[R] Re: [openMosix-general] openMosix and R: File I/O issues?

[A.J. Rossini]

Yes.  Read the docs -- it's not so much disliking I/O, as the need to
route I/O back to the originating node (depends on the type of I/O,
whether oMFS is enabled, etc).

James Thomas <james at staarfunds.com> writes:

> 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
>> >
>> >
>> >
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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
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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

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