okay, i did make -f Makefile_at clean and still got the problem.
it turned out Makefile's in directories under src/netcdf still had -m32 option and
I modified configure_at instead of .config.h and it worked.
however, test still does not work.
-----------------------------------------------------------------------------------------------------------
[naist-wavenet:~/apps/amber10/test] kenske% make -f Makefile_at test
( cd nab; make test )
=====================================================
Running test to make dna duplex:
/bin/sh: line 1: 9394 Segmentation fault ./duplex < duplex.in
make[1]: *** [duplex_test] Error 139
make: *** [test.nab] Error 2
-----------------------------------------------------------------------------------------------------------
Now I think i should try the AmberTools1.4.
Thank you for many helps so far!
kenske
>
> However, the error you're getting is a result of left-over object files
> built with the -m32 (or equivalent) flag, so you need to "make clean" to get
> rid of them.
>
> Good luck!
> Jason
>
> On Thu, May 20, 2010 at 10:03 PM, case <case.biomaps.rutgers.edu> wrote:
>
>> On Fri, May 21, 2010, Kensuke Nakamura wrote:
>>>>
>>>> These are architecture issues arising from the new 64-bit support in
>> snow
>>>> leopard. Look at the config.h and config_amber.h and remove all
>> instances
>>>> of "-m32" or "-march=i686" or i386, or anything else that looks like it
>>>> could be implying a 32-bit architecture (since uname -m returns i386
>> for Mac
>>>> OS X 10.6 unless you boot into the 64-bit kernel).
>>>
>>> I took -m32 out from config.h and make proceeded, before I get another
>> error..
>>> ld: warning: in ../netcdf/lib/libnetcdf.a, file was built for unsupported
>> file format which is not the architecture being linked (x86_64)
>>
>> It looks like you have left-over files from an earlier compile in the
>> netcdf
>> subdirectory. Be sure to type "make clean" (and make sure that
>> netcdf/lib/libnetcdf.a is removed) before continuing.
>>
>> ...good luck...dac
>>
>>
>> _______________________________________________
>> 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 Thu May 20 2010 - 20:30:04 PDT
