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

[Florian Haberl]

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) − 9131 − 85 26581
 Mailto: florian.haberl AT chemie.uni-erlangen.de
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