[Paraview] RAW (binary) file import issues

[Moreland, Kenneth]

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<mailto: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<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<mailto:S.D.Keyes at soton.ac.uk><https://www.outlook.soton.ac.uk/owa/<http://www.outlook.soton.ac.uk/owa/>redir.aspx?SURL=dhUg3da8XR77LeItLDzJQwhAwmH0Wx6PHrXeKfxx2tOD3LCr737TCG0AYQBpAGwAdABvADoAUwAuAEQALgBLAGUAeQBlAHMAQABzAG8AdABvAG4ALgBhAGMALgB1AGsA&URL=mailto%3aS.D.Keyes%40soton.ac.uk>
T: 07898720248
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