Thank you , thank you!
Yeah... A complete fresh reinstall worked fine!
Sometimes I get stuck in the trees and forget to see the forest.
Thanks again Jason!
Dean
> From: Dean Cuebas <deancuebas.missouristate.edu>
> Reply-To: AMBER Mailing List <amber.ambermd.org>
> Date: Fri, 12 Nov 2010 14:16:06 -0600
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Compiling Ambertools 1.4 on MacBook SnowLeopard10.6.4
>
> Dear users,
>
> Thanks very much for your help regarding compiling on Snow Leopard!
>
> Just wanted to clarify that
>
>> sudo gcc_select gcc-mp-4.4
>
> Didn't work, as the only compilers available using
>
> sudo gcc_select -l
>
> did not give gcc-mp.4.4, but did give
>
> mp-gcc44
>
> So I chose that (and I saw in a previous email on the list, that you (Jason)
> selected that also...)
>
> After ./configure -macAccelerate gnu and make install I get the following:
> ++++++++++++
> .
> .
> .
>
> ranlib arpack.a
> mv arpack.a /usr/local/amber11/lib
> gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o main.o
> main.c
> gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o rdparm.o
> rdparm.c
> gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o dispatch.o
> dispatch.c
> gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o help.o
> help.c
> gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o utility.o
> utility.c
> gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o second.o
> second.c
> gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o io.o io.c
> io.c:782: error: conflicting types for 'gzipFileSize'
> io.c:681: note: previous definition of 'gzipFileSize' was here
> io.c:814: error: conflicting types for 'bzip2FileSize'
> io.c:728: note: previous definition of 'bzip2FileSize' was here
> io.c:840: error: conflicting types for 'zipFileSize'
> io.c:755: note: previous definition of 'zipFileSize' was here
> make[1]: *** [io.o] Error 1
> make: *** [serial] Error 2
> ++++++++++++++++++++++++++++++++++++++
>
> Any reason for the errors???
>
> Make test shows a bunch of errors involving arpack
>
> Any suggestions?
>
> Thanks so much for your help!
>
> Dean
>
> PS. The above is compiling after applying the bugfix.all to the source
>
>
> Dr. Dean Cuebas, Associate Professor of Chemistry
> deancuebas.missouristate.edu, Ph 417-836-8567 FAX 417-836-5507
> Dept. of Chemistry, Missouri State University
> Springfield, Missouri 65897
>
>
>
>> From: Jason Swails <jason.swails.gmail.com>
>> Reply-To: AMBER Mailing List <amber.ambermd.org>
>> Date: Thu, 11 Nov 2010 10:36:37 -0600
>> To: AMBER Mailing List <amber.ambermd.org>
>> Subject: Re: [AMBER] Compiling Ambertools 1.4 on MacBook SnowLeopard10.6.4
>>
>> Hi Dean,
>>
>> I'm guessing this is the "hpc.sourceforge" site, and for some reason it
>> looks like they like to have only the bleeding-edge version of any GCC
>> compiler on there. Last time I tried downloading from there, it was 4.5,
>> experimental, now 4.5 is official release and 4.6 is experimental. I would
>> avoid using these compilers, as they're most likely to be buggy over
>> official releases.
>>
>> My far more preferred method is using MacPorts, which in my experience has
>> caught up to advances in Snow Leopard much more than alternatives (i.e.
>> Fink). Download MacPorts and install a GCC from there. I currently have
>> 4.3 through 4.6 installed, but 4.4 seems to work the best for me.
>>
>> sudo port -v install gcc44
>> sudo port -v install gcc_select
>> sudo gcc_select gcc-mp-4.4
>>
>> The above commands should install GCC 4.4.5, install a selection utility
>> that makes selecting a version of GCC compilers very easy, then using that
>> utility to select your newly installed GCC. These are native x86_64
>> binaries, unlike Fink's versions that I've seen (which are i386, but can
>> build x86_64 objects if explicitly passed -m64).
>>
>> Then you should be ready to build without hiccups.
>>
>> Hope this helps,
>> Jason
>>
>> On Thu, Nov 11, 2010 at 10:19 AM, Dean Cuebas
>> <deancuebas.missouristate.edu>wrote:
>>
>>> Dear users,
>>>
>>> I've tried to install Ambertools1.4 and have a compiler problem.
>>> I followed the instructions on amberonmac.blogspot.com SATURDAY, MAY 15,
>>> 2010 post.
>>>
>>>
>>> 1) Dowloaded and installed gcc-snwleo-intel-bin.tar.gz
>>> 2) type gcc -v and I get:
>>> ++++++++++++++++++++++++
>>> Using built-in specs.
>>> COLLECT_GCC=gcc
>>>
>>> COLLECT_LTO_WRAPPER=/usr/local/libexec/gcc/x86_64-apple-darwin10/4.6.0/lto-w
>>> rapper
>>> Target: x86_64-apple-darwin10
>>> Configured with: ../gcc-4.6-20100703/configure
>>> --enable-languages=fortran,c++ --host=x86_64-apple-darwin10
>>> --build=x86_64-apple-darwin10
>>> Thread model: posix
>>> gcc version 4.6.0 20100703 (experimental) (GCC)
>>> ++++++++++++++++++++++++++++++++++
>>> Which is a higher version of gcc than in the amberonmac demo.
>>>
>>> 3) Type gfortran -v and I get:
>>>
>>> +++++++++++++++++++++++++++++
>>> Using built-in specs.
>>> COLLECT_GCC=gfortran
>>>
>>> COLLECT_LTO_WRAPPER=/usr/local/libexec/gcc/x86_64-apple-darwin10/4.6.0/lto-w
>>> rapper
>>> Target: x86_64-apple-darwin10
>>> Configured with: ../gcc-4.6-20100703/configure
>>> --enable-languages=fortran,c++ --host=x86_64-apple-darwin10
>>> --build=x86_64-apple-darwin10
>>> Thread model: posix
>>> gcc version 4.6.0 20100703 (experimental) (GCC)
>>> ++++++++++++++++++++++++++++++++++++
>>>
>>> 4) I cd to the src directory of Ambertools and type
>>> ./configure -macAccelerate gnu
>>>
>>> +++++++++++++++++++++++++++++++++++++++++++++
>>> Your AMBERHOME environment variable should be set to /usr/local/amber11
>>>
>>>
>>> Obtaining the gnu suite version:
>>> gcc -v
>>> The version is 4.6.0
>>>
>>> Testing the gcc compiler:
>>> gcc -DUSE_AMBER_C9XCOMPLEX -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
>>> -o testp testp.c
>>> testp.c:1:19: fatal error: stdio.h: No such file or directory
>>> compilation terminated.
>>> ./configure: line 967: ./testp: No such file or directory
>>> Error: Unable to compile a C program using gcc -DUSE_AMBER_C9XCOMPLEX
>>> -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
>>> Please check your compiler settings or configure flags.
>>> ++++++++++++++++++++++++++++++++++++++++++++++
>>>
>>> Any help would be appreciated!
>>>
>>> Thanks in advance.
>>>
>>> Dean
>>> --
>>> Dr. Dean Cuebas, Associate Prof of Chemistry
>>> deancuebas.missouristate.edu, Ph 417-836-8567 FAX 417-836-5507
>>> Dept. of Chemistry, Missouri State University
>>> Springfield, Missouri 65897
>>>
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Graduate Student
>> 352-392-4032
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Nov 12 2010 - 14:30:03 PST
