[MINC-development] -O3 breaks N3

[Vladimir S. Fonov]

Another important observation,


when compiled with Debug flags sharpen_hist bails out with assert 
failure in Pool.cc:32 (  _elementSize >= sizeof(_Link *) )

since _elementSize in this case is 4 and sizeof(_Link *) is 8 (on 64 bit 
build).



On 12-04-18 11:58 PM, Claude LEPAGE 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
>> _______________________________________________
>> MINC-development mailing list
>> MINC-development at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development
>>
> _______________________________________________
> MINC-development mailing list
> MINC-development at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development


-- 
Best regards,
  Vladimir S. Fonov ~ vladimir.fonov <at> gmail.com