[MINC-users] minc "make check" error -- not just a Snow Leopard problem

[EJ Nikelski]

Hi all,

  Claude, I'm as sure as sure can get ...

jnikelski@[~]: otool -L /usr/local/bic/bin/minccalc
/usr/local/bic/bin/minccalc:
        /usr/local/bic/lib/libhdf5.6.dylib (compatibility version
7.0.0, current version 7.4.0)
        /usr/lib/libz.1.dylib (compatibility version 1.0.0, current
version 1.2.3)
        /usr/local/bic/lib/libnetcdf.4.dylib (compatibility version
5.0.0, current version 5.0.0)
        /usr/lib/libSystem.B.dylib (compatibility version 1.0.0,
current version 125.2.1)

    When you built netcdf and hdf5, did you not build the shared libs?
 If not, then that would explain the use of static linkage on the
system that you were working on.  Is this not the recommended linkage?
... or do we want everything (eg, hdf5/netcdf) statically linked?

-jim


On Thu, Feb 24, 2011 at 4:28 PM, Claude LEPAGE <claude at bic.mni.mcgill.ca> wrote:
> Jim,
>
> Are you sure about this? I believe my built is totally static for
> minc, volume_io, hdf5 and netcdf. Do "otool -L minccalc" and post
> the output.
>
> You probably got confused with our first attempt to build minc
> which had hdf5 and netcdf dynamic since I had /opt/local as part
> of the build path for configure.
>
> Claude
>
>
>> Hi Peter and List,
>>
>>    Peter, I think you might be onto something here.  The ldd
>> equivalent is called otool, and I've taken a look. The latest version
>> that I built with Claude links hdf5 and netcdf as dynamic -- all other
>> libs are statically linked into the executable (minc, volume_io).  In
>> the previous build, we had a very different configuration:
>> dynamic=3D(volume_io, minc2, hdf5), all the rest linked as static
>> (including netcdf). Apple seems to prefer linking dynamically, if it
>> can find a dynamic lib, else it grabs the static.
>>
>> What would be the suggested optimal linking? hdf5 and netcdf dynamic
>> and all of the mincy libs linked statically with the executable.  BTW,
>> running "make check" with the latest library configuration seems to
>> given me a different error. Progress?
>>
>> -jim
>>
>>
>> On Thu, Feb 24, 2011 at 2:45 PM, Peter Neelin <peter.neelin at gmail.com> wrot=
>> e:
>> > On Thu, Feb 24, 2011 at 1:45 PM, EJ Nikelski <nikelski at bic.mni.mcgill.ca>=
>>  wrote:
>> >
>> >> =A0 So, given the thumbs down from Peter, I looked a bit closer. As it
>> >> turns out, on Snow Leopard, even after ncopts=3D0 prior to the call to
>> >> ncvarid(), ncvarid() receives the default ncopts() value of 3 (i.e.,
>> >> display error message and *do not return* to calling program. So the
>> >> error return handling code is never entered. =A0Funnily enough, as this
>> >> works correctly under Linux, this *does* appear to be a Snow Leopard
>> >> problem after all.
>> >
>> > I wondered if there might be some funkiness with dynamically-loaded
>> > libraries in which ncopts is not truly global. Minc changes the
>> > variable but this is not seen by ncvarid() loaded from a different
>> > library. Could minc be defining its own ncopts? (Anyone know much
>> > about the weirdnesses of building shared libraries in Mac OS X?)
>> >
>> > I am assuming that we are dealing with shared libraries here - is that
>> > true? Or is the binary statically linked? (Does Snow Leopard have an
>> > ldd?)
>> >
>> > Peter
>> > --
>> > Peter Neelin
>> > (peter.neelin at gmail.com)
>> > _______________________________________________
>> > MINC-users at bic.mni.mcgill.ca
>> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>> >
>>
>>
>>
>> -- =
>>
>> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
>> =3D=3D=3D=3D=3D=3D=3D=3D
>> Jim Nikelski, Ph.D.
>> Postdoctoral Research Fellow
>> Bloomfield Centre for Research in Aging
>> Lady Davis Institute for Medical Research
>> Sir Mortimer B. Davis - Jewish General Hospital
>> McGill University
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
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>



-- 
=================================
Jim Nikelski, Ph.D.
Postdoctoral Research Fellow
Bloomfield Centre for Research in Aging
Lady Davis Institute for Medical Research
Sir Mortimer B. Davis - Jewish General Hospital
McGill University