[gmx-users] gmx4.5.4 installation help

Mark Abraham Mark.Abraham at anu.edu.au
Thu Jun 2 09:11:40 CEST 2011


On 2/06/2011 5:03 PM, Chandan Choudhury wrote:
> Hello gmx-users,
>
> I am trying to install gmx-4.5.4 on a HPC Linux cluster x86_64.
> 1. I installed fftw 3.2.2
>              ./configure --prefix /soft/sudip/abc/execs/fftw/  
> --enable-single --enable-threads
> 2. Installing Gromacs : CPPFLAGS and LDFLAGS were written in bashrc file
>     a)         ./configure --prefix=/soft/sudip/abc/execs/gromacs/
>        execute successfully without any complain.
>     b) make
>              /usr/bin/ld: 
> /soft/sudip/abc/execs/fftw/lib/libfftw3f.a(apiplan.o): relocation 
> R_X86_64_32 against `a local symbol' can not be used when making a 
> shared object; recompile with -fPIC
>              /soft/sudip/abc/execs/fftw/lib/libfftw3f.a: could not 
> read symbols: Bad value
>              collect2: ld returned 1 exit status
>              make[3]: *** [libmd.la <http://libmd.la>] Error 1
>              make[3]: Leaving directory 
> `/soft/sudip/abc/untar/gromacs-4.5.4/src/mdlib'
>              make[2]: *** [all-recursive] Error 1
>              make[2]: Leaving directory 
> `/soft/sudip/abc/untar/gromacs-4.5.4/src'
>              make[1]: *** [all] Error 2
>              make[1]: Leaving directory 
> `/soft/sudip/abc/untar/gromacs-4.5.4/src'
>              make: *** [all-recursive] Error 1
>
>       shows problem.
>
> Couldnot understand the origin of problem. Kndly let me know if some 
> information is missing.

See http://www.gromacs.org/Downloads/Installation_Instructions, where 
this problem is discussed.

Mark
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