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?
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
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu May 20 2010 - 21:00:03 PDT
