R computing: AMD or Intel?

Maxim.K

I am building an office PC, for which the heaviest task will be running Monte Carlo Markov Chain (MCMC) estimations in R. Clearly, a CPU-intensive task, and R is known for being limited to a single core.

Given that the budget is limited, which CPU is better suited for the task, AMD or Intel? In particular, I am looking at Intel Core i3 4130 with two cores clocked at 3.4 Ghz and at AMD FX-6300, six cores clocked at 3.5 Ghz and unlocked multiplier. Which one is better in terms of performance in heavy computational tasks, given the limitations of R?

Thank you.

EDIT: The only bit of information I could find on the issue is this FAQ item:

2.23 Why does R never use more than 50% of my CPU? This is a misreading of Windows' confusing Task Manager. R's computation is single-threaded, and so it cannot use more than one CPU. What the task manager shows is not the usage in CPUs but the usage as a percentage of the apparent total number of CPUs. We say "apparent" as it treats so-called "hyper-threaded" CPUs such as two CPUs per core, and most modern CPUs have at least two cores.

Am I to understand that if R can only use a single CPU thread, Intel's hyper-threading is of no consequence, and therefore AMD's higher clock will have the advantage?

EDIT2: And here are a couple of somewhat relevant benchmarks, though they don't compare CPUs, just the speed with and without hyper-threading.

EDIT3: this topic is about the same problem, albeit expressed in different terms. Without much resolution though.

EDIT4: I have found the answer, but since I doubt the question will be reopened, I'll reference it here. Please see my comment to the main post below.

The proper answer would be AMD (given this particular choice). If there are computational difficulties, e.g. the need to run very long MCMC chains, one can use JAGS or BUGS with R packages such as BRugs, R2WinBUGS, runjags, and rjags. In this case it is possible to run multiple chains for the same parameter on different cores and combine them post-factum. This vid explains it. The more cores, the more chains, hence AMD with six cores is preferable to Intel with 4 (hyperthreaded) cores.

For example, on a six core AMD I would run six chains simultaneously:

library(R2WinBUGS)
re.sim<-bugs(data, inits, parameters, "model.bug", n.chains=6, n.iter=100000,
n.burnin=3000, n.thin=2, debug=F, program="openbugs")

On the Intel CPU I would be able to run only four chains simultaneously, and with lower clock. It might be interesting to note that runjags library allows parallel execution, including multi-machine clusters.

I believe that people who marked this post as off-topic percieved it as a very broad question, while in fact it is an extremely narrow one, requiring the knowledge of R, software R interfaces with, what MCMC is and does, and how all of this combines in regard to uzilizing CPU power. The answer I have provided is not subjective at all, and it is directly related to programming complex Bayesian models in R. Voted to reopen, marking as off-topic is likely due to ignorance of what MCMC entails, focussing instead on the "AMD vs Intel" red herring.

Hans Roggeman

According to CPU benchmarks you are better off with the AMD between the two, independent of whether you use the parallel computing packages in R such as parallel or not.

EDIT (wrt. comments etc. - doing it here because I cannot post links long enough in comment):

Hyper-threading should in theory help you somewhat but as the graphs in the article you hint at show, it is unlikely to help you as much as actually using R in a multicore truly parallel mode (Revolution R does some of that for you whenever it can - that is probably why the CART is so much faster). You can use R across multiple cores with MCMC as indicated in an example in this pdf and some packages seem to use it in the background for you. So more cores looks better here ceteris paribus.

Collected from the Internet

Please contact [email protected] to delete if infringement.

edited at
0

Comments

0 comments
Login to comment

Related

From Dev

AMD processor to an Intel processor

From Dev

Difference between intel and AMD multithreading

From Dev

Is there a difference between AMD and Intel processors?

From Dev

Changing cpu from intel to amd

From Dev

Installing AMD & Intel dual graphics

From Dev

Changing cpu from intel to amd

From Dev

Ubuntu 17.04 and AMD Radeon R5 340X and Intel HD Graphics 4600

From Dev

AMD A4-5300 and GPU computing on BOINC

From Dev

Mixed AMD and Intel nodes in a cluster... considerations?

From Dev

Intel's HAXM equivalent for AMD on Windows OS

From Dev

Windows command line affected by AMD/Intel differences?

From Dev

amd gpu but display on intel integrated graphics

From Dev

AMD / Intel switchable graphics problem in Ubuntu 14.04

From Dev

Is there any alternative to intel or amd for server processors?

From Dev

Intel x86 or AMD64?

From Dev

what is correct architecture of my pc AMD or INTEL?

From Dev

Update Intel-microcode with amd CPU

From Dev

GPU Intel&AMD in device manager but only Intel in dxdiag

From Dev

Dell Inspiron 15 5559 problem at shutdown and logout (Intel Skylake and AMD Radeon R5 M335)

From Dev

R computing not so fast

From Dev

Computing geometric series in R

From Dev

What EXACTLY is the difference between intel's and amd's ISA, if any?

From Dev

Strange registry value for PROCESSOR_ARCHITECTURE for Intel and AMD processor

From Dev

OpenGL 3+ failure on Intel/AMD C++

From Dev

Which cache-coherence-protocol does Intel and AMD use?

From Dev

Why can an executable run on both Intel and AMD processors?

From Dev

Are AMD processors less well supported than Intel processors?

From Dev

Are AMD processors less well supported than Intel processors?

From Dev

Where can I find the instruction sets for Intel or AMD microprocessors?

Related Related

  1. 1

    AMD processor to an Intel processor

  2. 2

    Difference between intel and AMD multithreading

  3. 3

    Is there a difference between AMD and Intel processors?

  4. 4

    Changing cpu from intel to amd

  5. 5

    Installing AMD & Intel dual graphics

  6. 6

    Changing cpu from intel to amd

  7. 7

    Ubuntu 17.04 and AMD Radeon R5 340X and Intel HD Graphics 4600

  8. 8

    AMD A4-5300 and GPU computing on BOINC

  9. 9

    Mixed AMD and Intel nodes in a cluster... considerations?

  10. 10

    Intel's HAXM equivalent for AMD on Windows OS

  11. 11

    Windows command line affected by AMD/Intel differences?

  12. 12

    amd gpu but display on intel integrated graphics

  13. 13

    AMD / Intel switchable graphics problem in Ubuntu 14.04

  14. 14

    Is there any alternative to intel or amd for server processors?

  15. 15

    Intel x86 or AMD64?

  16. 16

    what is correct architecture of my pc AMD or INTEL?

  17. 17

    Update Intel-microcode with amd CPU

  18. 18

    GPU Intel&AMD in device manager but only Intel in dxdiag

  19. 19

    Dell Inspiron 15 5559 problem at shutdown and logout (Intel Skylake and AMD Radeon R5 M335)

  20. 20

    R computing not so fast

  21. 21

    Computing geometric series in R

  22. 22

    What EXACTLY is the difference between intel's and amd's ISA, if any?

  23. 23

    Strange registry value for PROCESSOR_ARCHITECTURE for Intel and AMD processor

  24. 24

    OpenGL 3+ failure on Intel/AMD C++

  25. 25

    Which cache-coherence-protocol does Intel and AMD use?

  26. 26

    Why can an executable run on both Intel and AMD processors?

  27. 27

    Are AMD processors less well supported than Intel processors?

  28. 28

    Are AMD processors less well supported than Intel processors?

  29. 29

    Where can I find the instruction sets for Intel or AMD microprocessors?

HotTag

Archive