<html>
<head>
<meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
<blockquote type="cite"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">File
sizes and linear offsets use a type MPI_Offset, which according
to the specification should be large enough to hold the size of
any file supported by the file system.</span></blockquote>
<br>
hmm, that may be but there are places in MPI I/O that limit to size
of signed int, here is cut direct from the mpi 3 standard:<br>
<blockquote>int MPI_File_read_all(MPI_File fh, void *buf, int count,<br>
MPI_Datatype datatype, MPI_Status *status)<br>
</blockquote>
the count argument is a signed int, so one can't read more than
INT_MAX in one go, and here is the VTK code where that is used<br>
<br>
291 // Figure out how many bytes to read.<br>
292 vtkIdType length = this->GetDataScalarTypeSize();<br>
293 length *= this->NumberOfScalarComponents;<br>
294 length *= extent[1]-extent[0]+1;<br>
295 length *= extent[3]-extent[2]+1;<br>
296 if (this->GetFileDimensionality() == 3) length *=
extent[5]-extent[4]+1;<br>
297 <br>
298 if (length > VTK_INT_MAX)<br>
299 {<br>
300 vtkErrorMacro(<< "Cannot read more than " <<
VTK_INT_MAX<br>
301 << " bytes at a time.");<br>
302 }<br>
303 <br>
304 // Do the read. This is a coordinated parallel operation for
efficiency.<br>
305 MPICall(MPI_File_read_all(file.Handle, buffer,
static_cast<int>(length),<br>
306 MPI_BYTE, MPI_STATUS_IGNORE));<br>
<br>
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
the VTK code checks for over flow. however as that is not the error
reported by the user, I have to admit that I am wrong about Sam's
problem. Sorry about that.<br>
<br>
Burlen<br>
<br>
<br>
<div class="moz-cite-prefix">On 11/22/2016 02:11 PM, Moreland,
Kenneth wrote:<br>
</div>
<blockquote
cite="mid:44db108eb6024280b31a555bdbc95754@ES08AMSNLNT.srn.sandia.gov"
type="cite">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<meta name="Generator" content="Microsoft Word 15 (filtered
medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Consolas;
panose-1:2 11 6 9 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman",serif;
color:black;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
pre
{mso-style-priority:99;
mso-style-link:"HTML Preformatted Char";
margin:0in;
margin-bottom:.0001pt;
font-size:10.0pt;
font-family:"Courier New";
color:black;}
p.msonormal0, li.msonormal0, div.msonormal0
{mso-style-name:msonormal;
mso-margin-top-alt:auto;
margin-right:0in;
mso-margin-bottom-alt:auto;
margin-left:0in;
font-size:12.0pt;
font-family:"Times New Roman",serif;
color:black;}
span.HTMLPreformattedChar
{mso-style-name:"HTML Preformatted Char";
mso-style-priority:99;
mso-style-link:"HTML Preformatted";
font-family:Consolas;
color:black;}
span.EmailStyle20
{mso-style-type:personal-reply;
font-family:"Calibri",sans-serif;
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
<div class="WordSection1">
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Although
we have certainly run into issues with communicating large
messages, I’m not sure this is the issue with MPI-I/O. File
sizes and linear offsets use a type MPI_Offset, which
according to the specification should be large enough to
hold the size of any file supported by the file system.
Although it is true that creating the 3D subarray uses
32-bit indices, those are for each of the separate
dimensions, and 2000 falls well below that limit.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Besides,
it looks like that error happens when checking an ifstream
object, so it looks like the reader is bypassing the MPI-I/O
path anyway.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">I
would follow Berk’s suggesting of looking into the
filesystem before diving into the guts of MPI-I/O.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">-Ken<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<div>
<div style="border:none;border-top:solid #E1E1E1
1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext">From:</span></b><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext">
ParaView [<a class="moz-txt-link-freetext" href="mailto:paraview-bounces@paraview.org">mailto:paraview-bounces@paraview.org</a>]
<b>On Behalf Of </b>Burlen Loring<br>
<b>Sent:</b> Tuesday, November 22, 2016 12:55 PM<br>
<b>To:</b> Geveci, Berk (External Contact)
<a class="moz-txt-link-rfc2396E" href="mailto:berk.geveci@kitware.com"><berk.geveci@kitware.com></a>; Keyes S.D.
<a class="moz-txt-link-rfc2396E" href="mailto:S.D.Keyes@soton.ac.uk"><S.D.Keyes@soton.ac.uk></a><br>
<b>Cc:</b> <a class="moz-txt-link-abbreviated" href="mailto:paraview@paraview.org">paraview@paraview.org</a><br>
<b>Subject:</b> [EXTERNAL] Re: [Paraview] RAW (binary)
file import issues<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:12.0pt">I've hit that
before. the RAW reader uses MPI-I/O, and MPI uses signed int
everywhere in its API, so there are limits that you end up
hitting. For instance to partition the data among processors
one must give MPI-I/O the starting offset of the data in the
file as a signed int, and that is limited to 2^31.
<br>
<br>
Burlen<o:p></o:p></p>
<div>
<p class="MsoNormal">On 11/22/2016 11:20 AM, Berk Geveci
wrote:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal">Hmmm that happens to be around 4 GB
which makes me wonder if there is a limit somewhere in
that reader... Any chance you can try this on a Linux
machine?<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">On Thu, Nov 17, 2016 at 10:30 AM,
Keyes S.D. <<a moz-do-not-send="true"
href="mailto:S.D.Keyes@soton.ac.uk" target="_blank">S.D.Keyes@soton.ac.uk</a>>
wrote:<o:p></o:p></p>
<blockquote style="border:none;border-left:solid #CCCCCC
1.0pt;padding:0in 0in 0in
6.0pt;margin-left:4.8pt;margin-right:0in">
<p class="MsoNormal">Dear all,<br>
<br>
I am encountering issues when trying to import large 8
bit RAW volumes to Paraview 5.1.2 (64 bit).<br>
<br>
The file I wish to import has xyz dimensions of
2000x2000x1920 voxels (Unsigned char), 7.5GB. I am
running a machine with 192 GB RAM and 12 CPU cores.<br>
<br>
I can import up to a 2000x2000x1000 crop of this file,
but I encounter the following message when I attempt
larger z dimensions:<br>
<br>
ERROR: In
C:\bbd\df0abce0\source-paraview\VTK\IO\Image\vtkImageReader2.cxx,
line 592<br>
<br>
vtkPVImageReader (0000000007767F90): Initialize: Could
not open file <a moz-do-not-send="true"
href="file://cseg_2/ERC/SLS_201606/Myco_2/CT2PpR3h1_/Hyphalseg_Raw_2000_2000_1920_8bit_SKELETON_FILT_PARAVIEW_TEST.raw">\\cseg_2\ERC\SLS_201606\Myco_2\CT2PpR3h1_\Hyphalseg_Raw_2000_2000_1920_8bit_SKELETON_FILT_PARAVIEW_TEST.raw</a><br>
<br>
<br>
I cannot find an obvious memory ceiling within the
paraview settings - any ideas as to whether there is
some effective upper limit to import file size?<br>
<br>
Sam<br>
<br>
Samuel D Keyes, MEng, PhD<br>
New Frontiers Fellow<br>
Bioengineering / μVIS Centre for Computed Tomography<br>
University of Southampton<br>
E: <a moz-do-not-send="true"
href="mailto:S.D.Keyes@soton.ac.uk">S.D.Keyes@soton.ac.uk</a><<a
moz-do-not-send="true" href="https://">https://</a><a
moz-do-not-send="true"
href="http://www.outlook.soton.ac.uk/owa/">www.outlook.soton.ac.uk/owa/</a>redir.aspx?SURL=dhUg3da8XR77LeItLDzJQwhAwmH0Wx6PHrXeKfxx2tOD3LCr737TCG0AYQBpAGwAdABvADoAUwAuAEQALgBLAGUAeQBlAHMAQABzAG8AdABvAG4ALgBhAGMALgB1AGsA&URL=mailto%3aS.D.Keyes%40soton.ac.uk><br>
T: 07898720248<br>
_______________________________________________<br>
Powered by <a moz-do-not-send="true"
href="http://www.kitware.com" target="_blank">www.kitware.com</a><br>
<br>
Visit other Kitware open-source projects at <a
moz-do-not-send="true"
href="http://www.kitware.com/">http://www.kitware.com/</a>opensource/opensource.html<br>
<br>
Please keep messages on-topic and check the ParaView
Wiki at: <a moz-do-not-send="true"
href="http://paraview.org/Wiki/ParaView"
target="_blank">
http://paraview.org/Wiki/ParaView</a><br>
<br>
Search the list archives at: <a
moz-do-not-send="true"
href="http://markmail.org/search/?q=ParaView"
target="_blank">
http://markmail.org/search/?q=ParaView</a><br>
<br>
Follow this link to subscribe/unsubscribe:<br>
<a moz-do-not-send="true"
href="http://public.kitware.com/mailman/listinfo/paraview"
target="_blank">http://public.kitware.com/mailman/listinfo/paraview</a><o:p></o:p></p>
</blockquote>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<p class="MsoNormal"><br>
<br>
<br>
<o:p></o:p></p>
<pre>_______________________________________________<o:p></o:p></pre>
<pre>Powered by <a moz-do-not-send="true" href="http://www.kitware.com">www.kitware.com</a><o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Visit other Kitware open-source projects at <a moz-do-not-send="true" href="http://www.kitware.com/opensource/opensource.html">http://www.kitware.com/opensource/opensource.html</a><o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Please keep messages on-topic and check the ParaView Wiki at: <a moz-do-not-send="true" href="http://paraview.org/Wiki/ParaView">http://paraview.org/Wiki/ParaView</a><o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Search the list archives at: <a moz-do-not-send="true" href="http://markmail.org/search/?q=ParaView">http://markmail.org/search/?q=ParaView</a><o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Follow this link to subscribe/unsubscribe:<o:p></o:p></pre>
<pre><a moz-do-not-send="true" href="http://public.kitware.com/mailman/listinfo/paraview">http://public.kitware.com/mailman/listinfo/paraview</a><o:p></o:p></pre>
</blockquote>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
Powered by <a class="moz-txt-link-abbreviated" href="http://www.kitware.com">www.kitware.com</a>
Visit other Kitware open-source projects at <a class="moz-txt-link-freetext" href="http://www.kitware.com/opensource/opensource.html">http://www.kitware.com/opensource/opensource.html</a>
Please keep messages on-topic and check the ParaView Wiki at: <a class="moz-txt-link-freetext" href="http://paraview.org/Wiki/ParaView">http://paraview.org/Wiki/ParaView</a>
Search the list archives at: <a class="moz-txt-link-freetext" href="http://markmail.org/search/?q=ParaView">http://markmail.org/search/?q=ParaView</a>
Follow this link to subscribe/unsubscribe:
<a class="moz-txt-link-freetext" href="http://public.kitware.com/mailman/listinfo/paraview">http://public.kitware.com/mailman/listinfo/paraview</a>
</pre>
</blockquote>
<br>
</body>
</html>