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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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