Posted by
Stephan Preibisch on
Jun 09, 2014; 4:38pm
URL: http://imagej.273.s1.nabble.com/SPIM-multi-view-deconvolution-via-GPU-tp5008097p5008100.html
Hi Doug,
there are two reasons (that I can see right now) why it doesn’t work:
1) The precompiled version that I put online was compiled for CUDA5.5, thanks to Liren Zhu for compiling and sharing the Windows DLL with me!
2) You have to put the DLL into the Fiji directory directly, not the plugins directory (see
http://www.nature.com/nmeth/journal/v11/n6/full/nmeth.2929.html#supplementary-information, chapter Implementation Details).
After placing the DLL in the right location, it might still not run due to the version mismatch. You have a few options now. You could downgrade to CUDA 5.5. Alternatively, I could nicely ask Liren if he maybe did compile it for CUDA6 already and cc you on this one? I do not have a Windows computer with CUDA running, so I cannot really compile it. You could also install Ubuntu 14.04 where I have a working library.
Maybe there is also a way to adapt the compiler call for Linux as shown in the paper to Windows so that you can do it yourself.
Cheers,
Stephan
---
Dr. Stephan Preibisch
HFSP Fellow
Robert H. Singer / Eugene Myers lab
Albert Einstein College of Medicine / HHMI Janelia Farm / MPI-CBG
email:
[hidden email] /
[hidden email] /
[hidden email]
web:
http://www.preibisch.net/On Jun 9, 2014, at 12:24 , Douglas Richardson <
[hidden email]> wrote:
> Hi Stephan,
>
> 6.0.1
>
> -Doug
>
>
> On Mon, Jun 9, 2014 at 11:37 AM, Stephan Preibisch <
[hidden email]>
> wrote:
>
>> Hi Doug,
>>
>> which version of CUDA do you have installed on your machine?
>>
>> Cheers,
>> Stephan
>>
>> On Jun 9, 2014, at 11:30 , Douglas Richardson <
[hidden email]>
>> wrote:
>>
>>> Hello all,
>>>
>>>
>>> Sorry to bother everyone as I know you're busy with ImageJ 2.0 questions,
>>> but here's a hopefully small issue I've been having:
>>>
>>>
>>>
>>> I recently just installed a processing station with an NVIDIA Titan Black
>>> GPU. I'm trying to run the "SPIM multi-view deconvolution" algorithm on
>> the
>>> it but am having some problems.
>>>
>>> Whenever I try to run deconvolution on the GPU I receive the following
>>> error:
>>>
>>>
>>>
>>> ChannelPattern:
>>>
>>> Channels: (0)
>>>
>>> ChannelsToRegister:
>>>
>>> ChannelsRegister: (0)
>>>
>>> ChannelsToFuse:
>>>
>>> ChannelsFuse: (0)
>>>
>>> Z-stretching = 4.824561403508772
>>>
>>> channel 0 takes it from channel 0
>>>
>>> Cannot find CUDA JNA library: java.lang.UnsatisfiedLinkError: Unable to
>>> load library 'Convolution3D_fftCUDAlib': The specified module could not
>> be
>>> found.
>>>
>>>
>>>
>>> I’ve downloaded the CUDA_code_conv3d files from the Nature Methods
>> website
>>> and placed all of the files from the ‘precompiled’ folder into the
>>> ‘Fiji.app’ folder or the ‘Fiji.app\plugins’ but I get the same error no
>>> matter which location the files are in.
>>>
>>>
>>>
>>> Any ideas as to what I’m doing wrong? I'm still running v1.49b on a
>>> Windows 7 64bit machine.
>>>
>>>
>>>
>>> Thanks for the help!
>>>
>>>
>>>
>>> -Doug
>>>
>>> --
>>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>
>> --
>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>
>
> --
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