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

[Dirk Eddelbuettel]

On 8 May 2008 at 11:54, Faheem Mitha wrote:
| 
| 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 

I think what you see is actually Open MPI which polls all cpus all the time
_on purpose_.  I am a bit hazy on the details but IIRC this may change in the
upcoming 1.3 release.  CC'ing Manuel who may remember better than I do.

| rmpi is now using openmpi. Any reason for not continuing to use lam as before?

LAM is discontinued and the LAM authors recomemnd migration to Open MPI, see
the LAM website.

You can of course rebuild locally against LAM, or continue to use the old packages.
 
| Should I submit a formal bug report for this?

There is no bug here -- though I agree that I also dislike this Open MPI
feature but it is in fact by design.  Check the Open MPI lists, it comes
there a bit.

Dirk

| 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
| 
| _______________________________________________
| R-SIG-Debian mailing list
| R-SIG-Debian at r-project.org
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian

-- 
Three out of two people have difficulties with fractions.