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List: insight-users
Subject: Re: [ITK-users] Variable Matrix Access Violiotation
From: Francois Budin <francois.budin () kitware ! com>
Date: 2017-09-12 12:42:27
Message-ID: CAHwLD2WTsS9-ar2ZVuL8F6j4AMEedRqBP65BtGzKGr=u1JqLPw () mail ! gmail ! com
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Hello Fabian,
In your case the limitation is really the fact that you compile your
project in 32bits. Using another kind of structure will lead to the same
issue as long as it is build in 32bits. So my advice is to compile your
project (and ITK) in 64 bits. It will work then (it works on my computer).
Hope this helps,
François
On Mon, Sep 11, 2017 at 5:30 PM, Fabian Torres <fabian.trobles@gmail.com>
wrote:
> Hi.
>
>
>
> Thanks for your responses; all of them gave me some perspective on the
> problem.
>
> Indeed the size of my matrix is around 3GB and I do have enough memory
> space to allocate it.
>
>
>
> So I think the problem lies in the integer overflow and that my program is
> compiled in 32-bit mode, so my win32 cannot allocate that size of matrix.
>
>
>
> So what do you recommend? use another kind of structure that it is not an
> itk matrix and compiling this project in 64bits?
>
>
>
> Thank you very much. I do appreciate the time you took for this subject.
>
> On Mon, Sep 11, 2017 at 1:08 PM, Lowekamp, Bradley (NIH/NLM/LHC) [C] <
> blowekamp@mail.nih.gov> wrote:
>
>> Yes, unsigned int's max is ~4GB, so it "could" work. But working with
>> unsigned integers in the 2GB-3GB range is problematic and trick when
>> subtraction and offsets need to be computed. It is a big red flag to me.
>>
>>
>>
>> Another possibility, is that the program was just compiled in 32-bit
>> mode. I don't think a win32 application can allocate that much memory.
>>
>>
>>
>> Brad
>>
>>
>>
>>
>>
>>
>>
>> *From: *Francois Budin <francois.budin@kitware.com>
>> *Date: *Monday, September 11, 2017 at 1:57 PM
>> *To: *"Lowekamp, Bradley (NIH/NLM/LHC) [C]" <blowekamp@mail.nih.gov>
>> *Cc: *Fabian Torres <fabian.trobles@gmail.com>, "insight-users@itk.org" <
>> insight-users@itk.org>
>>
>> *Subject: *Re: [ITK-users] Variable Matrix Access Violiotation
>>
>>
>>
>> @Brad: I looked in the source code and the types of the column and row
>> size variables are "unsigned int" which should allow up to 2^32-1 so 4GB,
>> isn't that correct?
>>
>>
>>
>> On Mon, Sep 11, 2017 at 1:47 PM, Lowekamp, Bradley (NIH/NLM/LHC) [C] <
>> blowekamp@mail.nih.gov> wrote:
>>
>> Oh! I think you are experiencing integer overflow with that size of a
>> matrix. The value Francois (correctly) computed 3,200,000,000 is ~3GB which
>> is greater than numeric_traits<int>::max(), which for 32-bit singed
>> integers is 2,147,483,647. The internal implementation of this class is
>> vnl_matrix, so the integer limitation lies within that library. So you
>> matrix is too big for this library.
>>
>>
>>
>> When I looked at this e-mail earlier I miss computed the size, so I
>> didn't realized this problem.
>>
>>
>>
>> HTH,
>>
>> Brad
>>
>>
>>
>>
>>
>> *From: *Francois Budin <francois.budin@kitware.com>
>> *Date: *Monday, September 11, 2017 at 1:38 PM
>> *To: *Fabian Torres <fabian.trobles@gmail.com>
>> *Cc: *"insight-users@itk.org" <insight-users@itk.org>
>> *Subject: *Re: [ITK-users] Variable Matrix Access Violiotation
>>
>>
>>
>> Hello Fabian,
>>
>> You are most likely allocating more memory than what your computer can
>> allocates. If you compute the memory required for your matrix, it will be
>> at least:
>>
>> 8 (long doubles on Visual Studio C++ are the same size as doubles) *
>> 2*100*100*2*100*100 = 3 200 000 000 Bytes
>>
>> This means that you need to have at least that much memory available.
>>
>> If your computer does not have this amount of memory available, you will
>> run into errors.
>>
>> Hope this helps,
>>
>> Francois
>>
>>
>>
>>
>>
>> On Wed, Aug 30, 2017 at 12:24 PM, Fabian Torres <fabian.trobles@gmail.com>
>> wrote:
>>
>> Hi evryone.
>>
>>
>>
>> I ´m using itk VariableMatrix to do some image processing. But I have some
>> problems initializing my matrices.
>>
>> When I use small sizes like this I do not have any problem
>>
>>
>>
>> //matrix A
>>
>> regionSize[0] = 15;
>>
>> regionSze[1] = 15;
>>
>> VariableSizeMatrix<long double> matA;
>>
>> matA.SetSize(2*regionSize[0]*regionSize[1],2*regionSize[0]*r
>> egionSize[1]);
>>
>> matA.Fill(0.0);
>>
>>
>>
>> But when I use bigger sizes like:
>>
>>
>>
>> regionSize[0] = 100;
>>
>> regionSze[1] = 100;
>>
>>
>>
>> I get an Acces Violation exception
>>
>> Access violation reading location 0xcdcdcdc1.
>>
>>
>>
>> I'm using Visualstudio 2008 and ITK 4.4
>>
>>
>>
>> Does this has something to do with memory allocation?
>>
>> Is there a way a could verify if I have enough memory to allocate my
>> matrix?
>>
>>
>>
>> Thanks.
>>
>>
>>
>> --
>>
>> Fabián Torres Robles
>> MaestrÃa en Ciencias en IngenierÃa Electrónica
>> IngenierÃa en Sistemas Electrónicos
>> Tel. 58081280, 0445534661338
>> E-mail fabian.trobles@gmail.com, dae.wong@gmail.com
>>
>>
>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
>>
>>
>>
>>
>
>
>
> --
> Fabián Torres Robles
> MaestrÃa en Ciencias en IngenierÃa Electrónica
> IngenierÃa en Sistemas Electrónicos
> Tel. 58081280, 0445534661338
> E-mail fabian.trobles@gmail.com, dae.wong@gmail.com
>
[Attachment #5 (text/html)]
<div dir="ltr"><div><div><div>Hello Fabian,<br><br></div>In your case the limitation \
is really the fact that you compile your project in 32bits. Using another kind of \
structure will lead to the same issue as long as it is build in 32bits. So my advice \
is to compile your project (and ITK) in 64 bits. It will work then (it works on my \
computer).<br><br></div>Hope this helps,<br></div>François<br></div><div \
class="gmail_extra"><br><div class="gmail_quote">On Mon, Sep 11, 2017 at 5:30 PM, \
Fabian Torres <span dir="ltr"><<a href="mailto:fabian.trobles@gmail.com" \
target="_blank">fabian.trobles@gmail.com</a>></span> wrote:<br><blockquote \
class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc \
solid;padding-left:1ex"><div dir="ltr"><p class="MsoNormal" \
style="margin-bottom:0.0001pt;line-height:normal"><span \
style="font-size:12pt;font-family:Arial,sans-serif;background-image:initial;background \
-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial">Hi.</span><span \
style="font-size:12pt;font-family:"Times New \
Roman",serif"><span></span></span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span \
style="font-size:12pt;font-family:Arial,sans-serif"><span> </span></span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span \
style="font-size:12pt;font-family:Arial,sans-serif">Thanks for your responses; all of \
them gave me some perspective on the problem.<span></span></span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span \
style="font-size:12pt;font-family:Arial,sans-serif">Indeed the size of my matrix is \
around 3GB and I do have enough memory space to allocate it.<span></span></span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span \
style="font-size:12pt;font-family:Arial,sans-serif"><span> </span></span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span \
style="font-size:12pt;font-family:Arial,sans-serif">So I think the problem lies in \
the integer overflow and that my program is compiled in 32-bit mode, so my win32 \
cannot allocate that size of matrix.<span></span></span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span \
style="font-size:12pt;font-family:Arial,sans-serif"><span> </span></span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span \
style="font-size:12pt;font-family:Arial,sans-serif">So what do you recommend? use \
another kind of structure that it is not an itk matrix and compiling this project in \
64bits?<span></span></span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span \
style="font-size:12pt;font-family:Arial,sans-serif"><span> </span></span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span \
style="font-size:12pt;font-family:Arial,sans-serif">Thank you very much. I do \
appreciate the time you took for this subject.<span></span></span></p></div><div \
class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div \
class="gmail_quote">On Mon, Sep 11, 2017 at 1:08 PM, Lowekamp, Bradley (NIH/NLM/LHC) \
[C] <span dir="ltr"><<a href="mailto:blowekamp@mail.nih.gov" \
target="_blank">blowekamp@mail.nih.gov</a>></span> wrote:<br><blockquote \
class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc \
solid;padding-left:1ex">
<div bgcolor="white" link="blue" vlink="purple" lang="EN-US">
<div class="m_-8667220397485991787m_-8487906454607124523WordSection1">
<p class="MsoNormal">Yes, unsigned int's max is ~4GB, so it "could" work. But \
working with unsigned integers in the 2GB-3GB range is problematic and trick when \
subtraction and offsets need to be computed. It is a big red flag to \
me.<u></u><u></u></p> <p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Another possibility, is that the program was just compiled in \
32-bit mode. I don't think a win32 application can allocate that much \
memory.<u></u><u></u></p> <p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Brad<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal" style="margin-left:.5in"><b><span \
style="font-size:12.0pt;color:black">From: </span></b><span \
style="font-size:12.0pt;color:black">Francois Budin <<a \
href="mailto:francois.budin@kitware.com" \
target="_blank">francois.budin@kitware.com</a>><br> <b>Date: </b>Monday, September \
11, 2017 at 1:57 PM<br> <b>To: </b>"Lowekamp, Bradley (NIH/NLM/LHC) [C]" \
<<a href="mailto:blowekamp@mail.nih.gov" \
target="_blank">blowekamp@mail.nih.gov</a>><br> <b>Cc: </b>Fabian Torres <<a \
href="mailto:fabian.trobles@gmail.com" \
target="_blank">fabian.trobles@gmail.com</a>>, "<a \
href="mailto:insight-users@itk.org" target="_blank">insight-users@itk.org</a>" \
<<a href="mailto:insight-users@itk.org" \
target="_blank">insight-users@itk.org</a>></span></p><div><div \
class="m_-8667220397485991787h5"><br> <b>Subject: </b>Re: [ITK-users] Variable Matrix \
Access Violiotation<u></u><u></u></div></div><p></p> </div><div><div \
class="m_-8667220397485991787h5"> <div>
<p class="MsoNormal" style="margin-left:.5in"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:.5in">@Brad: I looked in the source code and \
the types of the column and row size variables are "unsigned int" which \
should allow up to 2^32-1 so 4GB, isn't that correct?<u></u><u></u></p> </div>
<div>
<p class="MsoNormal" style="margin-left:.5in"><u></u> <u></u></p>
<div>
<p class="MsoNormal" style="margin-left:.5in">On Mon, Sep 11, 2017 at 1:47 PM, \
Lowekamp, Bradley (NIH/NLM/LHC) [C] <<a href="mailto:blowekamp@mail.nih.gov" \
target="_blank">blowekamp@mail.nih.gov</a>> wrote:<u></u><u></u></p> <blockquote \
style="border:none;border-left:solid #cccccc 1.0pt;padding:0in 0in 0in \
6.0pt;margin-left:4.8pt;margin-right:0in"> <div>
<div>
<p class="MsoNormal" style="margin-left:.5in">
Oh! I think you are experiencing integer overflow with that size of a matrix. The \
value Francois (correctly) computed 3,200,000,000 is ~3GB which is greater than \
numeric_traits<int>::max(), which for 32-bit singed integers is 2,147,483,647. \
The internal implementation of this class is vnl_matrix, so the integer limitation \
lies within that library. So you matrix is too big for this \
library.<u></u><u></u></p> <p class="MsoNormal" style="margin-left:.5in">
<u></u><u></u></p>
<p class="MsoNormal" style="margin-left:.5in">
When I looked at this e-mail earlier I miss computed the size, so I didn't realized \
this problem.<u></u><u></u></p> <p class="MsoNormal" style="margin-left:.5in">
<u></u><u></u></p>
<p class="MsoNormal" style="margin-left:.5in">
HTH,<u></u><u></u></p>
<p class="MsoNormal" style="margin-left:.5in">
Brad<u></u><u></u></p>
<p class="MsoNormal" style="margin-left:.5in">
<u></u><u></u></p>
<p class="MsoNormal" style="margin-left:.5in">
<u></u><u></u></p>
<div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal" style="margin-left:1.0in">
<b><span style="font-size:12.0pt;color:black">From: </span></b><span \
style="font-size:12.0pt;color:black">Francois Budin <<a \
href="mailto:francois.budin@kitware.com" \
target="_blank">francois.budin@kitware.com</a>><br> <b>Date: </b>Monday, September \
11, 2017 at 1:38 PM<br> <b>To: </b>Fabian Torres <<a \
href="mailto:fabian.trobles@gmail.com" \
target="_blank">fabian.trobles@gmail.com</a>><br> <b>Cc: </b>"<a \
href="mailto:insight-users@itk.org" target="_blank">insight-users@itk.org</a>" \
<<a href="mailto:insight-users@itk.org" \
target="_blank">insight-users@itk.org</a>><br> <b>Subject: </b>Re: [ITK-users] \
Variable Matrix Access Violiotation</span><u></u><u></u></p> </div>
<div>
<div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">
<u></u><u></u></p>
</div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt;margin-left:1.0in">
Hello Fabian,<u></u><u></u></p>
</div>
<p class="MsoNormal" style="margin-left:1.0in">
You are most likely allocating more memory than what your computer can allocates. If \
you compute the memory required for your matrix, it will be at \
least:<u></u><u></u></p> </div>
<p class="MsoNormal" style="margin-bottom:12.0pt;margin-left:1.0in">
8 (long doubles on Visual Studio C++ are the same size as doubles) * \
2*100*100*2*100*100 = 3 200 000 000 Bytes<u></u><u></u></p> </div>
<p class="MsoNormal" style="margin-left:1.0in">
This means that you need to have at least that much memory \
available.<u></u><u></u></p> </div>
<p class="MsoNormal" style="margin-bottom:12.0pt;margin-left:1.0in">
If your computer does not have this amount of memory available, you will run into \
errors.<u></u><u></u></p> </div>
<p class="MsoNormal" style="margin-left:1.0in">
Hope this helps,<u></u><u></u></p>
</div>
<p class="MsoNormal" style="margin-left:1.0in">
Francois<u></u><u></u></p>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">
<u></u><u></u></p>
</div>
</div>
</div>
</div>
</div>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">
<u></u><u></u></p>
<div>
<p class="MsoNormal" style="margin-left:1.0in">
On Wed, Aug 30, 2017 at 12:24 PM, Fabian Torres <<a \
href="mailto:fabian.trobles@gmail.com" \
target="_blank">fabian.trobles@gmail.com</a>> wrote:<u></u><u></u></p> <blockquote \
style="border:none;border-left:solid #cccccc 1.0pt;padding:0in 0in 0in \
6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0in;margin-bottom:5.0pt"> <div>
<p class="MsoNormal" style="margin-left:1.0in">
Hi evryone. <u></u><u></u></p>
<div>
<p class="MsoNormal" style="margin-left:1.0in">
<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">
I ´m using itk VariableMatrix to do some image processing. But I have some problems \
initializing my matrices.<u></u><u></u></p> </div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">
When I use small sizes like this I do not have any problem<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">
<u></u><u></u></p>
</div>
<div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">
//matrix A<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">
regionSize[0] = 15;<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">
regionSze[1] = 15;<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">
VariableSizeMatrix<long double> matA;<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">
matA.SetSize(2*regionSize[0]*r<wbr>egionSize[1],2*regionSize[0]*r<wbr>egionSize[1]);<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">
matA.Fill(0.0);<u></u><u></u></p>
</div>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">
<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">
But when I use bigger sizes like:<u></u><u></u></p>
</div>
<div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">
<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">
regionSize[0] = 100;<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">
regionSze[1] = 100;<u></u><u></u></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">
<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">
I get an Acces Violation exception<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">
Access violation reading location 0xcdcdcdc1.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">
<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">
I'm using Visualstudio 2008 and ITK 4.4<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">
<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">
Does this has something to do with memory allocation?<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">
Is there a way a could verify if I have enough memory to allocate my \
matrix?<u></u><u></u></p> </div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">
<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">
Thanks.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">
<span style="color:#888888"> </span><u></u><u></u></p>
</div>
<p class="MsoNormal" style="margin-left:1.0in">
<span class="m_-8667220397485991787m_-8487906454607124523m-7819910353623902563hoenzb"><span \
style="color:#888888">-- </span></span><u></u><u></u></p> <div>
<div>
<div>
<p class="MsoNormal" style="margin-left:1.0in">
<span style="color:#888888">Fabián Torres Robles<br>
MaestrÃa en Ciencias en IngenierÃa Electrónica<br>
IngenierÃa en Sistemas Electrónicos<br>
Tel. 58081280, 0445534661338<br>
E-mail <a href="mailto:fabian.trobles@gmail.com" \
target="_blank">fabian.trobles@gmail.com</a>, <a href="mailto:dae.wong@gmail.com" \
target="_blank">dae.wong@gmail.com</a> </span> <u></u><u></u></p>
</div>
</div>
</div>
</div>
</div>
<p class="MsoNormal" style="margin-bottom:12.0pt;margin-left:1.0in">
<br>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br><div \
class="m_-8667220397485991787gmail_signature" data-smartmail="gmail_signature"><div \
dir="ltr"><div>Fabián Torres Robles<br>MaestrÃa en Ciencias en IngenierÃa \
Electrónica<br>IngenierÃa en Sistemas Electrónicos<br>Tel. 58081280, \
0445534661338<br>E-mail <a href="mailto:fabian.trobles@gmail.com" \
target="_blank">fabian.trobles@gmail.com</a>, <a href="mailto:dae.wong@gmail.com" \
target="_blank">dae.wong@gmail.com</a> <div \
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