[gmx-users] Installation of Gromacs into BG/L

Hiroshi Fujisaki fujisaki at bu.edu
Wed Sep 20 22:16:12 CEST 2006


Dear Florian,

Thanks for your help. It worked!
I should have tried fftw-3.1.2 first ...

Best wishes,

> hi,
> 
> On Wednesday 20 September 2006 16:07, Hiroshi Fujisaki wrote:
> > Dear Gromacs users,
> >
> > I am now trying to install gromacs into our BlueGene facility,
> > but I fail when I do make. (configure seems to be fine.)
> > The link to the FFTW library does not seem to work.
> > I use fftw-2.1.5. I attach the excerpt of the make log file here
> > (the last part of the log).
> 
> Have yout tried it with fftw 3.1.2 version?
> perhaps some problem with linking to X?
> 
> so configure  --without-x and malloc
> 
> >
> > ###########################################################################
> >#########
> >
> > cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -maltivec
> > -mabi=altivec -mcpu=7450 -mtune=970 -o mdrun glaasje.o gctio.o init_sh.o
> > ionize.o do_gct.o relax_sh.o repl_ex.o xutils.o md.o mdrun.o genalg.o 
> > -L/bgl/local/fftw-2.1.5/lib ../mdlib/.libs/libmd_d.a -L/usr/X11R6/lib
> > ../gmxlib/.libs/libgmx_d.a -lnsl /bgl/local/fftw-2.1.5/lib/librfftw.a
> > /bgl/local/fftw-2.1.5/lib/libfftw.a -lm /usr/X11R6/lib/libXm.so -lXt -lSM
> > -lICE -lXext -lXp -lX11
> > /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0x56): In function
> > `read_int': /u/walkup/download/fftw-2.1.5/fftw/wisdom.c:224: undefined
> > reference to `__ctype_b'
> > /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0x62):/u/walkup/downloa
> >d/fftw-2.1.5/fftw/wisdom.c:224: undefined reference to `__ctype_b'
> > /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0x9e):/u/walkup/downloa
> >d/fftw-2.1.5/fftw/wisdom.c:229: undefined reference to `__ctype_b'
> > /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0xfa): In function
> > `eat_blanks': /u/walkup/download/fftw-2.1.5/fftw/wisdom.c:209: undefined
> > reference to `__ctype_b'
> > /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0x102):/u/walkup/downlo
> >ad/fftw-2.1.5/fftw/wisdom.c:209: undefined reference to `__ctype_b'
> > /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0x126):/u/walkup/downlo
> >ad/fftw-2.1.5/fftw/wisdom.c:209: more undefined references to `__ctype_b'
> > follow /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0x26a): In
> > function `toupper':
> > /bgl/BlueLight/ppcfloor/blrts-gnu/powerpc-bgl-blrts-gnu/sys-include/ctype.h
> >:176: undefined reference to `__ctype_toupper'
> > /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0x276):/bgl/BlueLight/p
> >pcfloor/blrts-gnu/powerpc-bgl-blrts-gnu/sys-include/ctype.h:176: undefined
> > reference to `__ctype_toupper'
> > /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0x28e): In function
> > `tolower':
> > /bgl/BlueLight/ppcfloor/blrts-gnu/powerpc-bgl-blrts-gnu/sys-include/ctype.h
> >:170: undefined reference to `__ctype_tolower'
> > /bgl/local/fftw-2.1.5/lib/libfftw.a(wisdom.o)(.text+0x29a):/bgl/BlueLight/p
> >pcfloor/blrts-gnu/powerpc-bgl-blrts-gnu/sys-include/ctype.h:170: undefined
> > reference to `__ctype_tolower'
> > /bgl/local/fftw-2.1.5/lib/libfftw.a(rader.o)(.text+0x128): In function
> > `fftwi_twiddle_rader': /u/walkup/download/fftw-2.1.5/fftw/rader.c:273:
> > undefined reference to `__divi64'
> > /bgl/local/fftw-2.1.5/lib/libfftw.a(rader.o)(.text+0x244):/u/walkup/downloa
> >d/fftw-2.1.5/fftw/rader.c:321: undefined reference to `__divi64'
> > /bgl/local/fftw-2.1.5/lib/libfftw.a(rader.o)(.text+0x470): In function
> > `fftw_twiddle_rader': /u/walkup/download/fftw-2.1.5/fftw/rader.c:190:
> > undefined reference to `__divi64'
> > /bgl/local/fftw-2.1.5/lib/libfftw.a(rader.o)(.text+0x590):/u/walkup/downloa
> >d/fftw-2.1.5/fftw/rader.c:238: undefined reference to `__divi64'
> > /bgl/local/fftw-2.1.5/lib/libfftw.a(rader.o)(.text+0x8ac): In function
> > `create_rader_aux': /u/walkup/download/fftw-2.1.5/fftw/rader.c:115:
> > undefined reference to `__divi64'
> > /bgl/local/fftw-2.1.5/lib/libfftw.a(rader.o)(.text+0xa7c):/u/walkup/downloa
> >d/fftw-2.1.5/fftw/rader.c:59: more undefined references to `__divi64' follow
> > collect2: ld returned 1 exit status
> > make[3]: *** [mdrun] Error 1
> > make[3]: Leaving directory
> > `/project2/gaussden/fujisaki/src/gromacs-3.3.1/src/kernel' make[2]: ***
> > [all-recursive] Error 1
> > make[2]: Leaving directory
> > `/project2/gaussden/fujisaki/src/gromacs-3.3.1/src' make[1]: *** [all]
> > Error 2
> > make[1]: Leaving directory
> > `/project2/gaussden/fujisaki/src/gromacs-3.3.1/src' make: ***
> > [all-recursive] Error 1
> >
> > ###########################################################################
> >#############
> >
> > I appreciate your help.
> >
> > Best wishes,
> 
> Greetings,
> 
> Florian
> -- 
> -------------------------------------------------------------------------------
>  Florian Haberl                        
>  Computer-Chemie-Centrum   
>  Universitaet Erlangen/ Nuernberg
>  Naegelsbachstr 25
>  D-91052 Erlangen
>  Telephone:  	+49(0) $BchC(B9131 $BchC(B85 26581
>  Mailto: florian.haberl AT chemie.uni-erlangen.de
> -------------------------------------------------------------------------------
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-- 
Hiroshi Fujisaki <fujisaki at bu.edu>




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