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
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Received on Fri Nov 12 2010 - 12:30:04 PST
