[gmx-users] Compiling GROMACS 4.5.6 in Cluster

[Justin Lemkul]

On 9/12/14 2:28 PM, Agnivo Gosai wrote:
> Dear Users
>
> I am facing a problem while compiling the GROMACS source code in my
> university cluster. I am laying down my installation procedure step by step
> :-
>
> 1. Downloaded fftw 3.3.4
> 2. exported paths of C-compiler and Fortran-compiler
> 3. Used the following command line to configure FFTW
> *./configure --prefix=/home/agosai/GROMACS/fftw-3.3.4-double
> --enable-threads --with-pic=-fPIC*
> There were no errors.
> Proceeded with make and then make install.
>
> 4.  Downloaded and unzipped GROMACS 4.5.6 source code
> 5. exported c++ compiler paths.
> 6. Defined path to FFTW compilation as follows :-
>
> *export CPPFLAGS="-I/home/agosai/GROMACS/fftw-3.3.4-double/include"export
> LDFLAGS="-L/home/agosai/GROMACS/fftw-3.3.4-double/lib"*
> 7. Tried compiling GROMACS as follows :-
> *./configure --prefix=/home/agosai/GROMACS/gromacs-4.5.6-double
> --disable-float --program-suffix=-4.5.6-double --with-fft=fftw3*
>
> There were no errors.
> 8. Then used "make"
>   Following messages came :-
>
>
>
>
>
>
>
>
>
> *ld: /home/agosai/GROMACS/fftw-3.3.4-double/lib/libfftw3.a(mapflags.o):
> relocation R_X86_64_32S against `.rodata' can not be used when making a
> shared object;


> recompile with -fPIC

This is the key message.

http://www.gromacs.org/Documentation/Installation_Instructions_4.5#Details_for_building_the_FFTW_prerequisite

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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