[gmx-users] Help, Errors while compiling gromacs under Mac OS X 10.5 Leopard

Thu May 13 07:16:15 CEST 2010

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 | 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 | 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 | 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>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>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    http://folding.bmc.uu.se/
>>
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
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>>
>
>
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