[gmx-users] Gromacs 4.0 installation problem

Mark Abraham Mark.Abraham at anu.edu.au
Thu Oct 30 02:05:26 CET 2008

Chavatte Philippe wrote:
> Hi,
> We are trying to install gromacs 4.0 on our new SGI cluster running under
> RHEL5.
> The configure script run fine (./configure –prefix =/install-dir).
> But an error occurs during the building (make) :
> cc -DHAVE_CONFIG_H -I. -I../../src  -I../../include
> -DGMXLIBDIR=\"/data1/soft/linux/gromacs-4.0/share/top\"
> -I/data1/soft/linux/fftw-3.1.3/include  -O3 -fomit-frame-pointer
> -finline-functions -Wall -Wno-unused -funroll-all-loops -MT grompp.o -MD
> -MP -MF .deps/grompp.Tpo -c -o grompp.o grompp.c
> mv -f .deps/grompp.Tpo .deps/grompp.Po
> /bin/sh ../../libtool --tag=CC   --mode=link cc  -O3 -fomit-frame-pointer
> -finline-functions -Wall -Wno-unused -funroll-all-loops 
> -L/data1/soft/linux/fftw-3.1.3/lib   -o grompp grompp.o
> libgmxpreprocess.la ../mdlib/libmd.la ../gmxlib/libgmx.la  -L/usr/lib64
> -lnsl -lfftw3f -lm   -lX11
> cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused
> -funroll-all-loops -o grompp grompp.o  -L/data1/soft/linux/fftw-3.1.3/lib
> ./.libs/libgmxpreprocess.a -L/usr/lib64 ../mdlib/.libs/libmd.a
> ../gmxlib/.libs/libgmx.a -lnsl
> /data1/soft/linux/fftw-3.1.3/lib/libfftw3f.a -lm -lX11
> /usr/bin/ld: cannot find -lX11

That's indicative of something weird going on. configure should have 
looked for this library and found it. Nonetheless, it's only used in one 
utility in GROMACS (ngmx) and there are plenty of other bits of 
visualization software that can replace it. One work-around is simply to 
"configure --without-x --and-your-other-options" and GROMACS will not 
attempt to build ngmx, and not require this library for the rest of the 


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