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

[Mark Abraham]

On 30/05/2012 1:50 AM, a a wrote:
> 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 CPPFLAGS="-I/home/softwares/fftw301/include"
> export LDFLAGS="-L/home/softwares/fftw301/lib"
>
> Should I type in another lines?

They won't help until you start a new shell. Or, instead, use them on 
the command line like the installation instructions suggest - since you 
don't need these settings on an ongoing basis.

>
> 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?

Definitely not. "make install" is the only command for which you should 
be root, and only then if the installation location requires it. Unless 
you like pain from risking needing to reinstall your trashed system.

Mark

>
> Please kindly give me some more guidance.
>
> Many thanks,
>
> Catherine
>
>
> ------------------------------------------------------------------------
> 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 --prefix=/home/softwares/fftw301
>     make
>     make install
>
>     In the .bash file:
>     export CPPFLAGS="-I/home/softwares/fftw301/include"
>     export LDFLAGS="-L/home/softwares/fftw301/lib"
>
>     go to the following directory /home/softwares/gromacs-4.5.5:
>     ./configure --enable-shared --prefix=/home/softwares/g455
>     make
>     ============================================= ==============
>
>     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 value
>     collect2: ld returned 1 exit status
>     make[3]: *** [libmd.la] Error 1
>     make[3]: Leaving directory `/home/softwares/gromacs-4.5.5/src/mdlib'
>     make[2]: *** [all-recursive] Error 1
>     make[2]: Leaving directory `/home/softwares/gromacs-4.5.5/src'
>     make[1]: *** [all] Error 2
>     make[1]: Leaving directory `/home/softwares/gromacs-4.5.5/src'
>     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.
>
> Mark
>
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