[gmx-users] problem installing gromacs

[Mark Abraham]

Samik Bhattacharya wrote:
> 
> --- On Thu, 13/8/09, st <y1gao at ucsd.edu> wrote:
> 
> From: st <y1gao at ucsd.edu>
> Subject: [gmx-users] problem installing gromacs
> To: gmx-users at gromacs.org
> Date: Thursday, 13 August, 2009, 1:42 AM
> 
> 
> 
>  
> Hi There,
>  
> I have some problems 
> installing gromacs on the linux server. 
>  
> fftw installed with no error, but when I install 
> gromacs,
> I got the following error:
> *****************************************
> /bin/sh ../../libtool --tag=CC   --mode=link 
> cc  -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused 
> -funroll-all-loops  -L/home/y1gao/soft/fftw/lib   -o grompp 
> grompp.o libgmxpreprocess_d.la ../mdlib/l
> cc -O3 -fomit-frame-pointer 
> -finline-functions -Wall -Wno-unused -funroll-all-loops -o .libs/grompp 
> grompp.o  -L/home/y1gao/soft/fftw/lib ./.libs/libgmxpreprocess_d.a 
> -L/usr/X11R6/lib ../mdlib/.libs/libmd_d.so /n
> _d.so -lnsl -lfftw3 -lm -lSM 
> -lICE -lX11  -Wl,--rpath 
> -Wl,/home/y1gao/soft/gromacs//lib
> .../mdlib/.libs/libmd_d.so: undefined 
> reference to `__libm_sse2_sincos'
> .../mdlib/.libs/libmd_d.so: undefined 
> reference to `__libm_sse2_log'
> .../mdlib/.libs/libmd_d.so: undefined reference 
> to `_intel_fast_memcpy'
> collect2: ld returned 1 exit status
> make[3]: *** 
> [grompp] Error 1
> make[3]: Leaving directory 
> `/nas/y1gao/installation_files/gromacs-4.0.4/gromacs-4.0.4/src/kernel'
> make[2]: 
> *** [all-recursive] Error 1
> make[2]: Leaving directory 
> `/nas/y1gao/installation_files/gromacs-4.0.4/gromacs-4.0.4/src'
> make[1]: *** 
> [all] Error 2
> make[1]: Leaving directory 
> `/nas/y1gao/installation_files/gromacs-4.0.4/gromacs-4.0.4/src'
> make: *** 
> [all-recursive] Error 1
> *******************************************
>  
> I used the combinations of the following fftw and 
> gromacs:
> fftw 3.2.1; fftw3.2.2
> gromacs 3.3.3; gromacs 4.0.4
>  
> gcc version 3.4.6
>  
> 
> 
> try with make links after make install of gromacs. probably this may help.....
> good luck

No. The object-linking process is failing. So making file system 
symlinks after object-linking and installation will not help.

Mark