Hi, I was wondering if anyone has had good experiences using R on Linux with dual AMD64 (Opteron) processors. I'm thinking of buying a couple of such servers, but I'd like to make sure R would work fine. The "R Installation and Administration" guide notes that there may be some problems with BLAS libraries. That's all I could find about R on AMD64. Please share your experience using R on AMD64. Many thanks, Jerome Asselin
We've succesfully installed R on a dual Opteron machine running SuSE SLES 8 and managed to compile ATLAS without any problems. R can access (just about) all of the 6GB of memory on the machine. -roger Asselin Jerome wrote:> Hi, > > I was wondering if anyone has had good experiences using R on Linux > with dual AMD64 (Opteron) processors. I'm thinking of buying a > couple of such servers, but I'd like to make sure R would work > fine. > > The "R Installation and Administration" guide notes that there may > be some problems with BLAS libraries. That's all I could find about > R on AMD64. > > Please share your experience using R on AMD64. > > Many thanks, Jerome Asselin > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do > read the posting guide! http://www.R-project.org/posting-guide.html > >
On Fri, 23 Jul 2004, Asselin Jerome wrote:> Hi, > > I was wondering if anyone has had good experiences using R on Linux with > dual AMD64 (Opteron) processors. I'm thinking of buying a couple of such > servers, but I'd like to make sure R would work fine. > > The "R Installation and Administration" guide notes that there may be > some problems with BLAS libraries. That's all I could find about R on > AMD64.Actually it says with ATLAS BLAS, not generically.> Please share your experience using R on AMD64.Quite a few people, including us, are using R on such servers routinely with no problems at all. There are still some issues about how to squeeze the maximum performance out of them (e.g. which BLAS to use -- we are using Goto's -- and which compiler to use, e.g. Portland Group or Intel). -- Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595
Professor Ripley, which operating system are you using for these servers, please? Thanks, Andrew ----- Original Message ----- From: Prof Brian Ripley <ripley at stats.ox.ac.uk> Date: Saturday, July 24, 2004 5:41 pm Subject: Re: [R] R on AMD64 (Opteron)> On Fri, 23 Jul 2004, Asselin Jerome wrote: > > > Hi, > > > > I was wondering if anyone has had good experiences using R on > Linux with > > dual AMD64 (Opteron) processors. I'm thinking of buying a couple > of such > > servers, but I'd like to make sure R would work fine. > > > > The "R Installation and Administration" guide notes that there > may be > > some problems with BLAS libraries. That's all I could find about > R on > > AMD64. > > Actually it says with ATLAS BLAS, not generically. > > > Please share your experience using R on AMD64. > > Quite a few people, including us, are using R on such servers > routinelywith no problems at all. There are still some issues > about how to squeeze > the maximum performance out of them (e.g. which BLAS to use -- we > are > using Goto's -- and which compiler to use, e.g. Portland Group or > Intel). > -- > Brian D. Ripley, ripley at stats.ox.ac.uk > Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ > University of Oxford, Tel: +44 1865 272861 (self) > 1 South Parks Road, +44 1865 272866 (PA) > Oxford OX1 3TG, UK Fax: +44 1865 272595 > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://www.stat.math.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting- > guide.html
Also, I'm curious... Not that this would be my first choice for a server, but... Anyone running Windows XP 64-Bit Edition? Any success compiling R? On Sat, 24 Jul 2004 18:07:18 +1000, Andrew Robinson <andrewr at uidaho.edu> wrote:> Professor Ripley, > > which operating system are you using for these servers, please? > Thanks, > > Andrew > > > > ----- Original Message ----- > From: Prof Brian Ripley <ripley at stats.ox.ac.uk> > Date: Saturday, July 24, 2004 5:41 pm > Subject: Re: [R] R on AMD64 (Opteron) > > > On Fri, 23 Jul 2004, Asselin Jerome wrote: > > > > > Hi, > > > > > > I was wondering if anyone has had good experiences using R on > > Linux with > > > dual AMD64 (Opteron) processors. I'm thinking of buying a couple > > of such > > > servers, but I'd like to make sure R would work fine. > > > > > > The "R Installation and Administration" guide notes that there > > may be > > > some problems with BLAS libraries. That's all I could find about > > R on > > > AMD64. > > > > Actually it says with ATLAS BLAS, not generically. > > > > > Please share your experience using R on AMD64. > > > > Quite a few people, including us, are using R on such servers > > routinelywith no problems at all. There are still some issues > > about how to squeeze > > the maximum performance out of them (e.g. which BLAS to use -- we > > are > > using Goto's -- and which compiler to use, e.g. Portland Group or > > Intel). > > -- > > Brian D. Ripley, ripley at stats.ox.ac.uk > > Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ > > University of Oxford, Tel: +44 1865 272861 (self) > > 1 South Parks Road, +44 1865 272866 (PA) > > Oxford OX1 3TG, UK Fax: +44 1865 272595 > > > > ______________________________________________ > > R-help at stat.math.ethz.ch mailing list > > https://www.stat.math.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide! http://www.R-project.org/posting- > > guide.html > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://www.stat.math.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html >-- Jose Quesada, PhD. jquesada at andrew.cmu.edu Research associate http://lsa.colorado.edu/~quesadaj Dept. of Social and Decision Sciences http://www.andrew.cmu.edu/~jquesada Carnegie Mellon University Porter Hall Phone: 412 268 6011 office PH208-J Fax: 412 268 6938 5000 Forbes ave. 15213, Pittsburgh, PA -- * I have finally put online an exhibition project with my newer paintings * http://lsa.colorado.edu/~quesadaj/CMUexhibitionProject/ Jose Quesada, PhD. jquesada at andrew.cmu.edu Research associate http://lsa.colorado.edu/~quesadaj Dept. of Social and Decision Sciences http://www.andrew.cmu.edu/~jquesada Carnegie Mellon University Porter Hall Phone: 412 268 6011 office PH208-J Fax: 412 268 6938 5000 Forbes ave. 15213, Pittsburgh, PA
Just one more thing for folks intending to try Opterons with >1 cpu: You'll probably want to use a NUMA kernel, rather than a SMP one. Cheers, Andy> From: Prof Brian Ripley > > We are using Fedora Core 2 and some version(s) of SuSe Linux > on various > dual Opteron servers. We also have a copy of RHEL, but AFAIK are not > currently using it. I've been using a dual Opteron 248 under FC2 > > I don't know that Windows XP 64-Bit Edition is actually released yet > (although there have beem public betas). However, as Peter D > says, one > would need a suitable compiler, binutils etc and the MinGW project is > unlikely to provide them any time soon (if ever, although the > project's > FAQ suggests that it does intend to). > > On Sat, 24 Jul 2004, Jose Quesada wrote: > > > Also, I'm curious... > > Not that this would be my first choice for a server, but... > > Anyone running Windows XP 64-Bit Edition? Any success compiling R? > > > > > > > > On Sat, 24 Jul 2004 18:07:18 +1000, Andrew Robinson > <andrewr at uidaho.edu> wrote: > > > Professor Ripley, > > > > > > which operating system are you using for these servers, please? > > > Thanks, > > > > > > Andrew > > > > > > > > > > > > ----- Original Message ----- > > > From: Prof Brian Ripley <ripley at stats.ox.ac.uk> > > > Date: Saturday, July 24, 2004 5:41 pm > > > Subject: Re: [R] R on AMD64 (Opteron) > > > > > > > On Fri, 23 Jul 2004, Asselin Jerome wrote: > > > > > > > > > Hi, > > > > > > > > > > I was wondering if anyone has had good experiences using R on > > > > Linux with > > > > > dual AMD64 (Opteron) processors. I'm thinking of > buying a couple > > > > of such > > > > > servers, but I'd like to make sure R would work fine. > > > > > > > > > > The "R Installation and Administration" guide notes that there > > > > may be > > > > > some problems with BLAS libraries. That's all I could > find about > > > > R on > > > > > AMD64. > > > > > > > > Actually it says with ATLAS BLAS, not generically. > > > > > > > > > Please share your experience using R on AMD64. > > > > > > > > Quite a few people, including us, are using R on such servers > > > > routinelywith no problems at all. There are still some issues > > > > about how to squeeze > > > > the maximum performance out of them (e.g. which BLAS to > use -- we > > > > are > > > > using Goto's -- and which compiler to use, e.g. > Portland Group or > > > > Intel). > > > > -- > > > > Brian D. Ripley, ripley at stats.ox.ac.uk > > > > Professor of Applied Statistics, > http://www.stats.ox.ac.uk/~ripley/ > > > > University of > Oxford, Tel: +44 1865 272861 (self) > > > > 1 South Parks Road, +44 1865 272866 (PA) > > > > Oxford OX1 3TG, UK Fax: +44 1865 272595 > > -- > Brian D. Ripley, ripley at stats.ox.ac.uk > Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ > University of Oxford, Tel: +44 1865 272861 (self) > 1 South Parks Road, +44 1865 272866 (PA) > Oxford OX1 3TG, UK Fax: +44 1865 272595 > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://www.stat.math.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! > http://www.R-project.org/posting-guide.html > >
> From: Jerome Asselin > > From: "Liaw, Andy" <andy_liaw at merck.com> > > > Just one more thing for folks intending to try Opterons with >1 cpu: > You'll > > probably want to use a NUMA kernel, rather than a SMP one. > > > > Cheers, > > Andy > > Thanks for the advice, but is there another reason why you > write this beside > a large (I mean >8) number of CPUs? > > At http://lse.sourceforge.net/numa/faq/ I read, > > What is the difference between NUMA and SMP? > The NUMA architecture was designed to surpass the scalability > limits of the > SMP architecture. With SMP, which stands for Symmetric > Multi-Processing, all > memory access are posted to the same shared memory bus. This > works fine for > a relatively small number of CPUs, but the problem with the shared bus > appears when you have dozens, even hundreds, of CPUs > competing for access to > the shared memory bus. NUMA alleviates these bottlenecks by > limiting the > number of CPUs on any one memory bus, and connecting the > various nodes by > means of a high speed interconnect.I was told by folks at Penguin Computing (where we bought our Opterons) and AMD that because of the way memory controller is integrated in the Opteron, when running two CPU intensive processes on a dual CPU box, one cpu will be at near 100% while the other will be only around 90%, if you use a SMP kernel. Indeed that's what we saw when we ran two R processes simultaneously. Switching to the NUMA kernel for the most part `solves' that problem. Andy
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