[gmx-users] problem installing gromacs

Samik Bhattacharya samikbhat at yahoo.co.in
Thu Aug 13 06:19:28 CEST 2009

--- 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 
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 
.../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 
*** [all-recursive] Error 1
make[2]: Leaving directory 
make[1]: *** 
[all] Error 2
make[1]: Leaving directory 
make: *** 
[all-recursive] Error 1
I used the combinations of the following fftw and 
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

The command I used are:
To install fftw:
 $ ./configure 
--enable-threads --enable-sse2 -prefix 
 $ 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 
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