[gmx-users] installation of gromacs on windows using cygwin

Mark Abraham Mark.Abraham at anu.edu.au
Sat Nov 6 08:42:28 CET 2010

On 5/11/2010 10:48 PM, bharat gupta wrote:
> I followed the same instructions given in the gromacs manual , step by 
> step ... I first tried installing gromacs with the first command given 
> in the manual and then again I installed with the options for FLAGS 
> but finally ended up with the following error in both the above 
> mentioned conditions :-
> checking dynamic linker characteristics... Win32 ld.exe

I think here's a problem.  Your cygwin installation doesn't have a 
proper linker installed. win32 ld.exe is not up to the job, IIRC. You 
need (at least) the gcc and binutils packages.

When asking for free help, you should copy and paste into these emails 
the command that is failing. If you'd really followed the instructions, 
we expect they'd have worked. So in the absence of evidence that you've 
done it right, we'll have to assume you've made a typo. We don't want to 
guess what you've done wrong :-)


> checking how to hardcode library paths into programs... immediate
> appending configuration tag "F77" to libtool
> checking for special C compiler options needed for large files... no
> checking for _FILE_OFFSET_BITS value needed for large files... no
> checking for _LARGEFILE_SOURCE value needed for large files... no
> checking for sqrt in -lm... yes
> checking for fftw3.h... configure: error: Cannot find the default 
> external FFT l
> ibrary (fftw3).
> Other alternatives are 'fftw2', or 'mkl' for Intel MKL.
> You are STRONGLY recommended to use one of these - fftw is free.
> Use CPPFLAGS and LDFLAGS if the library is installed in a
> non-standard location. (see FAQ at http://www.gromacs.org)
> If you dont care about performance you can also specify 'fftpack'
> to use a slower set of FFTs built into Gromacs.
> (Just install FFTW3 unless you really know what you are doing).
> I have installed fftw2.1.5  ...
> Pls help me rectify the error
> -- 
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
> E-mail : monu46010 at yahoo.com <mailto:monu46010 at yahoo.com>

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