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!
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?
thanks a lot!!
Matthieu
Dirk
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