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GPU programming on Matlab (Mac/Window): What are my options?

Asked by Dushyant on 19 Apr 2018
Latest activity Commented on by Walter Roberson
on 18 May 2018

Hi,

I usually use "Mac pro 2016" and "window computer at my office" to code on Matlab. I would like to get some GPU power to implement some of my reconstruction idea for medical image reconstruction.

I do plan to use L-BFGS-B solver, which takes 90% of my computation time. Using CPU, it takes 14-15 hours.With implementation of the new idea, I expect computation time to go by 2-3 times.

I have no idea about GPU programming. So, I would appreciate some advice from some GPU programmer. I have budget of $1300-1400.

i) Would it be possible to buy some dedicated NVIDIA card and use it for Mac and/or PC? Could I get more GPU power this way. ii) Should I go for some gaming laptop with "NVIDIA GeForce GTX 1060 graphics with 6GB GDDR5 VRAM"?

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Answer by Joss Knight
on 28 Apr 2018
 Accepted Answer

Others may have a longer answer to your question, but certainly it is possible to get an NVIDIA GPU for a desktop PC with a PCI bus. You can even get something that will work with your Mac or Windows laptop, you just need to buy a caddy to put the card in, for instance the Razer Core. Getting this working with a Mac is a bit more complicated than with Windows, you can find instructions online.

Once you have your GPU installed, check out the MATLAB GPU product page to get started.

The GTX 1060 is adequate to get started with image processing, computer vision and deep learning because it has good single precision performance. For simulation, solvers, and other problems where high accuracy double precision is essential, you may need to look at a more expensive card in the Quadro or Tesla range. There is also the Titan V.

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Answer by Dushyant on 17 May 2018
Edited by Walter Roberson
on 17 May 2018

Dr. Knight,

Thanks a lot for answering.

I have few more queries and your answer would be appreciated.

Do you think that I can buy two of "GF GTX 1080 - 8 GB" and use that in egpu box (Akitio Node Pro) together?

GPU: https://www.cdwg.com/product/GIGABYTE-GTX-1080-TURBO-OC-8GB-PCIE/4446980

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I see https://www.zdnet.com/pictures/gallery-top-10-external-gpu-enclosures/

It looks like I read the specifications incorrectly; the Akitio Node uses Thunderbolt 3, not USB 3.0. And that is a problem for you, as your Mac Pro ("late 2013") design only has Thunderbolt 2 according to Apple https://support.apple.com/kb/sp697 . Thunderbolt 3 is not common at all on MS Windows machines. Most of the enclosures listed in the summary article are Thunderbolt 3.

I see a note on the Cubix Xpander description that it should be compatible with the Mac Pro tower systems, but it does look to require a card slot. It is the only one listed in that particular summary article that supports multiple GPU.

For any system such as these, communications between main memory and the GPU can be a bottleneck, so with multiple external GPU you would prefer that you were using a different host controller to talk to each external GPU.

I have MacBook pro 2016. It has 4 Thunderbolt 3 ports. So, I guess that I am fine there. However, I am concerned about my window with USB-2 port. That is my main computation machine as a lots of things do not work on Mac.

Any idea if I can easily upgrade some card on my window?

Though it it works on Mac, then I am all set. I am asking just in case it does not work out.

It appears to me that Thunderbolt 3 cards need PCIe 3.0 x4 at minimum. Asus appears to make some interface cards that are specific to their motherboards; and I see, for example, http://www.asrock.com/mb/spec/product.asp?Model=Thunderbolt%203%20AIC

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