[gmx-users] gmx user

Mark Abraham Mark.Abraham at anu.edu.au
Sun Nov 1 09:41:34 CET 2009

pawan raghav wrote:
> Dear all,
> I am a new user of GROMACS and suffering from severe problem about 
> fftw-3.2.2 installation. Actually I have installed cygwin on windows XP 
> with gcc, gdb, and make packages rest all are leaved default. Now when I 
> have used configure command then it would give last line as
> config.status: executing libtool commands
> then returned back to my current working directory, after that when used 
> make command it gives an error i.e.
> ../libtool: line 111: CDPATH: command not found
> libtool: Version mismatch error. This is libtool 2.2.6 Debian-2.2.6a-4 
> but the
>  > libtool: definition of this LT_INIT comes from an older release.
>  > libtool: You should recreate aclocal.m4 with macros from libtool 2.2.6
>  > libtool: and run autoconf again.
>  > make[2]: *** [align.lo] Error 63
>  > make[2]: Leaving directory `/cygdrive/c/fftw-3.2.2/kernel
>  > make[1]: *** [all-recursive] Error 1
>  > make[1]: Leaving directory `/cygdrive/c/fftw-3.2.2/'
>  > make: *** [all] Error 2

It looks like you've copied this directory from some other machine. Get 
rid of it, download a tarball from fftw.org and follow the installation 
instructions here 

Also, do yourself a favour and get out of the DOS habit of putting 
everything in the root of the filesystem.


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