[gmx-users] Help, Errors while compiling gromacs under Mac OS X 10.5 Leopard
Erik Marklund
erikm at xray.bmc.uu.se
Fri May 14 09:42:42 CEST 2010
Am I missing something here? You're not getting any error messages, so
what's the problem?
Erik Marklund
Emily Curtis skrev:
> I've added a few flags and fixed some of the error messages but now I
> am getting these messages. Does anyone have any ideas about what I am
> doing wrong?
>
> creating highway
> Making all in contrib
> make[3]: Nothing to be done for `all'.
> make[3]: Nothing to be done for `all-am'.
> Making all in admin
> make[1]: Nothing to be done for `all'.
> Making all in scripts
> cat ./GMXRC.in | sed 's, at bindir\@,/Users/emily/gromacstrial/bin,' > GMXRC
> cat ./GMXRC.csh.in <http://GMXRC.csh.in> | sed
> 's, at libdir\@,/Users/emily/gromacstrial/lib,' | \
> sed 's, at bindir\@,/Users/emily/gromacstrial/bin,' | \
> sed 's, at datadir\@,/Users/emily/gromacstrial/share,' | \
> sed 's, at mandir\@,/Users/emily/gromacstrial/share/man,' > GMXRC.csh
> cat ./GMXRC.bash.in <http://GMXRC.bash.in> | sed
> 's, at libdir\@,/Users/emily/gromacstrial/lib,' | \
> sed 's, at bindir\@,/Users/emily/gromacstrial/bin,' | \
> sed 's, at datadir\@,/Users/emily/gromacstrial/share,' | \
> sed 's, at mandir\@,/Users/emily/gromacstrial/share/man,' > GMXRC.bash
> cat ./GMXRC.zsh.in <http://GMXRC.zsh.in> | sed
> 's, at libdir\@,/Users/emily/gromacstrial/lib,' | \
> sed 's, at bindir\@,/Users/emily/gromacstrial/bin,' | \
> sed 's, at datadir\@,/Users/emily/gromacstrial/share,' | \
> sed 's, at mandir\@,/Users/emily/gromacstrial/share/man,' > GMXRC.zsh
> Making all in share
> Making all in top
> make[2]: Nothing to be done for `all'.
> Making all in tutor
> Making all in nmr1
> make[3]: Nothing to be done for `all'.
> Making all in nmr2
> make[3]: Nothing to be done for `all'.
> Making all in speptide
> make[3]: Nothing to be done for `all'.
> Making all in water
> make[3]: Nothing to be done for `all'.
> Making all in gmxdemo
> make[3]: Nothing to be done for `all'.
> Making all in methanol
> make[3]: Nothing to be done for `all'.
> Making all in mixed
> make[3]: Nothing to be done for `all'.
> make[3]: Nothing to be done for `all-am'.
> Making all in template
> cat ./Template.mak | \
> sed 's, at LDFLAGS\@,-L/Users/emily/gromacstrial/lib
> -L/Developer/opt/intel/Compiler/11.1/067/Frameworks/mkl/lib/em64t
> -framework Accelerate,' | \
> sed 's, at LIBS\@,-lmd -lgmx -lxml2 -L/usr/X11/lib -R/usr/X11/lib
> -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lm -lSM -lICE -lX11
> ,' | \
> sed 's, at CFLAGS\@,-O3 -fomit-frame-pointer -finline-functions -Wall
> -Wno-unused -funroll-all-loops -I/usr/include/libxml2
> -I/Users/emily/gromacstrial/include
> -I/Users/emily/gromacstrial/include/gromacs,' | \
> sed 's, at CC\@,cc,' | \
> sed 's, at host\@,x86_64-apple-darwin,' >Makefile.x86_64-apple-darwin
> Making all in html
> Making all in .
> make[3]: Nothing to be done for `all-am'.
> Making all in images
> make[3]: Nothing to be done for `all'.
> Making all in online
> make[3]: Nothing to be done for `all'.
> make[2]: Nothing to be done for `all-am'.
> Making all in man
> Making all in man1
> make[2]: Nothing to be done for `all'.
> make[2]: Nothing to be done for `all-am'.
> make[1]: Nothing to be done for `all-am'.
> nom27267d:gromacs-4.0.7-mbh emily$
>
>
> On Wed, May 12, 2010 at 10:10 AM, Emily Curtis
> <emilymariecurtis at gmail.com <mailto:emilymariecurtis at gmail.com>> wrote:
>
> Here are all of the messages I get when I type "make". I have
> been trying to figure this out based on mailing list emails but I
> cant seem to find what I need to fix. Thank you for your help.
>
> Emily-Curtis-MacBook-Pro:gromacs-4.0.7-mbh emily$ make
> Making all in include
> Making all in .
> make[2]: Nothing to be done for `all-am'.
> Making all in types
> make[2]: Nothing to be done for `all'.
> Making all in src
> make all-recursive
> Making all in gmxlib
> Making all in nonbonded
> Making all in nb_kernel_ia32_sse
> /bin/sh ../../../../libtool --mode=compile cc -O3
> -fomit-frame-pointer -finline-functions -Wall -Wno-unused
> -funroll-all-loops -c -o nb_kernel010_ia32_sse.lo
> nb_kernel010_ia32_sse.s
> cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused
> -funroll-all-loops -c nb_kernel010_ia32_sse.s -o
> nb_kernel010_ia32_sse.o
> nb_kernel010_ia32_sse.s:88:suffix or operands invalid for `push'
> nb_kernel010_ia32_sse.s:90:suffix or operands invalid for `push'
> nb_kernel010_ia32_sse.s:91:suffix or operands invalid for `push'
> nb_kernel010_ia32_sse.s:92:suffix or operands invalid for `push'
> nb_kernel010_ia32_sse.s:93:suffix or operands invalid for `push'
> nb_kernel010_ia32_sse.s:94:suffix or operands invalid for `push'
> nb_kernel010_ia32_sse.s:95:suffix or operands invalid for `push'
> nb_kernel010_ia32_sse.s:796:suffix or operands invalid for `pop'
> nb_kernel010_ia32_sse.s:797:suffix or operands invalid for `pop'
> nb_kernel010_ia32_sse.s:798:suffix or operands invalid for `pop'
> nb_kernel010_ia32_sse.s:799:suffix or operands invalid for `pop'
> nb_kernel010_ia32_sse.s:800:suffix or operands invalid for `pop'
> nb_kernel010_ia32_sse.s:801:suffix or operands invalid for `pop'
> nb_kernel010_ia32_sse.s:866:suffix or operands invalid for `push'
> nb_kernel010_ia32_sse.s:868:suffix or operands invalid for `push'
> nb_kernel010_ia32_sse.s:869:suffix or operands invalid for `push'
> nb_kernel010_ia32_sse.s:870:suffix or operands invalid for `push'
> nb_kernel010_ia32_sse.s:871:suffix or operands invalid for `push'
> nb_kernel010_ia32_sse.s:872:suffix or operands invalid for `push'
> nb_kernel010_ia32_sse.s:873:suffix or operands invalid for `push'
> nb_kernel010_ia32_sse.s:1345:suffix or operands invalid for `pop'
> nb_kernel010_ia32_sse.s:1346:suffix or operands invalid for `pop'
> nb_kernel010_ia32_sse.s:1347:suffix or operands invalid for `pop'
> nb_kernel010_ia32_sse.s:1348:suffix or operands invalid for `pop'
> nb_kernel010_ia32_sse.s:1349:suffix or operands invalid for `pop'
> nb_kernel010_ia32_sse.s:1350:suffix or operands invalid for `pop'
> make[5]: *** [nb_kernel010_ia32_sse.lo] Error 1
> make[4]: *** [all-recursive] Error 1
> make[3]: *** [all-recursive] Error 1
> make[2]: *** [all-recursive] Error 1
> make[1]: *** [all] Error 2
> make: *** [all-recursive] Error 1
>
>
> On Wed, May 12, 2010 at 3:46 AM, Erik Marklund
> <erikm at xray.bmc.uu.se <mailto:erikm at xray.bmc.uu.se>> wrote:
>
> Hi,
>
> These error messages are not very informative, they just state
> that something went wrong in the linking process. There ought
> to be more descriptive messages prior to these linker errors.
> Post those, then perhaps we can help you out.
>
> Erik
>
> Emily Curtis skrev:
>
> Dr. Bonner,
>
> I am trying to install gromacs on a mac. I am running
> Leopard. I can configure successfully, however, when I
> type "make" I am getting the same errors that you reported:
>
> make[5]: *** [nb_kernel010_ppc_altivec.lo] Error 1
> make[4]: *** [all-recursive] Error 1
> make[3]: *** [all-recursive] Error 1
> make[2]: *** [all-recursive] Error 1
> make[1]: *** [all] Error 2
> make: *** [all-recursive] Error 1
>
> I read the gcc manual but I can't figure out what flags I
> need to include. Did you ever figure out the flags you
> needed to include to fix this? I appreciate your help
>
> Emily
>
>
>
> --
> -----------------------------------------------
> Erik Marklund, PhD student
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: +46 18 471 4537 fax: +46 18 511 755
> erikm at xray.bmc.uu.se <mailto:erikm at xray.bmc.uu.se>
> http://folding.bmc.uu.se/
>
> --
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>
--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
erikm at xray.bmc.uu.se http://folding.bmc.uu.se/
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