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What computer should I buy to make MATLAB simulations run fast?

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Robert
Robert on 13 Sep 2012
I use MATLAB to run large population models. I represent populations as matrices which may have as many as 4,000 rows and up to hundreds of columns. Some simulations may track up to hundreds of matrices. I often subject the matrices to basic math operations in which entries are treated as scalars (e.g., exp(A), A.^2, etc.), or to commands such as sum, cumsum, max, flipdim, and sortrow.
I have the opportunity to buy a new computer on which to run these simulations, and I want to buy something that will run my simulations as quickly as possible. My organization is committed to the Mac platform. I would like to keep the total price in the US$4,000 to $8,000 range (after an institutional discount), although I could go slightly over if there were good reason to do so. On the other hand, I don’t want to throw money away on hardware that won’t make a meaningful difference in simulation speed.
The IT office at my institution has recommended:
Mac Pro
12-core with 2x 6-core Intel Xeon 2.4GHz processors
16GB RAM
ATI Radeon HD 5770 – dual output
(~$3,400 base price; upgrade to 2.66GHz +$1,000; 3.06GHz +$2,000)
2x 1TB drives (to change to 0.5GB Solid State +$800 per drive)
2x Dell UltraSharp U2711 69cm(27") monitors (~$1,400)
Does this seem reasonable? Is it worth the extra money to get the faster processors? Are there things I should cut because they won’t help very much, or add because they will?

Answers (4)

Walter Roberson
Walter Roberson on 13 Sep 2012
If you are looking at the Mac Pro, see if you can wait several months. The Mac Pro has not been refreshed for the Sandy Bridge architecture, or for the higher speed base graphics. There is also no official support on the Mac Pro for CUDA, and putting in a Tesla apparently requires hardware mods, it has been written here.
Apple did specifically indicate earlier this year that they are working on a Mac Pro refresh, but did not give a time frame.
When I was trying to decide what to buy earlier this year, I looked at benchmarks. They are, as always, somewhat confusing. The new MacBook Pro (laptop!) was nearly as fast for general work, and was faster for disk work if you got the SSD version, and was faster for some graphics. The Mac Pro only really shone in total computation power for tasks that could use the full 12 cores.
I do not know much about programming with CUDA, but what you describe your tasks as seems likely to me to be able to program relatively easily with CUDA; if that is correct it might change the balance of your decision.
  3 Comments
Walter Roberson
Walter Roberson on 13 Sep 2012
The point about SSD reminds me of backup issues. The Mac Pro does not support Thunderbolt yet, and even if it did, Thunderbolt backup devices that can operate at full speed are very expensive ($3000). Most of the Thunderbolt-equipped drives on the market are only 5400 rpm, and only get a slight bit more performance than Firewire 800 can give. And Firewire 800 is rather a lot slower than SSD drives.
Whether the speed of the backup devices makes any significant difference to you will depend a lot on your use patterns and on whether you happen to have other backup infrastructure already in place.

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Sean de Wolski
Sean de Wolski on 13 Sep 2012
Edited: Sean de Wolski on 13 Sep 2012
Is it worth the extra money to get the faster processors?
From my experience: Yes.
  1 Comment
Azzi Abdelmalek
Azzi Abdelmalek on 13 Sep 2012
I agree with that. Faster=Much money, other considerations are subjectives

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Jan
Jan on 13 Sep 2012
Edited: Jan on 13 Sep 2012
I do not use Matlab on Macs, but the experiences in this forum seems like Matlab is more stable under Windows.
I've seen Matlab programs running extremly fast on a Pentium and others hanging around stalled by false cache-sharing on quad-cores. While a SSD is fundamental for a fast start of the operating system and programs, paying a good programmer to optimize the code is a better investment than buying the hottest computer. A Terra-Giga-maschine will run 2 or 6 times faster than a standard computer, while this forum has improved the speed of some functions by a factor of 100.
Just as an example: FEX: mmx
  2 Comments
Jan
Jan on 13 Sep 2012
Sorry, Paul, you are right. My answer does miss the point that the OP wants a computer recommendation. I wanted to point out, that the "speed" does not only depend on the processor, but on the complete system including the setup, startup, design- and programming-time.
I've seen too many high-power computers wasting their time with omitted pre-allocation, and this really hurts me. A PhD student asked for a faster computer, because his optimization routines took 3 weeks. A short inspection revealed, that he has driven the internal ODE solvers with maximum accuracy all of the time. Reducing the accuracy at first and increasing it stepwise, when the optimization gets nearer to a solution, reduced the runtime to several hours.
A redundant power-supply can save days of work, a smart method for storing intermediate results on the disk also. In opposite to this, 12 cores can only run twice as fast as 6 cores.
But my preference of brain-power compared to maschine-power has an exception: 16GB RAM for 12 cores is too lean. Any disk-swapping kills efficiency, therefore it must be avoided carefully. Buy much more RAM!

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Paul Metcalf
Paul Metcalf on 13 Sep 2012
Your IT office are like any other IT office. They have no idea what they're talking about and should stick to configuring word for admin staff. You want the fastest clock rate possible + an SSD HD. You want the largest amount of on chip Level 2 and Level 3 RAM as possible. 8GB RAM is probably sufficient if you need to compromise. Unfortunately, HP sell slightly faster chips than Apple, but the Apple is a much better machine overall. What you want is this: (I'm going down the Apple Store config page) Mac Pro Single Processor Six Core Xeon @ 3.33GHz 8GB RAM 512GB Solid State HD Everything else doesn't matter. Enjoy your new machine. Paul

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