Login  Register

Re: SPIM multi view deconvolution via GPU

Posted by bnorthan on Jun 11, 2014; 9:48pm
URL: http://imagej.273.s1.nabble.com/SPIM-multi-view-deconvolution-via-GPU-tp5008097p5008147.html

Hi Stephan

Thanks, I will try it out.  Also, looking at your code in
"Multi_View_Deconvolution.java" I saw a comment (around line 825 where it
loads the libary) "under linux automatically checks lib/linux64".  So that
mean it only checks the Fiji/lib directory under linux??


On Wed, Jun 11, 2014 at 5:20 PM, Stephan Preibisch <[hidden email]>
wrote:

> Thanks a lot Brian for the help!
>
> the behavior is unfortunately very different under Windows and Linux as we
> figured out.
>
> The new version of my plugin that is currently developed handles it much
> better I think, it actively looks for it and you can change the path. It
> will be released very soon, if you want to try it ahead of time let me
> know, I can send you jars (or here is the source
> https://github.com/fiji/spimreconstruction/tree/revised-spimdata)! It is
> much more flexible and powerful and iterates with the BigDataViewer.
>
> Cheers,
> Stephan
>
> On Jun 11, 2014, at 17:11 , Brian Northan <[hidden email]> wrote:
>
> > Hi Douglas
> >
> > Any luck fixing your problem?  I had a similar problem working with a
> cuda
> > plugin.
> >
> > First I was getting an error something like "can't find library.so"
> >
> > 1.  I had to put the native libraries in a "lib" directory directly under
> > the Fiji directory.  So perhaps put the .dll in the "lib" directory.
> >
> > Then I got an error something like "can't find cudart.so"
> >
> > 2.  I had to add the location of the Cuda library to my system library
> > path.  The ubuntu cuda installer didn't do this automatically.  Not sure
> > the behaviour is the same in Windows or not.  But you might want to check
> > and see if the location of the cuda libaries has been added to the system
> > path.
> >
> > 3.  You mention you couldn't get the newest graphics card to work with
> Cuda
> > 5.5.  I think that might be because cuda 5.5 installs an older version of
> > the nvidia drivers.  I think you can get the newer cards working with
> Cuda
> > 5.5.  This info is for GTX 750 Ti but perhaps relevant for you as well.
> >
> > "The GTX 750 Ti is not supported by the driver (319.37) that is included
> > with the cuda 5.5 toolkit installer package. Download the latest driver
> > installer package for GeForce 750 Ti from www.nvidia.com and run that to
> > replace your 319.37 driver (only). You should have better results. Yes,
> > CUDA 5.5 is compatible with the newer driver you are installing."
> >
> >
> >
> >
> > On Tue, Jun 10, 2014 at 11:17 AM, Johannes Schindelin <
> > [hidden email]> wrote:
> >
> >> Hi Douglas,
> >>
> >> On Mon, 9 Jun 2014, Douglas Richardson wrote:
> >>
> >>> Wayne: Sorry, I'll stick to the Fiji bug reporter from now on.......
> >>
> >> The ImageJ mailing list is the best place to discuss these things: as
> you
> >> pointed out, Stephan keeps an eye on this list. He does not keep an eye
> on
> >> the Fiji bugzilla. SPIM registration is an ImageJ plugin after all, a
> >> plugin that just happens to be available in the Fiji distribution of
> >> ImageJ for users' convenience.
> >>
> >> There are other users of the SPIM deconvolution plugin that will benefit
> >> from seeing this discussion and its outcome. There is a lot of expertise
> >> on this mailing list and the use of CUDA is on the rise in biological
> >> image processing. I think this is in fact a perfect place to discuss
> this.
> >>
> >> The strength of the ImageJ mailing list has always been that it is a
> >> friendly place with a wide range of expertise about everything related
> to
> >> ImageJ, and sometimes even beyond.
> >>
> >> Let's continue to keep it that way,
> >> Johannes
> >>
> >> --
> >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >>
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html