[MINC-development] -O3 breaks N3

[Alex Zijdenbos]

See? In the end it always comes down to a problem with the compiler ;-)

By the way I am working on eliminating EBTKS from N3; I am also
planning a (drop-in) replacement for inormalize which also depends on
EBTKS; and hope to get to classify as well. We can then hopefully toss
EBTKS overboard altogether, which I am sure will make lots of people
very happy.

I am not promising a particular timeline yet though.

-- A

On Thu, Apr 19, 2012 at 12:51 PM, Vladimir S. FONOV
<vladimir.fonov at gmail.com> wrote:
> Hello,
>
>
> finally, I was able to achieve the same results, by recompiling EBTKS
> as a static library (before I had it built as a shared library).
>
> So, now both versions produce exactly the same output.
>
> On Thu, Apr 19, 2012 at 10:59 AM, Vladimir S. FONOV
> <vladimir.fonov at gmail.com> wrote:
>> Hello,
>>
>>
>> I managed to track problem further. First, it turns out that on new
>> build  volume_stats -nocache produced very different results then
>> default (and consistent with old build). So, I disabled caching.
>>
>> On top of that, I discovered that the output of sharpen_hist changed
>> significantly.
>>
>> If i give the following command line:
>>
>> sharpen_hist -blur -fwhm .2 -noise 0.01 -range 762.440430 1646.982788
>> hist.txt hist.sharp.txt
>>
>> the output is very different for two  versions (and none of them makes
>> any sense whatsoever).
>>
>> See attached file hist.txt, hist_old.sharp.txt and hist_new.shart.txt
>>
>> the graph showing the histogram is here:
>> http://www.bic.mni.mcgill.ca/~vfonov/temp/histograms.png
>>
>>
>>
>>
>> On Wed, Apr 18, 2012 at 11:58 PM, Claude LEPAGE
>> <claude at bic.mni.mcgill.ca> wrote:
>>> Hi,
>>>
>>> I think the damping of 1.0e-7 might be a little bit too
>>> aggressive and not enough damping can cause the matrix
>>> system to be ill-conditioned. While it works in most cases,
>>> a value of 1.0e-6 will give similar results and will be
>>> more robust numerically. Can you try that?
>>>
>>> Claude
>>>
>>>> Hello Everybody,
>>>>
>>>> Turns out that N3 is broken with -O2. Actually , compiling
>>>> http://packages.bic.mni.mcgill.ca/tgz/N3-1.12.0.tar.gz
>>>> using standard ./configure & make
>>>>
>>>> produces a code which seem to work, but essentially corrects nothing at
>>>> least when applied to icmb 00100 t1w scan :
>>>> (
>>>> /data/ipl/user01/rotor/icbm_recovery/shell-pipe-analy-circa2006/native/mni_icbm_00100.001.t1.mnc.gz
>>>> on the bic system)
>>>>
>>>> it produces an imp file :
>>>>
>>>> MNI Field File
>>>> %Wed Apr 18 18:40:53 2012>>> /opt/minc2/bin/nu_estimate_np_and_em
>>>> -parzen -log -sharpen 0.1 0.01 -iterations 100 -stop 0.0001 -shrink 4
>>>> -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute
>>>> -clobber -nokeeptmp -tmpdir /tmp/nu_correct_7795/
>>>> mni_icbm_00100.001.t1.mnc auto_mni_icbm_00100.001.t1.nuc.imp
>>>> Version = 0.9.0;
>>>> Field_Type = B_Spline;
>>>> Distance = 200;
>>>> Domain =
>>>>       -81.519097598907     89.3619937534825
>>>>       -95.84404     164.15596
>>>>       -155.813426545559     107.579156148442;
>>>> Coefficients =
>>>>      6.93367797718816e-310
>>>>      6.93367797718816e-310
>>>>                          0
>>>>                          0
>>>>                          0
>>>> ...(all zeroes)
>>>>                          0;
>>>>
>>>> When compiled on ubuntu 11.04 , gcc version 4.5.2
>>>>
>>>> Interestingly, the same tool compiled on Debian 5, gcc version 4.3.4
>>>> works as expected.
>>>>
>>>>
>>>>
>>>>
>>>> On 12-04-15 07:41 AM, Andrew Janke wrote:
>>>> > Absolutely...
>>>> >
>>>> > Claude, remember also the bug we fixed in EBTKS's spline
>>>> > implementation a long time back that was causing crashed on some files
>>>> > with certain magic dimensions. I can't think of how this might break
>>>> > anything (we added an episilon IIRC) but it was a change we had to
>>>> > make.
>>>> >
>>>> > I for one am keen to keep N3 as it is and I don't see it being a
>>>> > problem to force -02 behaviour during the compile. I have used N4 but
>>>> > often revert to N3, probably because it's a beast I know.
>>>>
>>>>
>>>> --
>>>> Best regards,
>>>>
>>>> Vladimir S. FONOV ~ vladimir <dot> fonov <at> gmail <dot> com
>>>> _______________________________________________
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>>>> MINC-development at bic.mni.mcgill.ca
>>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>>>>
>>> _______________________________________________
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>>
>>
>>
>> --
>> Best regards,
>>
>>  Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com
>
>
>
> --
> Best regards,
>
>  Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com
> _______________________________________________
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