[Paraview] RAW (binary) file import issues

[Ken Martin]

I believe Visual studio 2010 does not properly handle file seeks/etc beyond
32 bit even on 64 bit builds. If you are using VS 2010 or earlier that is
possibly the issue. I believe it is fixed in VS 2013 and later.

On Tue, Nov 22, 2016 at 5:11 PM, Moreland, Kenneth <kmorel at sandia.gov>
wrote:

> 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.
>
>
>
> 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.
>
>
>
> I would follow Berk’s suggesting of looking into the filesystem before
> diving into the guts of MPI-I/O.
>
>
>
> -Ken
>
>
>
> *From:* ParaView [mailto:paraview-bounces at paraview.org] *On Behalf Of *Burlen
> Loring
> *Sent:* Tuesday, November 22, 2016 12:55 PM
> *To:* Geveci, Berk (External Contact) <berk.geveci at kitware.com>; Keyes
> S.D. <S.D.Keyes at soton.ac.uk>
> *Cc:* paraview at paraview.org
> *Subject:* [EXTERNAL] Re: [Paraview] RAW (binary) file import issues
>
>
>
> 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.
>
> Burlen
>
> On 11/22/2016 11:20 AM, Berk Geveci wrote:
>
> 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?
>
>
>
> On Thu, Nov 17, 2016 at 10:30 AM, Keyes S.D. <S.D.Keyes at soton.ac.uk>
> wrote:
>
> Dear all,
>
> I am encountering issues when trying to import large 8 bit RAW volumes to
> Paraview 5.1.2 (64 bit).
>
> 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.
>
> I can import up to a 2000x2000x1000 crop of this file, but I encounter the
> following message when I attempt larger z dimensions:
>
> ERROR: In C:\bbd\df0abce0\source-paraview\VTK\IO\Image\vtkImageReader2.cxx,
> line 592
>
> vtkPVImageReader (0000000007767F90): Initialize: Could not open file
> \\cseg_2\ERC\SLS_201606\Myco_2\CT2PpR3h1_\Hyphalseg_Raw_
> 2000_2000_1920_8bit_SKELETON_FILT_PARAVIEW_TEST.raw
>
>
> 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?
>
> Sam
>
> Samuel D Keyes, MEng, PhD
> New Frontiers Fellow
> Bioengineering / μVIS Centre for Computed Tomography
> University of Southampton
> E: S.D.Keyes at soton.ac.uk<https://www.outlook.soton.ac.uk/owa/re
> dir.aspx?SURL=dhUg3da8XR77LeItLDzJQwhAwmH0Wx6PHrXeKfxx2tOD3LCr737TCG0AYQBp
> AGwAdABvADoAUwAuAEQALgBLAGUAeQBlAHMAQABzAG8AdABvAG4ALgBhAGMA
> LgB1AGsA&URL=mailto%3aS.D.Keyes%40soton.ac.uk>
> T: 07898720248
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-- 
Ken Martin PhD
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Kitware Inc.
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