R help - Apr 2004 - openMosix and R: File I/O issues?

Hi there,

We're attempting to run an LVQ analysis over a cluster of machines via R 
and openMosix.  R spawns several child processes simply by writing 
commands to several files and using system() to start a slave process. 
 The processes migrate perfectly, and often finish with no reported 
errors, writing their results into respective files for the parent 
process to piece together.  However, occasionally we have had the 
problem that the results from a child process never make it into a file. 
 The process finishes, and exits, with no errors - but the file never 
turns up.  Repeated tests with the same data have shown that the 
specific process that dies is random, and stress tests of R I/O have 
shown that there are no issues there.  Does anyone know of I/O issues 
with openMosix, either specifically related to R or not?

using:
openMosix kernel 2.4.21
R 1.8.1
RedHat Enterprise Edition

Thanks,
Jim

Other than OpenMOSIX disliking I/O, I havn't seen any problems.  I
would suspect network hardware and drivers -- while generally robust, cluster
computations stress it much more than daily use, with less tolerance
for problems.

best,
-tony


Jim Thomas <james at staarfunds.com> writes:
> Hi there,
>
> We're attempting to run an LVQ analysis over a cluster of machines via
> R and openMosix.  R spawns several child processes simply by writing
> commands to several files and using system() to start a slave
> process. The processes migrate perfectly, and often finish with no
> reported errors, writing their results into respective files for the
> parent process to piece together.  However, occasionally we have had
> the problem that the results from a child process never make it into a
> file. The process finishes, and exits, with no errors - but the file
> never turns up.  Repeated tests with the same data have shown that the
> specific process that dies is random, and stress tests of R I/O have
> shown that there are no issues there.  Does anyone know of I/O issues
> with openMosix, either specifically related to R or not?
>
> using:
> openMosix kernel 2.4.21
> R 1.8.1
> RedHat Enterprise Edition
>
> Thanks,
> Jim
>
>
>
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-- 
rossini at u.washington.edu            http://www.analytics.washington.edu/ 
Biomedical and Health Informatics   University of Washington
Biostatistics, SCHARP/HVTN          Fred Hutchinson Cancer Research Center
UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable
FHCRC  (M/W): 206-667-7025 FAX=206-667-4812 | use Email

CONFIDENTIALITY NOTICE: This e-mail message and any attachme...{{dropped}}

Thanks for the response.  Are there any documented reasons as to why oM
"dislikes" I/O?  Our network hardware works fine with SNOW and rMPI,
so our problem must lie somewhere within the mosix framework.

Jim

---- "(A.J. Rossini)" <rossini at blindglobe.net>
wrote:
>
> 
> Other than OpenMOSIX disliking I/O, I havn't seen any problems.  I
> would suspect network hardware and drivers -- while generally robust,
cluster
> computations stress it much more than daily use, with less tolerance
> for problems.
> 
> best,
> -tony
> 
> 
> Jim Thomas <james at staarfunds.com> writes:
> 
> > Hi there,
> >
> > We're attempting to run an LVQ analysis over a cluster of machines
via
> > R and openMosix.  R spawns several child processes simply by writing
> > commands to several files and using system() to start a slave
> > process. The processes migrate perfectly, and often finish with no
> > reported errors, writing their results into respective files for the
> > parent process to piece together.  However, occasionally we have had
> > the problem that the results from a child process never make it into a
> > file. The process finishes, and exits, with no errors - but the file
> > never turns up.  Repeated tests with the same data have shown that the
> > specific process that dies is random, and stress tests of R I/O have
> > shown that there are no issues there.  Does anyone know of I/O issues
> > with openMosix, either specifically related to R or not?
> >
> > using:
> > openMosix kernel 2.4.21
> > R 1.8.1
> > RedHat Enterprise Edition
> >
> > Thanks,
> > Jim
> >
> >
> >
> > -------------------------------------------------------
> > This SF.Net email is sponsored by: IBM Linux Tutorials
> > Free Linux tutorial presented by Daniel Robbins, President and CEO of
> > GenToo technologies. Learn everything from fundamentals to system
> >
administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
> > _______________________________________________
> > openMosix-general mailing list
> > openMosix-general at lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/openmosix-general
> >
> 
> -- 
> rossini at u.washington.edu            http://www.analytics.washington.edu/
> Biomedical and Health Informatics   University of Washington
> Biostatistics, SCHARP/HVTN          Fred Hutchinson Cancer Research Center
> UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable
> FHCRC  (M/W): 206-667-7025 FAX=206-667-4812 | use Email
> 
> CONFIDENTIALITY NOTICE: This e-mail message and any attachments may be
> confidential and privileged. If you received this message in error,
> please destroy it and notify the sender. Thank you.
> 
>