[R-sig-Debian] rmpi/snow grabs all available CPU

[Faheem Mitha]

Hi,

I'm testing affyPara on Debian lenny with

R 2.7 from unstable, and the corresponding bioconductor packages from
bioconductor.org downloaded using biocLite as per usual.

The command

cl = makeMPIcluster(k)

succeeds, but spawns k R slaves which promptly soak up all available CPU, which 
is odd since they are not doing anything yet. This looks like a bug to me. 
Similar behaviour is shown by a different machine, also running lenny,

This is probably an issue with rmpi/snow. I notice that the Debian package of 
rmpi is now using openmpi. Any reason for not continuing to use lam as before?

Should I submit a formal bug report for this?

I'm happy to run further tests, and provide further information as necessary.

                                                    Take care, Faheem.

************************************************************************
> sessionInfo()
R version 2.7.0 (2008-04-22)
x86_64-pc-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;L
C_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

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

other attached packages:
[1] Rmpi_0.5-5           affyPara_1.0.0       snow_0.2-9
[4] affy_1.18.0          preprocessCore_1.2.0 affyio_1.8.0
[7] Biobase_2.0.0

******************************************************************

lenny:/home/faheem# dpkg -l| grep r-
ii  r-base-core                   2.7.0-1                 GNU R core of 
statistical computing language
ii  r-base-dev                    2.7.0-1                 GNU R installation of 
auxiliary GNU R packag
ii  r-cran-boot                   1.2.33-1                GNU R package for 
bootstrapping functions fr
ii  r-cran-cluster                1.11.10-1               GNU R package for 
cluster analysis by Rousse
ii  r-cran-codetools              0.2-1-1                 GNU R package 
providing code analysis tools
ii  r-cran-foreign                0.8.25-1                GNU R package to 
read/write data from other
ii  r-cran-kernsmooth             2.22.22-1               GNU R package for 
kernel smoothing and densi
ii  r-cran-lattice                0.17-7-1                GNU R package for 
'Trellis' graphics
ii  r-cran-mgcv                   1.3-31-1                GNU R package for 
multiple parameter smoothi
ii  r-cran-nlme                   3.1.88-1                GNU R package for 
(non-)linear mixed effects
ii  r-cran-rmpi                   0.5-5-2                 GNU R package 
interfacing MPI libraries for
ii  r-cran-rpart                  3.1.41-1                GNU R package for 
recursive partitioning and
ii  r-cran-survival               2.34-1-1                GNU R package for 
survival analysis
ii  r-cran-vr                     7.2.42-1                GNU R package 
accompanying the Venables and
ii  r-recommended                 2.7.0-1                 GNU R collection of 
recommended packages [me