[Rtk-users] rtkForwardProjections Segmentation fault...

[Simon Rit]

Hi Steven,
Big dataset. I unfortunately do not have a 6 GB card at hand to test it,
the maximum I have is a 3 GB card. I still believe it is a simple memory
issue. I noticed that there were some checks missing so I have added them
<https://github.com/SimonRit/RTK/commit/6e040cbaf77a3105871f3f42721ef426806d000b>.
Could you try again with the attached script instead of the one you have
sent? It does only one projection which will require less memory and it
works on my 3 GB card with half your volume. With the full volume, it fails
but the new checks describe the memory issue as expected. There have been
some changes in the management of the memory indeed and it will now create
the full stack in the GPU memory with the example you sent. Streaming
should be possible, we can work on it after you confirm it is a memory
issue if you want.
About the aliasing, I noticed that your voxels are finely resolved. I have
tried to change the hard-coded value "float t_step = 1" to 0.1 in
rtkCudaForwardProjectionImageFilter.cxx and it removes them. I have now made
that configurable
<https://github.com/SimonRit/RTK/commit/fb62489657397df2c9f6d1d1bf0711bbc8fd7673>
through the option --step of rtkforwardprojections.
Simon


On Thu, Jul 17, 2014 at 11:09 PM, Steven Pollmann <spollmann at robarts.ca>
wrote:

> Hello RTK Users,
>
> We have noticed some problems with RTK's forward projection software
> (rtkForwardProjections) using CUDA.  Originally, using a build we have been
> using from July 2013 (v1,0 rc3, commit ID
> 2dabe6a04cf33c0da45907efdf03d427b4473adc dated July 03, 2013), GPU Forward
> Projection would complete, but would leave some sort of aliasing artifacts
> in the projections that were not present when rtkForwardProjections was run
> using only the CPU methods (Joseph method, or RayCastInterpolator, changing
> --method commandline option, at the time).
>
> The next time we tried using a newer build of openRTK to perform some
> forward projections using the GPU/CUDA was later in the year.  However, I
> believe some CUDA memory management changes were made, and a forward
> projection could no longer be attempted due to running out of memory (and
> rtkForwardProjections being unable to chunk. or split up the volume to
> forward project).  (Our GPU at the time was an Nvidia GTX 770 with 4GB
> vram).
>
> More recently, we acquired an Nvidia GTX Titan Black with 6GB vram,
> running driver version 337.25 on Xubuntu 14.04, and I attempted a forward
> projection using the latest OPENRTK (v1.0.0, July 10, 2014 commit
> 8646fbdc3b01b439ae37c1d7084e2e68d155c3a5).  We no longer get the "out of
> memory" errors (this build still causes the GTX770 to complain of memory),
> but rather a Segmentation Fault when trying to do the forward projection.
>  The Segmentation Fault occurs after it has read in the 3D Volume, when it
> is "Projection Volume...".  The failure is immediate.  Again, if using just
> the CPU to do the forward projections, everything seems to work fine.
>
> Anyhow, I was wondering if anyone had any insight into this issue?
>
> Our scanners produce fairly large volumes (1024x1024x680) that we are
> interested in performing some iterative reconstructions on.
>
> I've uploaded a sample dataset (a Rubiks Cube volume) onto Google drive at
> the following link.  Due to the rtkForwardProjections program being unable
> to "chunk", or "divide" the dataset, I think you would need a substantial
> amount of video memory (6GB or more) to test this dataset, and experience
> the Segmentation Fault.
>
>
> https://drive.google.com/folderview?id=0B2rwn1Vax7UydVhudHlSZGlXVDQ&usp=sharing
>
> There, you should be able to download the Rubiks MHD and Raw Volume file,
> the Geometry File, and a script file containing the forward projection
> commands we are using.
>
> Let me know if any other information would be useful.
>
> Thanks!
>
> Steve
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>
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