[R-sig-hpc] socket cluster/gotoblas2 configuration confusion

Claudia Beleites claudia.beleites at ipht-jena.de
Wed Nov 23 15:44:45 CET 2011

Dear all,

I'm just doing my first steps with parallelized calculations and got 
quite confused.

Here's what I want, what I have and what I did:

- I want to parallelize calculations on a Centos server with 2 x 6 cores 
and 8 GB RAM (it is actually part of a cluster, but I have access only 
to this node, and the other nodes do not (yet) have R installed).

- My Data is too large to work with in one piece.
But it comes in separate files of suitable size: I can work nicely with 
2 to 3 samples in memory at the same time.

- So my idea was to start up a snow socket cluster with 2 or 3 workers.

- In addition I want to use an optimized and blas. Linear algebra is 
only a small part of the analysis so it does make sense to have the 
socket cluster with as many workers as possible and have the linear 
algebra parts use up to n / nworkers cores.

So I built R 2.14.0 using gotoblas2 and set $GOTO_NUM_THREADS to 6. 
Matrix multiplication in a fresh R session now is much faster and CPU 
usage shows the expected 6 cores working:

 > system.time ({m <- matrix (1:9e6, 3e3); m%*%m; NULL})
        User      System verstrichen
       5.219       0.126       1.111

However, the socket clusters seem not to use the GOTO_NUM_THREADS:
 > library (snow)
 > cl <- makeCluster(2,type="SOCK")
 > tm <- snow.time(clusterEvalQ(cl, {m <- matrix (1:9e6, 3e3); m%*%m; 
 > tm
elapsed    send receive  node 1  node 2
   9.553   0.001   0.010   9.510   9.543
 > tm$data
      send_start send_end recv_start recv_end exec
[1,]          0    0.001      9.511    9.512 9.51

      send_start send_end recv_start recv_end  exec
[1,]      0.001    0.001      9.544    9.553 9.543

 > tm$elapsed

CPU usage shows 2 cores working, and the times correspond to that.

What configuration do I need to do in order to make the blas use more 
threads for the worker processes? Anything else I should do differently?

 > sessionInfo ()
R version 2.14.0 (2011-10-31)
Platform: x86_64-unknown-linux-gnu (64-bit)

  [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=de_DE.UTF-8        LC_COLLATE=de_DE.UTF-8
  [7] LC_PAPER=C                 LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] snow_0.3-8

Additional questions:
- Is there some command like sessionInfo () that yields information 
about the blas (particularly NUM_THREADS)?
- Is there some command that I can use to tell the blas how many threads 
to use during an R session? Can I set environment variables from within 
R? Searching didn't help as I got only info about R environments...) 
Would that actually help here?

Thanks a lot for your help.


Claudia Beleites
Institute of Photonic Technology
Albert-Einstein-Str. 9
07745 Jena

email: claudia.beleites at ipht-jena.de
phone: +49 3641 206-133
fax:   +49 2641 206-399

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