind to teach me how? I also
> > found I don't have the X11R6 folder in the location indicated in config.h.
> > Where should I find the X11R6? Should I modify the path instead to get it
> > run?
> >
> >
> > ========================================================================================================
> > ./configure_at gcc
> > Setting AMBERHOME to /home/annie/Amber10/amber10
> >
> >
> > Testing the C compiler:
> > gcc -m32 -o testp testp.c
> > OK
> >
> > Obtaining the C++ compiler version:
> > g++ -v
> > The version is ../src/configure
> > 4.4.1
> > [: 520: -lt: unexpected operator
> > OK
> >
> > Testing the g77 compiler:
> > g77 -O2 -fno-automatic -finit-local-zero -o testp testp.f
> > ./configure_at: 538: g77: not found
> > ./configure_at: 539: ./testp: not found
> > Unable to compile a Fortran program using g77 -O2 -fno-automatic
> > -finit-local-zero
> >
> > Testing the gfortran compiler:
> > gfortran -O1 -fno-automatic -o testp testp.f
> > OK
> >
> > Testing flex:
> > OK
> >
> > Configuring netcdf; (may be time-consuming)
> >
> > NETCDF configure succeeded.
> >
> > The configuration file, config.h, was successfully created.
> >
> > The next step is to type 'make -f Makefile_at'
> >
> >
> > ========================================================================================================
> >
> > # AmberTools configuration file, created with: ./configure_at gcc
> >
> >
> > ###############################################################################
> >
> > # (1) Location of the installation
> >
> > BINDIR=/home/annie/Amber10/amber10/bin
> > LIBDIR=/home/annie/Amber10/amber10/lib
> > INCDIR=/home/annie/Amber10/amber10/include
> > DATDIR=/home/annie/Amber10/amber10/dat
> > NABHOME=/home/annie/Amber10/amber10/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)/arpack.a $(LIBDIR)/lapack.a
> > $(LIBDIR)/blas.a $(LIBDIR)/f2c.a
> >
> >
> > ###############################################################################
> >
> > # (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= -m32 -DBINTRAJ $(AMBERBUILDFLAGS)
> > OCFLAGS=-O3 -m32 -DBINTRAJ $(AMBERBUILDFLAGS)
> > NABFLAGS=
> > LDFLAGS=
> >
> > LEX= flex
> > YACC= $(BINDIR)/yacc
> > AR= ar rv
> > M4= m4
> > RANLIB=ranlib
> >
> > # 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= -O1 -fno-automatic $(LOCALFLAGS) $(AMBERBUILDFLAGS)
> > FREEFORMAT_FLAG= -ffree-form
> > LM=-lm
> >
> > BUILD_SLEAP=install_sleap
> > XHOME= /usr/X11R6
> > XLIBS= -L/usr/X11R6/lib
> > MAKE_XLEAP=install_xleap
> >
> > NETCDF=netcdf.mod
> > NETCDFLIB=../netcdf/lib/libnetcdf.a
> > G77=hasG77
> >
> > # default rules for Fortran and C compilation:
> >
> > .f.o:
> > $(FC) -c $(FFLAGS) -o $. $<
> >
> > .c.o:
> > $(CC) -c $(CFLAGS) -o $. $<
> >
> > ~
> > ~
> >
> > ===============================================================================================================
> >
> >
> > _________________________________________________________________
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> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue Jun 08 2010 - 08:00:03 PDT
