Re: [R] Problems building R 2.2.1 with libgoto and SSE2 enabled

From: Prof Brian Ripley <>
Date: Thu 23 Feb 2006 - 20:27:00 EST

[This sort of highly technical non-R issue would be better discussed on the R-devel list. See the R posting guide.]

Do note the comments in the R-admin manual. R requires proper results with IEEE754 specials (Infs and NaNs) and switching on fast arithmetic options often calls failures because of this. It is not clear from your description what compiler you are using (presumably some version of gcc), and how it handles this. Since gcc's AMD64 code makes use of such extensions it may be safe, but we don't know about your compiler/CPU combination. Generally the advice is that it takes more time to investigate wrong results from over-optimization (as now, and it is not just your time in this case) than to make use of safer options.

However, without knowing what the failure is (look in the tests/ file) we can only speculate.

Building ATLAS should take only a couple of hours at most for platforms where there are good defaults, and that includes P4 on Linux. I had a lot of problems on Opteron, basically because my machine was too fast for the timing loops (and you also need to ensure that PIC code is used).

On Thu, 23 Feb 2006, Ivan Adzhubey wrote:

> Hi,
> I am trying to build R 2.2.1 with Kazushige Goto's BLAS library (libgoto) and
> encountered a problem: I have two computers with the almost identical
> hardware (P4 Northwood CPU, i875 chipset, 2GB DDR400 RAM) and identical Linux
> OS. I have the latest version of libgoto for this CPU installed on both boxes
> ( and I am using gcc compiler flags "-O2
> -march=pentium4 -mfpmath=sse -msse2" to enable use of SSE2 extensions. With
> one computer that works perfectly, while on the other one "make check"
> constantly fails on lm-test. If I remove "-mfpmath=sse -msse2" part from the
> gcc flags then all checks pass on the second computer too. Any hints on what
> may cause the error? Anyone willing to share his/her experience on building
> and using R with SSE2 and on libgoto performance in particular? I was
> planning to give ATLAS a try but pre-built binaries are not available for my
> distro and on my AMD Opteron cluster it took almost 48 hours to build. I am
> not sure my home computer (the one that gives me errors with libgoto/SSE2)
> would survive this.
> TIA,
> Ivan
> ______________________________________________
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> PLEASE do read the posting guide!

Brian D. Ripley,        
Professor of Applied Statistics,
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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Received on Thu Feb 23 20:42:26 2006

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