Re: [R] [OT] R on Atlas library
Hi Allan, Thank you for your response. Finally I succeeded. These were the commands to compile Atlas and R: Atlas: ../configure -t 4 -Fa alg -fPIC make make install (-fPIC is needed to wrap some of objects of lapack.a as into a shared lib) R: ../configure --with-blas=/usr/local/lib/libptf77blas.a /usr/local/lib/libatlas.a -lpthread make make install Using your benchmark example, all CPUs seem to be used. It is now working at such a high speed that I could not entirely be sure, top refreshes only every 5 s. Cheers Matthias Am 09.08.2010 11:51, schrieb Allan Engelhardt: I don't know about the specific function (a simple, stand-alone reproducible example is always helpful, see the posting guide for details), but ATLAS certainly uses all my cores on a test like this: s - 7500 # Adjust for your hardware a - matrix(rnorm(s*s), ncol = s, nrow = s) b - crossprod(a) # Uses all cores here. My configuration of R with ATLAS on Linux (Fedora) is described at http://www.cybaea.net/Blogs/Data/Faster-R-through-better-BLAS.html Maybe your distribution has single-threaded ATLAS and you forgot to rebuild it with enable_native_atlas 1 or the equivalent for your platform? Allan On 06/08/10 15:12, Matthias Gondan wrote: Dear List, I am aware this is slightly off-topic, but I am sure there are people who already had the problem and who perhaps solved it. I am running long-lasting model fits using constrOptim command. At work there is a linux computer (Quad Core, debian) on which I already have compiled R and Atlas, in the hope that things will go faster on that machine. Atlas offers the possibility to be compiled for multiple cores, I used that option, but without success. Performance meter (top) for Linux shows 25% CPU usage, and there is no loss of performance if I run 4 instances of R doing heavy matrix multiplications. Performance drops when a 5th instance of R is doing the same job, so I assume my attempt was not successful. I am sure I did something wrong. Is there anybody who sucessfully runs R with Atlas and all processors? A short description of the necessary steps would be helpful. Searching around the internet was not very encourageing. Some people wrote that it is not so simple to have Atlas fully exploit a multicore computer. I hope this is not too unspecific. Best wishes, Matthias -- Dr. rer. nat. Matthias Gondan Institut für Psychologie Universität Regensburg D-93050 Regensburg Tel. 0941-943-3856 Fax 0941-943-3233 Email: matthias.gon...@psychologie.uni-regensburg.de http://www.psychologie.uni-r.de/Greenlee/team/gondan/gondan.html __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] [OT] R on Atlas library
I don't know about the specific function (a simple, stand-alone reproducible example is always helpful, see the posting guide for details), but ATLAS certainly uses all my cores on a test like this: s - 7500 # Adjust for your hardware a - matrix(rnorm(s*s), ncol = s, nrow = s) b - crossprod(a) # Uses all cores here. My configuration of R with ATLAS on Linux (Fedora) is described at http://www.cybaea.net/Blogs/Data/Faster-R-through-better-BLAS.html Maybe your distribution has single-threaded ATLAS and you forgot to rebuild it with enable_native_atlas 1 or the equivalent for your platform? Allan On 06/08/10 15:12, Matthias Gondan wrote: Dear List, I am aware this is slightly off-topic, but I am sure there are people who already had the problem and who perhaps solved it. I am running long-lasting model fits using constrOptim command. At work there is a linux computer (Quad Core, debian) on which I already have compiled R and Atlas, in the hope that things will go faster on that machine. Atlas offers the possibility to be compiled for multiple cores, I used that option, but without success. Performance meter (top) for Linux shows 25% CPU usage, and there is no loss of performance if I run 4 instances of R doing heavy matrix multiplications. Performance drops when a 5th instance of R is doing the same job, so I assume my attempt was not successful. I am sure I did something wrong. Is there anybody who sucessfully runs R with Atlas and all processors? A short description of the necessary steps would be helpful. Searching around the internet was not very encourageing. Some people wrote that it is not so simple to have Atlas fully exploit a multicore computer. I hope this is not too unspecific. Best wishes, Matthias __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] [OT] R on Atlas library
Dear List, I am aware this is slightly off-topic, but I am sure there are people who already had the problem and who perhaps solved it. I am running long-lasting model fits using constrOptim command. At work there is a linux computer (Quad Core, debian) on which I already have compiled R and Atlas, in the hope that things will go faster on that machine. Atlas offers the possibility to be compiled for multiple cores, I used that option, but without success. Performance meter (top) for Linux shows 25% CPU usage, and there is no loss of performance if I run 4 instances of R doing heavy matrix multiplications. Performance drops when a 5th instance of R is doing the same job, so I assume my attempt was not successful. I am sure I did something wrong. Is there anybody who sucessfully runs R with Atlas and all processors? A short description of the necessary steps would be helpful. Searching around the internet was not very encourageing. Some people wrote that it is not so simple to have Atlas fully exploit a multicore computer. I hope this is not too unspecific. Best wishes, Matthias -- Dr. rer. nat. Matthias Gondan Institut für Psychologie Universität Regensburg D-93050 Regensburg Tel. 0941-943-3856 Fax 0941-943-3233 Email: matthias.gon...@psychologie.uni-regensburg.de http://www.psychologie.uni-r.de/Greenlee/team/gondan/gondan.html -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
