k-Wave

1. DanR
   

   Member
   Joined: Mar '11
   Posts: 9

   Brad,
   Could you summarize the current status of using the GPU and GPUmat with version b05? Code I ran a year ago no longer runs without an error. Reading the postings, I see that there have been changes that may account for this.

   Starting from scratch and following your posting on getting started with GPUmat, I get an error when casting to GPUsingle that tsearch is not supported in this version of Matlab (R2012a). It is suggested I set CartInterp to 'nearest' and try again. When I do so, I get another error about array dimensions from GPUtype/bsxfun.

   More recent postings have suggested using Jacket and that GPUmat is not being updated. I did find a newer version (0.28) as of Feb 2012 and downloaded it. No difference. It was suggested that the code example "example_na_optimising_performance" can be used to test the GPU, but looking at the choices, I don't see a cast to GPUsingle. I do see one to gsingle, which I gather is used with Jacket.

   Thanks for you help,
   Dan

   Posted 12 years ago #

2. Bradley Treeby
   

   Developer
   Joined: Mar '10
   Posts: 1,640

   Hi Dan,

   Out of the box, it doesn't work. The problem is that since B.0.4, the wavenumber and PML variables in k-Wave have been stored as vectors (instead of replicated matrices) and then applied using bsxfun. Unfortunately this function isn't natively supported by GPUmat, and development for the GPUmat project seems to have stopped. I've written a simple MATLAB replacement using repmat that gets GPUmat working, but it isn't particularly efficient.

   I've now uploaded this function to the k-Wave website and updated the post about using GPUmat (apologies for not doing this sooner!). You should still see an improvement for simulations in 3D, but the performance of Jacket is much better. We are planning on including support for the GPU functionality of the Parallel Computing Toolbox in the next release.

   Any questions or problems, please let us know!

   Brad.

   Posted 12 years ago #

3. DanR
   

   Member
   Joined: Mar '11
   Posts: 9

   Brad,
   Thanks for clearing things up for me. I have not used Jacket or the Matlab PCT. According to Accelereyes, Jacket is much better (of course). In your experience, which one might be faster for our 3D simulations? They are about the same price to us.

   Regards,
   Dan

   Posted 12 years ago #

4. Bradley Treeby
   

   Developer
   Joined: Mar '10
   Posts: 1,640

   Hi Dan,

   At this stage, we don't have much experience with using k-Wave and the PCT yet as the required GPU functions were only included in the latest version of MATLAB (2012a). What is your time frame for making a decision? If you leave it with me for a couple of weeks, I can try and incorporate a GPUarrary option into DataCast and run some comparisons.

   Brad.

   Posted 12 years ago #

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