[MINC-users] nu_correct (volume_stats) assertion failed

Mon May 17 17:02:34 EDT 2010

Off the top of my head (well, grep really):

N3
classify
inormalize

They're the 3 that have checks for EBTKS in configure.

Alex

On Mon, May 17, 2010 at 03:37:15PM -0400, Burt Cr?peault wrote:
> Date: Mon, 17 May 2010 15:37:15 -0400
> From: Burt Cr?peault <burt.crepeault at crulrg.ulaval.ca>
> Subject: Re: [MINC-users] nu_correct (volume_stats) assertion failed
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> 
> Well whaddaya know, that was it!
> 
> Rebuilt EBTKS static only, rebuilt N3 against it and voilà!
> 
> Once again, thank you all for this quick and (almost) painless fix.
> 
> By the way, just so that I don't have to build everything again, what other
> minc packages use ebtks?
> 
> Burt.
> 
> 
> 
> 
> On Mon, May 17, 2010 at 14:42, Alexandre CARMEL-VEILLEUX <
> acveilleux at mrs.mni.mcgill.ca> wrote:
> 
> > EBTKS is not built as a static library, I link directly to it. Maybe
> > that's the problem? Because otherwise your environment looks like
> > mine... I might have skipped a land mine by not dynamically linking
> > EBTKS.
> >
> > Alex
> >
> > On Mon, May 17, 2010 at 02:36:05PM -0400, Burt Cr?peault wrote:
> > > Date: Mon, 17 May 2010 14:36:05 -0400
> > > From: Burt Cr?peault <burt.crepeault at crulrg.ulaval.ca>
> > > Subject: Re: [MINC-users] nu_correct (volume_stats) assertion failed
> > > To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> > >
> > > Must be a case of bad fingers then because everything below appears very
> > > similar.
> > >
> > > One difference I can see is that yours doesn't list EBTKS as a library of
> > > volume_stats. Also, I built all the dependencies (libz, netcdf, hdf5)
> > > directly in the build path with the same prefix directive. To allow
> > > everything to work, I must set DYLD_LIBRARY_PATH and PERL5LIB as such:
> > >
> > > # echo $DYLD_LIBRARY_PATH
> > > /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib
> > >
> > > # echo $PERL5LIB
> > >
> > /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib:/Network/MEDICS/EX/etc/minc-2.0.18/Darwin/Library/Perl/Updates/5.8.8:/Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib/perl5/site_perl/5.8.8/darwin-thread-multi-2level
> > >
> > > # uname -a
> > > Darwin beryllium.crulrg.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul
> > 15
> > > 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386
> > >
> > > # gcc --version
> > > i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 (Apple Inc. build 5465)
> > >
> > > # strings /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib/libminc2.1.dylib
> > |
> > > grep '2\.0\.'
> > > 2.0.18
> > >
> > > # otool -L volume_stats
> > > volume_stats:
> > >     /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib/libvolume_io2.1.dylib
> > > (compatibility version 3.0.0, current version 3.2.0)
> > >     /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib/libminc2.1.dylib
> > > (compatibility version 3.0.0, current version 3.2.0)
> > >     /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib/libhdf5.0.dylib
> > > (compatibility version 1.0.0, current version 1.0.0)
> > >     /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib/libz.1.dylib
> > > (compatibility version 1.0.0, current version 1.2.5)
> > >     /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/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
> > > 111.0.0)
> > >     /Network/MEDICS/EX/etc/minc-2.0.18/Darwin/lib/libEBTKS.0.dylib
> > > (compatibility version 1.0.0, current version 1.0.0)
> > >     /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current
> > version
> > > 7.4.0)
> > >     /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current
> > version
> > > 1.0.0)
> > >
> > > # volume_stats -version
> > > Assertion failed at line 32 in file templates/Pool.cc
> > >
> > > Burt.
> > >
> > >
> > >
> > >
> > > On Mon, May 17, 2010 at 14:11, Alexandre CARMEL-VEILLEUX <
> > > acveilleux at mrs.mni.mcgill.ca> wrote:
> > >
> > > > What's the exact platform you're building on?
> > > >
> > > > I'm using:
> > > >
> > > > uname -a:
> > > > Darwin mrspc.bic.mni.mcgill.ca 9.8.0 Darwin Kernel Version 9.8.0: Wed
> > Jul
> > > > 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386
> > > >
> > > > gcc:
> > > > mrspc [/localscratch/compile/newtemp/bin] gcc --version
> > > > i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 (Apple Inc. build 5465)
> > > >
> > > > I've just built this tool line from scratch and it works:
> > > >
> > > > minc 2.0.18
> > > > ebtks 1.6.2
> > > > N3 1.11.0
> > > >
> > > >
> > > > It's all very weird.
> > > >
> > > > Alex
> > > >
> > > > Extraneous output:
> > > >
> > > >
> > > >
> > > > mrspc [/localscratch/compile/newtemp/bin] strings
> > > > /localscratch/compile/newtemp/lib/libminc2.1.dylib | grep '2\.0\.'
> > > > 2.0.18
> > > > mrspc [/localscratch/compile/newtemp/bin] otool -L volume_stats
> > > > volume_stats:
> > > >        /localscratch/compile/newtemp/lib/libvolume_io2.1.dylib
> > > > (compatibility version 3.0.0, current version 3.2.0)
> > > >        /localscratch/compile/newtemp/lib/libminc2.1.dylib
> > (compatibility
> > > > version 3.0.0, current version 3.2.0)
> > > >        /usr/local/lib/libhdf5.0.dylib (compatibility version 1.0.0,
> > current
> > > > version 1.0.0)
> > > >        /usr/lib/libz.1.dylib (compatibility version 1.0.0, current
> > version
> > > > 1.2.3)
> > > >        /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
> > > > version 111.1.4)
> > > >        /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current
> > > > version 7.4.0)
> > > >        /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current
> > > > version 1.0.0)
> > > > mrspc [/localscratch/compile/newtemp/bin] volume_stats -version
> > > > The program <volume_stats> was built from:
> > > > Package MNI N3, version 1.11.0, compiled by
> > > > acveilleux at mrspc.bic.mni.mcgill.ca (i686-apple-darwin9.8.0) on
> > 2010-05-17
> > > > at 14:03:52
> > > >
> > > >
> > > >
> > > > On Mon, May 17, 2010 at 01:47:24PM -0400, Burt Cr?peault wrote:
> > > > > Date: Mon, 17 May 2010 13:47:24 -0400
> > > > > From: Burt Cr?peault <burt.crepeault at crulrg.ulaval.ca>
> > > > > Subject: Re: [MINC-users] nu_correct (volume_stats) assertion failed
> > > > > To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> > > > >
> > > > > Ah, new builds, old libs... I used the exact same compiler flags, as
> > per
> > > > > your recommendations, so everything should work. Perhaps I should try
> > > > > another build using 2.0.15 as a basis. Still, it'd be nice to know
> > what
> > > > the
> > > > > problem is with 2.0.18.
> > > > >
> > > > > Burt.
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > On Mon, May 17, 2010 at 12:31, Alexandre CARMEL-VEILLEUX <
> > > > > acveilleux at mrs.mni.mcgill.ca> wrote:
> > > > >
> > > > > > I've just tested a build of N3-1.11.0 with ebtks-1.6.2 on my build
> > > > > > environment (Mac OS X 10.5.8, most of the libs as per the package I
> > > > made
> > > > > > last year, minc 2.0.15).
> > > > > >
> > > > > > 1.10.1 with 1.6.1 works for me
> > > > > > 1.11.0 with 1.6.1 works for me
> > > > > > 1.11.0 with 1.6.2 works for me
> > > > > >
> > > > > > Where works for me means: (a) -help works and (b) it prints out the
> > > > > > stats of a random minc file I had on hand.
> > > > > >
> > > > > > I used this to build both tools:
> > > > > >
> > > > > > ./configure CFLAGS="-O2 -arch x86_64 -m64" CXXFLAGS="-O2 -arch
> > x86_64
> > > > -m64"
> > > > > > \
> > > > > > --prefix=//localscratch/compile/newtemp \
> > > > > > --with-build-path=/localscratch/compile/newtemp:/usr/local/bic \
> > > > > > --with-minc2
> > > > > >
> > > > > > /locascratch/compile/newtemp is where I built the new EBTKS.
> > > > > >
> > > > > >
> > > > > > This is very annoying,
> > > > > >
> > > > > > Alex
> > > > > >
> > > > > > On Mon, May 17, 2010 at 12:12:02PM -0400, Burt Cr?peault wrote:
> > > > > > > Date: Mon, 17 May 2010 12:12:02 -0400
> > > > > > > From: Burt Cr?peault <burt.crepeault at crulrg.ulaval.ca>
> > > > > > > Subject: Re: [MINC-users] nu_correct (volume_stats) assertion
> > failed
> > > > > > > To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> > > > > > >
> > > > > > > I've put the original file here:
> > > > > > >
> > > > > >
> > > >
> > https://sodium.crulrg.ulaval.ca/WX/images.13671.bl.MR.T1.MP-RAGE.1034.1.10007.[mnc.rsh][mnc.dns].Br.80_p2.mnc.gz
> > > > > > >
> > > > > > > Andrew: yes, running a dry volume_stats command still fails.
> > > > > > >
> > > > > > > Burt.
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > On Mon, May 17, 2010 at 11:56, Andrew Janke <a.janke at gmail.com>
> > > > wrote:
> > > > > > >
> > > > > > > > > Can't wait to get this OS X 64-bit build going... Man this is
> > > > > > tough...
> > > > > > > > > (sigh)
> > > > > > > >
> > > > > > > > Welcome to the EBTKS ornery beast! :)  Well actually that
> > probably
> > > > > > > > isn't fair on Alex, it's at least half C++'s fault for
> > continually
> > > > > > > > changing the spec!.  (but I digress...)
> > > > > > > >
> > > > > > > > > neon:Darwin:# volume_stats
> > > > > > > > > Assertion failed at line 32 in file templates/Pool.cc
> > > > > > > > >
> > > > > > > > > I believe that Pool.cc file belongs to EBTKS, I'm using
> > version
> > > > > > 1.6.2. I
> > > > > > > > > checked the output generated during its build, no apparent
> > > > problem
> > > > > > there.
> > > > > > > > I
> > > > > > > > > built it again, just to make sure, and did the same for N3.
> > > > > > Everything
> > > > > > > > went
> > > > > > > > > well but the failed assertion error persists.
> > > > > > > >
> > > > > > > > > Any ideas?
> > > > > > > >
> > > > > > > > And this is just running volume_stats by itself?  ie: it was
> > trying
> > > > to
> > > > > > > > produce the -help output?
> > > > > > > >
> > > > > > > >
> > > > > > > > --
> > > > > > > > Andrew Janke
> > > > > > > > (a.janke at gmail.com || http://a.janke.googlepages.com/)
> > > > > > > > Canberra->Australia    +61 (402) 700 883
> > > > > > > > _______________________________________________
> > > > > > > > MINC-users at bic.mni.mcgill.ca
> > > > > > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > > > > > > >
> > > > > > > _______________________________________________
> > > > > > > MINC-users at bic.mni.mcgill.ca
> > > > > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > > > > > _______________________________________________
> > > > > > MINC-users at bic.mni.mcgill.ca
> > > > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > > > > >
> > > > > _______________________________________________
> > > > > MINC-users at bic.mni.mcgill.ca
> > > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > > > _______________________________________________
> > > > MINC-users at bic.mni.mcgill.ca
> > > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > > >
> > > _______________________________________________
> > > MINC-users at bic.mni.mcgill.ca
> > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users