(Current) Ubuntu : r-base-dev seems incompatible with atlas-base-dev.
Dear Dirk, Le vendredi 29 ao?t 2008 ? 17:37 -0500, Dirk Eddelbuettel a ?crit :
Emmanuel, On 30 August 2008 at 00:04, Emmanuel Charpentier wrote: | Dear list, | | Setup : Ubuntu Hardy + updates + backports + security + R repository on | a 3.2 GHz PIV dual-core processor. | | Bitten (again...) by the "I'll optimize my setup" bug, I tried to test | atlas. Following Dirk's advice on a not-so-recent post to R-help, I | tried "apt-get install -s atlas3-doc atlas3-base-dev" (I tend to | recompile some packages, so I need r-base-dev and I *think* I need | atlas3-base-dev to allow the recompiled packages to use it, but I might | be completely wrong...). Ahem ... : | | [ Snip... ] | | Les paquets suivants seront ENLEV?S : | libblas-dev liblapack-dev r-base-dev | | [ Snip again ... ] | | (for non-francophones : "The following packages will be REMOVED : ..."). | | However, atlas3-base *is* currently installed, and I never had problems | recompiling packages. Quick guess: you have the old atlas-* packages instead of the new libatlas-* packages. Try $ sudo apt-get install libatlas3gf-base libatlas-base-dev
Right on ! It happened that I had already libatlas3gf-base on my PIV system. libatlas-base-dev installed without a hitch. My asinine insistence on atlas* was probably due to the fact that this system has been installed quite a bit ago (dapper ? or even before that ? ) and has been upgraded since. It has ben, however, reinforced by a README.Atlas file which hasn't been updated since 2001 and points to atlas2-*. Maybe an upgrade of this file would be in order ? Anyway, installing libatlas3gf-sse2 didn't produce any difference in the "small" test hinted at in the README file. [ Snip ... ]
| Last but not least : Atlas does not seem to exist on other architectures | (I'm interested in amd64, of course...), at least in Debian and Ubuntu. | Are there similar projects for amd64 I'm not aware of ? Are you sure? This has built on many architectures for many years, and the reason it took so long to get to libatlas [ie the new build with the new Fortran compuler] was as far as I know the darn portability. All this works on my Debian (which gets R from my Debian packages) and Ubuntu (which gets R from CRAN) machines.
We are both right : no atlas* executable package in Ubuntu or Debian amd64 (there is, however, an altas2-base-dev (IIRC)...). But there is indeed a libatlas3gf-base and a -dev packages in Ubuntu amd64. That's what happens when you use "dpkg -l atlas*" instead of searching "atlas" in the synaptic GUI... I might have got the right hint by searching "*atlas*" instead... Installing it gave me more or less 3x acceleration of your matrix inversion test. Mmmm...
Hope this helps, Dirk
It sure did ! Thank you, Dirk ! Emmanuel Charpentier