[gmx-users] problem installing gromacs

st y1gao at ucsd.edu
Wed Aug 12 22:12:48 CEST 2009

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

The command I used are:
To install fftw:
 $ ./configure --enable-threads --enable-sse2 -prefix /home/y1gao/soft/fftw/lib
 $ make
$ make install

To install gromacs:
$ ./configure --enable-shared LDFLAGS='-L/home/y1gao/soft/fftw/lib' CPPFLAGS='-I/home/y1gao/soft/fftw/include' --enable-double --prefix=/home/y1gao/soft/gromacs/
$ make
$ make install
( error comes out here)


Could anyone help me find a way out? Thanks in advance.

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