On 16 March 2011 at 00:32, mat wrote: | Dirk, thanks a lot for answering to these (maybe trivial) questions!! | Very nice! Answers below | | Le 15. 03. 11 18:57, Dirk Eddelbuettel a écrit : | > On 15 March 2011 at 18:27, Matthieu Stigler wrote: | > | Hi | > | | > | I just read the thread on gotoBLAS, as well as the excellent vignette of | > | gcbd. I still have some confusion and would like to ask very basic | > | questions, hope I am not taking too much of your time. | > | | > | The point that retained my attention was the question of using implicit | > | (multi-threaded blas) versus explicit (parallel code) optimisation. As I | > | understood, the ideal would be to use a multi-threaded BLAS for simple | > | code, and restrict it to use one core when parallel R code is used? Do | > | > Right, as fine-grained parallelism (via BLAS) can clash with coarse-grained | > parallelism (via, say, multicore) where you could end up with 'overbooked' | > cpus. Being able to tell the BLAS implementation to _not_ use parallel code | > is a nice feature ... which Atlas for example does not have. | > | > | you agree? I could not find the presentation of R Bivand on this... Any | > | other references on this question? | > | | > | Secondly, I am a little bit confused about how this is done on Ubuntu. | > | First of all.... I am not sure of which BLAS is actually being used... a | > | dpkg -l indicated me that both liblas (-dev and 3gf) and libatlas | > | (3gf-base) are installed... Doing: | > | | > | $ ls -n /usr/lib/R/lib/ | > | total 2528 | > | -rw-r--r-- 1 0 0 2583076 2011-02-26 04:21 libR.so | > | | > | I don't see which one is used actually... how can I figure out? | > | > Use the 'ldd' command, not the 'ls' command, and run | > | > $ ldd /usr/lib/R/lib/libR.so | on one machine: | libblas.so.3gf => /usr/lib/atlas/libblas.so.3gf | > $ ldd /usr/lib/R/modules/lapack.so | liblapack.so.3gf => /usr/lib/atlas/liblapack.so.3gf (0x00007fcc50272000) | | so I guess this mean I am already using the atlas implementation of | BLAS? Good!
Looks like you do. | > That should show you e.g. your Atlas libblas and liblapack, if you have those | > packages installed. | > | > Also note that /usr/bin/R sets more LD_LIBRARY_PATH arguments meaning so it | > can potentially see more locations than the system default for ld.so | > reflected in the ldd output you just saw.. That is the trick which was used | > by the MKL package so that R saw those libraries but other programs did | > not... (as per the wishes of Intel who gave REvo permission to distribute MKL | > just for R on Ubuntu). | > | > Makes sense? | definitely! (although still need to meditate on the story of locations | for ld.so) | | Now the question is, once I install say gotBLAS through this script you | recommend, is it easy to switch from one BLAS to another, as you did in | your investigation, or does it require some tricky methods? The idea is to just use the package managers. By having a proper .deb package based on Goto (using the gotoblas2-helper) you can drop Goto in and out as you see fit. But do take a look at the benchmark results in the gcbd vignette -- the differences are not that big. Unless you really really need it, it may not be worth the sysadmin'ing hazzles. Dirk -- Dirk Eddelbuettel | [email protected] | http://dirk.eddelbuettel.com _______________________________________________ R-SIG-Debian mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-debian
