I don't think this calculation is memory-bound at all and I would be surprised if changing to a 32-bit environment would change things. I do have a 32-bit chroot environment on these machines (needed for things like wine and acroread) so I'll try that out but I think I will need to use Atlas as the accelerated BLAS rather than Goto's BLAS. I imagine the Opteron/Athlon 64 version of Goto's BLAS assumes a 64-bit environment.
On 3/3/06, Paul Gilbert <[EMAIL PROTECTED]> wrote: > Doug > > This is probably not your reason, but I am finding my dual core Athlon > 64 is much slower running 64 bit Linux and R than it was running 32 bit > Linux and R. All the programs are bigger. (Some, like the clock applet, > are a lot bigger for no obvious reason.) The difference is enough to > put my meager 1GB machine into swapping much more, with the result that > it is a lot slower. > > Paul > > Douglas Bates wrote: > > >I have been timing a particular model fit using lmer on several > >different computers and came up with a peculiar result - the model fit > >is considerably slower on a dual-core Athlon 64 using Goto's > >multithreaded BLAS than on a single-core processor. > > > >Here is the timing on a single-core Athlon 64 3000+ running under > >today's R-devel with version 0.995-5 of the Matrix package. > > > > > > > >>library(Matrix) > >>data(star, package = 'mlmRev') > >>system.time(fm1 <- lmer(math~gr+sx+eth+cltype+(yrs|id)+(1|tch)+(yrs|sch), > >>star, control = list(nit=0,grad=0,msV=1))) > >> > >> > > 0 241720.: 1.16440 0.335239 0.00000 1.78732 0.867209 0.382318 > > 0.00000 > > 1 239722.: 1.94952 5.00000e-10 0.00933767 1.65999 0.858003 > >0.341520 0.00908757 > > 2 239580.: 1.95924 0.0884059 0.00933767 1.65308 0.857487 > >0.339296 0.00954718 > > 3 239215.: 2.60877 0.0765848 0.0177699 1.45739 0.843562 > >0.275100 0.0236849 > > 4 239204.: 2.62582 0.106670 0.0239698 1.41976 0.841086 > >0.261033 0.0267073 > > 5 239176.: 2.63149 0.0787924 0.0367185 1.37952 0.838527 > >0.245076 0.0301134 > > 6 239141.: 2.64949 0.108534 0.0594586 1.28846 0.832543 > >0.208404 0.0375456 > > 7 239049.: 2.64794 0.0789214 0.121782 1.10436 0.819711 > >0.126101 0.0524965 > > 8 239004.: 2.66044 0.117957 0.181505 0.932202 0.798982 > >0.0718116 0.0628958 > > 9 238944.: 2.66310 0.0819653 0.334477 0.631735 0.740855 > >0.258359 0.0806590 > > 10 238893.: 2.72626 0.0975205 0.653432 0.703912 0.666067 > >0.109922 0.201809 > > 11 238892.: 2.74381 0.111146 0.666155 0.693544 0.662000 0.104060 > > 0.207591 > > 12 238888.: 2.75052 0.0990238 0.689199 0.694588 0.655781 > >0.106516 0.216460 > > 13 238861.: 2.80325 0.126935 1.05912 0.733914 0.556162 0.159296 > > 0.360938 > > 14 238832.: 2.82656 0.117617 1.59471 0.607916 0.441371 > >0.0749944 0.976142 > > 15 238811.: 2.87350 0.136332 1.59046 0.653141 0.353763 0.226061 > > 1.79285 > > 16 238810.: 2.87663 0.125135 1.58992 0.656808 0.352605 0.220488 > > 1.79282 > > 17 238806.: 2.89342 0.141551 1.58607 0.676523 0.344212 0.181833 > > 1.79268 > > 18 238804.: 2.90080 0.125137 1.56624 0.682921 0.261295 0.180598 > > 1.74325 > > 19 238802.: 2.91950 0.128569 1.56836 0.680436 0.336051 0.159940 > > 1.80400 > > 20 238801.: 2.92795 0.134762 1.56597 0.685121 0.331695 0.145547 > > 1.80414 > > 21 238801.: 2.93741 0.125667 1.56139 0.687827 0.332700 0.138854 > > 1.81495 > > 22 238800.: 2.94588 0.131757 1.55294 0.687909 0.330414 0.137834 > > 1.82826 > > 23 238799.: 2.96867 0.129716 1.52943 0.688678 0.323171 0.139912 > > 1.84615 > > 24 238799.: 2.98994 0.133378 1.52188 0.700038 0.337387 0.131403 > > 1.77623 > > 25 238799.: 3.00312 0.135308 1.51475 0.697550 0.311750 0.145683 > > 1.78037 > > 26 238799.: 3.00461 0.129920 1.51083 0.697666 0.306722 0.138745 > > 1.81188 > > 27 238799.: 3.00504 0.134882 1.50539 0.696745 0.302949 0.135897 > > 1.84405 > > 28 238799.: 3.00422 0.134013 1.47947 0.698115 0.303243 0.133806 > > 1.86486 > > 29 238799.: 3.00819 0.134378 1.48185 0.701871 0.307097 0.134637 > > 1.84996 > > 30 238799.: 3.01313 0.134279 1.49098 0.702883 0.304788 0.133682 > > 1.86254 > > 31 238799.: 3.01291 0.134253 1.49060 0.701818 0.303155 0.133771 > > 1.84613 > > 32 238799.: 3.01142 0.134314 1.48921 0.701782 0.303589 0.134439 > > 1.84653 > > 33 238799.: 3.01174 0.134315 1.48926 0.701641 0.304120 0.134145 > > 1.84635 > > 34 238799.: 3.01175 0.134304 1.48942 0.701740 0.303762 0.134185 > > 1.84649 > > 35 238799.: 3.01173 0.134307 1.48937 0.701724 0.303809 0.134206 > > 1.84647 > >[1] 43.10 3.78 48.41 0.00 0.00 > > > > > >(If you run the timing yourself and don't want to see the iteration > >output, take the msV=1 out of the control list. I keep it in there so > >I can monitor the progress.) > > > >If I time the same model fit on a dual-core Athlon 64 X2 3800+ with > >the same version of R, BLAS and Matrix package, the timing ends up > >with something like > > > >90 140 235 0 0 > > > >I do see that the multithreading is working on a calculation that is > >essentially BLAS-bound such as > > > > > > > >>mm <- Matrix(rnorm(1e6), nc = 1e3) > >>system.time(crossprod(mm)) > >> > >> > >[1] 0.57 0.02 0.60 0.00 0.00 > > > >On the X2 processor it still takes about 0.6 seconds user time but > >only 0.3 seconds elapsed time when the machine is otherwise idle and > >both cores are available for the calculation. > > > >Any suggestions why the dual-core processor is so much slower than the > >single core processor? > > > >By the way, I would be interested in accumulating timings of this > >model fit on other systems. If you do time it please send me > >(off-list) a summary of the version of R, version of the accelerated > >BLAS if you use them, processor speed and configuration (i.e. > >multiprocessor, multicore, etc.) and, if you know it, memory speed. > > > >This is an example of a complex multilevel model with crossed grouping > >factors fit to a relatively large (30000 observations on 10000 > >students, 1400 teachers and 80 schools) data set. > > > >______________________________________________ > >R-devel@r-project.org mailing list > >https://stat.ethz.ch/mailman/listinfo/r-devel > > > > > ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
