[gmx-users] gromacs-3.3 build on linux. make fails

[David van der Spoel]

susan james wrote:
> Hello,
> 
> I'm new to this list and hope I can get some help.
> 
> I'm seeking help with installing double precision gromacs-3.3
> on Centos-4 linux.
> 
> I'm using Lam-7.1.2 built with gcc4.
> 
> I built fftw with this configure string which succeeded:
> ./configure --prefix=/usr/local/fftw301-double --enable-threads
> 
> here's my gromacs configure string which succeeds:
> ./configure --enable-shared --without-motif-libraries --disable-float 
> --prefix=/usr/local/gromacs-double/3.3 --enable-mpi --with-fft=fftw3
> 
> The gromacs configure succeeds:
> ================================
> config.status: creating man/man1/Makefile
> config.status: creating src/config.h
> config.status: executing depfiles commands
> 
> * You are compiling a double precision version of Gromacs -
>   program names will be suffixed with _d to avoid overwriting single
>   precision files. You can override it with --program-suffix
> 
> * Seems you are compiling with MPI support. You can install the MPI-
>   enabled programs with suffixed names to have both MPI and non-MPI
>   versions. This is useful e.g. on supercomputers where you usually
>   cannot run MPI-linked programs on the login node.
>   Set a suffix with e.g. --program-suffix=_mpi (or _mpi_d for double).
>   You only need MPI for mdrun, so if you already have non-MPI stuff
>   installed you can issue make mdrun; make install-mdrun.
> ================================
> 
> the gromacs make fails.   the complete log is too large to send.
> and, more precisely, here's where make bailed out.
> ===================================
> mx_mpi_d.so -lnsl /usr/local/fftw301-double/lib/libfftw3.a -lm -lSM 
> -lICE -lX11 -Wl,--rpath -Wl,/usr/local/gromacs-double/3.3/lib
> ../gmxlib/.libs/libgmx_mpi_d.so: undefined reference to 
> `_nb_kerne010_x86_64_sse2'
> collect2: ld returned 1 exit status
> mpicc: No such file or directory
> make[3]: *** [grompp] Error 1
> make[3]: Leaving directory 
> `/root/src/gromacs/gromacs-3.3-double/gromacs-3.3/src/kernel'
> make[2]: *** [all-recursive] Error 1
> make[2]: Leaving directory 
> `/root/src/gromacs/gromacs-3.3-double/gromacs-3.3/src'
> make[1]: *** [all] Error 2
> make[1]: Leaving directory 
> `/root/src/gromacs/gromacs-3.3-double/gromacs-3.3/src'
> make: *** [all-recursive] Error 1
> =================================
> 
for some reason it did not compile the assembly bits. it could be due to 
gcc4, or maybe because you did a single precision compilation first. in 
the latter case try make distclean before running configure.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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