[gmx-users] configuration, make, installation problem

[David van der Spoel]

Nevena Todorova wrote:
> Hi there,
> i am trying to install (double precision, mpi )Gromacs 3.3 on an SGI Altix system and during this process i encounter few problems.
> 
> I configure the system using the commmand:
> ./configure --enable-mpi --enable-shared --disable-nice --disable-float --prefix=$HOME/g-3.3 --program-suffix=_d_mpi --with-fft=fftw2
> 
> and  it seems to be running without problems untill the end where it stops without an output line for a successful configuration. It is not giving me an errors for missing programs, or environment set ups.
> The end look like this:
> "config.status: creating share/top/Makefile
> config.status: creating share/html/Makefile
> config.status: creating share/html/images/Makefile
> config.status: creating share/html/online/Makefile
> config.status: creating man/Makefile
> config.status: creating man/man1/Makefile
> config.status: creating src/config.h
> config.status: executing depfiles commands
> "
> 
> If i try to run "make" after this, it is compiling for some time until it stops with the following output:
> ": multiple definition of `fftwnd_f77_destroy_plan_'
> nonbonded/.libs/libnonbonded.a(fftwf77.o)(.text+0x680): first defined here
> /opt/fftw-2.1.5/intel-9.0/lib/libdfftw.a(fftwf77.o)(.text+0x700): In function `fftwnd_f77_':
> : multiple definition of `fftwnd_f77_'
> nonbonded/.libs/libnonbonded.a(fftwf77.o)(.text+0x700): first defined here
> /opt/fftw-2.1.5/intel-9.0/lib/libdfftw.a(fftwf77.o)(.text+0x780): In function `fftwnd_f77_one_':
> : multiple definition of `fftwnd_f77_one_'
> nonbonded/.libs/libnonbonded.a(fftwf77.o)(.text+0x780): first defined here
> ld: nonbonded/.libs/libnonbonded.a(rplanner.o): @gprel relocation against dynamic symbol rfftw_plan_hook
> ld: nonbonded/.libs/libnonbonded.a(rplanner.o): @gprel relocation against dynamic symbol rfftw_plan_hook
> ld: nonbonded/.libs/libnonbonded.a(rplanner.o): @gprel relocation against dynamic symbol rfftw_plan_hook
> ld: nonbonded/.libs/libnonbonded.a(rplanner.o): @gprel relocation against dynamic symbol rfftw_plan_hook
> ld: nonbonded/.libs/libnonbonded.a(rplanner.o): @gprel relocation against dynamic symbol rfftw_plan_hook
> ld: nonbonded/.libs/libnonbonded.a(rplanner.o): @gprel relocation against dynamic symbol rfftw_plan_hook
> make[4]: *** [libgmx_mpi_d.la] Error 1
> make[4]: Leaving directory `/home/595/nxt595/gromacs-3.3/src/gmxlib'
> make[3]: *** [all-recursive] Error 1
> make[3]: Leaving directory `/home/595/nxt595/gromacs-3.3/src/gmxlib'
> make[2]: *** [all-recursive] Error 1
> make[2]: Leaving directory `/home/595/nxt595/gromacs-3.3/src'
> make[1]: *** [all] Error 2
> make[1]: Leaving directory `/home/595/nxt595/gromacs-3.3/src'
> make: *** [all-recursive] Error 1
> "
> 
> The installation guide on the Gromacs website is excellent, but i can not find a reason for these errors.
> I am new to Gromacs and i would appreciate it if anybody can help me out with this.
> How do i know if i have installed the programm successfully? Is there a conformation output in the very end, or is it a matter of testing it out???
> 
> Thanks in advance,
> Nevena 
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check the link command line. are the fftw libraries included twice? a 
safe way is to do your own fftw libraries (use version 3 in that case).

before doing anything else, do a make distclean, there could be 
leftovers from a single precision or non-mpi compilation

-- 
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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