[R-sig-hpc] digesting "parallel" package in R-2.14. how about you?

Christophe Dutang dutangc at gmail.com
Thu Jan 5 09:25:01 CET 2012

Dear Paul,

I have also started HPC few days ago. Please see my post https://stat.ethz.ch/pipermail/r-sig-hpc/2011-December/001186.html 
where I have tested an example from http://www.informatik.uni-ulm.de/ni/staff/HKestler/Reisensburg2009/PDF/multicore.pdf .

See also, my reply here https://stat.ethz.ch/pipermail/r-sig-hpc/attachments/20111205/dbba522a/attachment.pl for HPC on windows 7.

Hope it helps


Christophe Dutang
Ph.D. student at ISFA, Lyon, France
website: http://dutangc.free.fr

Le 5 janv. 2012 à 05:09, Paul Johnson a écrit :

> Have you been testing out R's new parallel package? I'm getting
> started and wonder about your experience.  The help page is very brief
> because most of the functions are not exported, so I'm finding it a
> bit difficult to use.
> Our cluster runs RMPI over OpenMPI.  Initially, I thought that would
> be a bad problem because parallel is intended for "sock" and "fork"
> clusters.  That seemed bad,  but parallel's makeCluster help page says
> it will call snow to make the cluster.  So I think that's OK for me,
> if I were using a snow cluster.  The parallel vignette also says its
> functions will work with clusters created by snow, so that's hopeful.
> In the past, I've blundered into conflicts between OpenMPI and the
> other frameworks that are drawn in by some packages.  OpenMPI doesn't
> play well with libraries that want to spawn thread, for example.
> OpenMPI is not compatible with OpenMP and the multicore package, but
> the parallel package uses those things. I worry they will slide in
> where I don't want them.
> Here's an example of an error I got today, I don't know yet what
> causes it, but I'm suspicious :)
> --------------------------------------------------------------------------
> An MPI process has executed an operation involving a call to the
> "fork()" system call to create a child process.  Open MPI is currently
> operating in a condition that could result in memory corruption or
> other system errors; your MPI job may hang, crash, or produce silent
> data corruption.  The use of fork() (or system() or other calls that
> create child processes) is strongly discouraged.
> The process that invoked fork was:
>  Local host:          compute-2-11.local (PID 8290)
>  MPI_COMM_WORLD rank: 0
> If you are *absolutely sure* that your application will successfully
> and correctly survive a call to fork(), you may disable this warning
> by setting the mpi_warn_on_fork MCA parameter to 0.
> --------------------------------------------------------------------------
> -- 
> Paul E. Johnson
> Professor, Political Science
> 1541 Lilac Lane, Room 504
> University of Kansas
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