[gmx-users] FW: gmx-users Digest, Vol 44, Issue 3

David van der Spoel spoel at xray.bmc.uu.se
Fri Dec 7 08:47:27 CET 2007 

Bonner, Carl E. wrote:
> Thanks for the quick response. 
> 
> I am using the MacPorts/DarwinPorts installation so I don't think I have
> direct access to the compiler this way.  I do have access to the Mac OS X
> binaries.  Can I use these since they are already compiled?  If so how do I
> go about this.  The MacPorts are convenient and worked well on my other Macs
> before I switched over to OS 10.5.

The compiler comes with the OS. Please check your installation CD and 
install Xcode tools.
> 
> Thanks for any assistance.
> 
> Carl
> 
> 
> Carl E. Bonner, Jr., Ph.D 
> Director, Center for Materials Research, 
> Professor of Chemistry and Materials Science 
> Norfolk State University 700 Park Avenue, Norfolk, VA 23504 
> (757) 823-2097 (voice) (757) 823-9054 (fax), 
> http://vigyan.nsu.edu/~cmr/cebonner.htm
> 
> 
> 
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org on behalf of
> gmx-users-request at gromacs.org
> Sent: Sun 12/2/2007 6:00 AM
> To: gmx-users at gromacs.org
> Subject: gmx-users Digest, Vol 44, Issue 3
>  
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> Today's Topics:
> 
>    1. Re: Help, Errors while compiling gromacs under Mac OS	X 10.5
>       Leopard (David van der Spoel)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Sun, 02 Dec 2007 09:56:17 +0100
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> 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: <47527331.90904 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> Bonner, Carl E. wrote:
>> I am trying to set up gromacs on a G4 powerbook 1.25 GB RAM, 60 MB Drive,
> I
>> have upgraded to OS X 10.5.  I am using the Darwinports installer. As
>> instructed, I have installed XCode tools, X11 SDK.  I got xmgrace to work,
>> however, gwyddion, rasmol and gromacs error on compilation.  For gromacs,
> I
>> get the following error:
> 
> This may mean that you have to change some compiler flags, since Leopard 
> comes with a new version of gcc. Previously one had to use -faltive. 
> Maybe you can read the gcc manual (man gcc) and the rerun
> make CFLAGS="-faltivec"
> or similar new flags. But I cannot find the right options right now..
> 
>>
>> Carl-Bonners-laptop-Computer:gromacs carlbonner$ sudo port install gromacs
>> Password:
>> --->  Building gromacs with target all
>> Error: Target org.macports.build returned: shell command " cd
>>
> "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports
>> .org_release_ports_science_gromacs/work/gromacs-3.3.1" && make all "
> returned
>> error 2
>> Command output: nb_kernel010_ppc_altivec.c:145: error: 'Vvdw6' undeclared
>> (first use in this function)
>> nb_kernel010_ppc_altivec.c:146: error: 'Vvdw12' undeclared (first use in
> this
>> function)
>> nb_kernel010_ppc_altivec.c:150: error: 'fs' undeclared (first use in this
>> function)
>> nb_kernel010_ppc_altivec.c:159: error: 'tmp1' undeclared (first use in this
>> function)
>> nb_kernel010_ppc_altivec.c:159: error: 'tmp2' undeclared (first use in this
>> function)
>> nb_kernel010_ppc_altivec.c:159: error: 'tmp3' undeclared (first use in this
>> function)
>> nb_kernel010_ppc_altivec.c:159: error: 'tmp4' undeclared (first use in this
>> function)
>> nb_kernel010_ppc_altivec.c: In function 'nb_kernel010nf_ppc_altivec':
>> nb_kernel010_ppc_altivec.c:293: error: 'vector' undeclared (first use in
> this
>> function)
>> nb_kernel010_ppc_altivec.c:293: error: syntax error before 'float'
>> nb_kernel010_ppc_altivec.c:312: error: 'nul' undeclared (first use in this
>> function)
>> nb_kernel010_ppc_altivec.c:331: error: 'shvec' undeclared (first use in
> this
>> function)
>> nb_kernel010_ppc_altivec.c:334: error: 'ix' undeclared (first use in this
>> function)
>> nb_kernel010_ppc_altivec.c:335: error: 'Vvdwtot' undeclared (first use in
>> this function)
>> nb_kernel010_ppc_altivec.c:339: error: 'iy' undeclared (first use in this
>> function)
>> nb_kernel010_ppc_altivec.c:339: error: 'iz' undeclared (first use in this
>> function)
>> nb_kernel010_ppc_altivec.c:353: error: 'dx' undeclared (first use in this
>> function)
>> nb_kernel010_ppc_altivec.c:353: error: 'dy' undeclared (first use in this
>> function)
>> nb_kernel010_ppc_altivec.c:353: error: 'dz' undeclared (first use in this
>> function)
>> nb_kernel010_ppc_altivec.c:357: error: 'rsq' undeclared (first use in this
>> function)
>> nb_kernel010_ppc_altivec.c:360: error: 'rinvsq' undeclared (first use in
> this
>> function)
>> nb_kernel010_ppc_altivec.c:361: error: 'rinvsix' undeclared (first use in
>> this function)
>> nb_kernel010_ppc_altivec.c:367: error: 'c6' undeclared (first use in this
>> function)
>> nb_kernel010_ppc_altivec.c:367: error: 'c12' undeclared (first use in this
>> function)
>> 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
>>
>> Is this a problem with my gromacs installation, Leopard, or the operator?
>>
>> Thanks for any help
>>
>> Carl E. Bonner, Jr., Ph.D 
>> Professor of Chemistry and Materials Science 
>> Norfolk State University 700 Park Avenue, Norfolk, VA 23504 
>> (757) 823-2097 (voice) (757) 823-9054 (fax), 
>> http://vigyan.nsu.edu/~cmr/cebonner.htm
>>
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> 
> 


-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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