On May 20, 2010, at 10:45 PM, Jason Swails wrote:
> 2010/5/20 Kensuke Nakamura <kensuke-nm.is.naist.jp>
>
>> 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.
>>
>
> Yes, because configure_at itself calls the configure script in the netcdf
> directory with its own flags. Thus, even if you modify config.h to remove
> the -m32 flags, they have still been passed to netcdf's configure script and
> will appear in its Makefiles. However, because OS X 10.6 came out well
> after AmberTools 1.2/Amber10 were released, this issue (which I still blame
> on OS X) couldn't be anticipated. Amber11 (and AmberTools 1.4) does not
> suffer from this, since the hurdle of architecture incompatibilities with OS
> X 10.6 came out during its development (and have subsequently been addressed
> prior to release).
>
> Although a question to potentially help future users that may struggle with
> this: Did you have to go into the netcdf directory itself and do a "make
> distclean" or something related? Or was "make clean" in $AMBERHOME/src
> enough?
>
I seem to remember having to do this while I was troubleshooting Amber 10.
> About the test problem, I believe the segfault associated with the NAB test
> you see failing is also fixed in AmberTools 1.4..
>
> Thanks!
> Jason
>
> P.S. perhaps another approach to building Amber10/AmberTools1.2 on Mac OS X
> 10.6 is to boot into the 64-bit kernel to perform the install (do this by
> holding the numbers 6 and 4 down when the computer is first turned on). That
> way the configure script will recognize a 64-bit kernel (uname -m returns
> x86_64 instead of i386)
>
>
>>
>> -----------------------------------------------------------------------------------------------------------
>> [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
>>>>
>>>>
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>>>> 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
>>
>> $BCfB<7z2p(B
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>>
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>> TEL: 0743-72-5257(Fax:5258)
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>>
>>
>>
>>
>>
>>
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>
>
>
> --
> 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 May 21 2010 - 06:30:05 PDT
