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

[lina]

Hi Emily,

I have no idea about your problems, but I noticed that the gromacs you
used might be the one my colleague had sent to you, he modified
something to fit my multicores processors, I guess you may do a try to
use the original and official one also. 

Good luck,

Lina 
> ------------------------------
> 
> Message: 3
> Date: Thu, 13 May 2010 01:16:15 -0400
> From: Emily Curtis <emilymariecurtis at gmail.com>
> Subject: Re: [gmx-users] Help, Errors while compiling gromacs under
> 	Mac OS X 	10.5 Leopard
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> 	<AANLkTimhh75nvbEpmmNxHcOlYC5j4s2s_70c08aFJ2WI at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> 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
> >>>