[gmx-users] How to install GROMACS in 64-bit?

a a patd_2 at hotmail.com
Tue May 29 17:50:16 CEST 2012

Dear Mark,

I have overlook it.  Sorry.

I have already added the following two sentences in .bashrc file in my home directory (when I login as user).

          export LDFLAGS="-L/home/softwares/fftw301/lib"

Should I type in another lines?

Did I do any common mistakes in using the command export with .bash shell?

Should I add these two lines at the root directory as it seems I have a role as root during installation?

Please kindly give me some more guidance.

Many thanks,


Date: Tue, 29 May 2012 18:48:15 +1000
From: Mark.Abraham at anu.edu.au
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] How to install GROMACS in 64-bit?

    On 29/05/2012 6:37 PM, a a wrote:
        Dear Sir/Madam,

        Thanks for the insightful comments from the experts.  
           Follows the steps, I found the source of error:

        This what I have done:

          In the following directory /home/softwares/fftw-3.0.1:
          ./configure --enable-shared
          make install

          In the .bash file:
          export LDFLAGS="-L/home/softwares/fftw301/lib"

          go to the following directory
          ./configure --enable-shared --prefix=/home/softwares/g455


          In the middle of the make, I found this error message:


          /usr/bin/ld: /usr/local/lib/libfftw3f.a(alloc.o):
            relocation R_X86_64_32 against `.rodata.str1.1' can not be
            used when making a shared object; recompile with -fPIC
          /usr/local/lib/libfftw3f.a: could not read symbols: Bad
          collect2: ld returned 1 exit status
          make[3]: *** [libmd.la] Error 1
          make[3]: Leaving directory
          make[2]: *** [all-recursive] Error 1
          make[2]: Leaving directory
          make[1]: *** [all] Error 2
          make[1]: Leaving directory
          make: *** [all-recursive] Error 1


        It seems to be a problem of 64 and 32 bit, my workstation
          is a 64 bit machine and the OS is also 64 bit, what should I
          do to make sure both the fftw-3.0.1
            library and GROMACS are compiled with 64 bit settings?

    I would start by observing that those error messages pertain to an
    installation of FFTW that configure found in /usr/local/lib, and not
    the one in /home/softwares. You have to sort that out first, since
    this error messages indicates the need to use FFTW configured with
    --enable-shared, per the link I gave last time.




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