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

susan james sjames at lbl.gov
Sat Feb 10 01:34:24 CET 2007


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 
collect2: ld returned 1 exit status
mpicc: No such file or directory
make[3]: *** [grompp] Error 1
make[3]: Leaving directory 
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory 
make[1]: *** [all] Error 2
make[1]: Leaving directory 
make: *** [all-recursive] Error 1

here's my env:

CAN SOMEONE HELP?  what am I missing?

thank you.

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