Hello! I need to purchase a new box, which I would like to optimize for good R performance. For the record, I will run Fedora Core 5 as and OS, and I wanted to know if anyone has experience with how the following affects R performance: - Is there a big advantage to having a 64-bit CPU over having a 32-bit? - Does an Opteron offer any advantages over an Athlon, and if yes, does it justify an investment of about US $75 more for equivalent listed speeds? - Have people successfully multithreaded R computations, such as to justify a dual-core CPU? I understand R itself does not multithread, but of course it should be possible to write code that paralellizes computations and I wanted to know if anyone has experience doing so and gained large speed advantages by it. Thanks, Toby Muhlhfoer
Hi,
64bit CPUs, such as opterons, help significantly with large databases
or if you are running multiple processes. But there is a speed
penalty if you are not.
Some packages can make use of multiple processors, such as my rgenoud
(genetic optimization using derivatives) and Matching packages, but
most do not. For these packages the speed up is significant. There
are also multithreaded BLAS which can be used reliably under LINUX,
but the speed benefit is usually small.
You may want to check out some benchmarks at:
http://sekhon.berkeley.edu/macosx/ (linux does very well).
Cheers,
JS.
======================================Jasjeet S. Sekhon
Associate Professor
Survey Research Center
UC Berkeley
http://sekhon.berkeley.edu/
V: 510-642-9974 F: 617-507-5524
======================================
Toby Muhlhofer writes:
> Hello!
>
> I need to purchase a new box, which I would like to optimize for good R
> performance.
>
> For the record, I will run Fedora Core 5 as and OS, and I wanted to know
> if anyone has experience with how the following affects R performance:
>
> - Is there a big advantage to having a 64-bit CPU over having a 32-bit?
>
> - Does an Opteron offer any advantages over an Athlon, and if yes, does
> it justify an investment of about US $75 more for equivalent listed
speeds?
>
> - Have people successfully multithreaded R computations, such as to
> justify a dual-core CPU? I understand R itself does not multithread, but
> of course it should be possible to write code that paralellizes
> computations and I wanted to know if anyone has experience doing so and
> gained large speed advantages by it.
>
> Thanks,
> Toby Muhlhfoer
>
>
From: Jasjeet Singh Sekhon> > > This would be true of 64-bit builds of R, not 64-bit CPUs. [...] > > This doesn't mean that a 32-bit build of R on a 64-bit > processor will be > > slower than a 32-bit build of R on a 32-bit processor. > > There is the issue, however, of running a 32bit application > on a 64bit OS. Under RedHat and SuSE this works > transparently and I've not noticed a performance issue, but > under Debian's or Ubuntu's chroot setup there is in my > experience a measurable performance hit. Of course, one > could simply run 32bit Debian along with 32bit R on an Opteron.It's my recollection that about a year ago there was still fierce debate about Debian on x86_64: One group got a pure 64-bit version to a usable state sooner than another group that was trying to make a standard conforming version that would run both 64- and 32-bit apps transparently. I don't know how that was resolved in the end, but that basically was enough for me to steer clear of any Debian-based distro for x86_64. Andy> Cheers, > Jas. > > ======================================> Jasjeet S. Sekhon > > Associate Professor > Travers Department of Political Science > Survey Research Center > UC Berkeley > > http://sekhon.berkeley.edu/ > V: 510-642-9974 F: 617-507-5524 > ======================================> > > > Thomas Lumley writes: > > On Wed, 5 Apr 2006, Jasjeet Singh Sekhon wrote: > > > > > > > > Hi, > > > > > > 64bit CPUs, such as opterons, help significantly with > large databases > > or if you are running multiple > processes. But there is a speed > > penalty if you are not. > > > This would be true of 64-bit builds of R, not 64-bit CPUs. > > > > On a 64-bit processor you can usually run either 64-bit or > 32-bit builds > > of R, and the 64-bit one will be able to access more > memory but will be > > slower. > > > > This doesn't mean that a 32-bit build of R on a 64-bit > processor will be > > slower than a 32-bit build of R on a 32-bit processor. > > > > -thomas > > > > Thomas Lumley Assoc. Professor, Biostatistics > > tlumley at u.washington.edu University of Washington, Seattle > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! > http://www.R-project.org/posting-guide.html > >