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

Huntsinger, Reid reid_huntsinger at merck.com
Wed Apr 21 21:25:24 CEST 2004

It's generally said that OM needs lots more swap than plain Linux. There has
to be someplace to juggle processes around. We use 4 GB nodes with something
like 12 GB swap; that plus round-robin logins to distribute home nodes
seemed to solve a lot of our problems. 

To use oMFS to allow processes to write from the node they've migrated to
you also need DFSA enabled. That sounds like a great idea but it seems to
cause problems in our setup--that is, with DFSA off we go a lot longer
without oMFS misbehavior or other odd phenomena than when DFSA is on. 

How many processes do you run at a time?

Reid Huntsinger

-----Original Message-----
From: Jim Thomas [mailto:james at staarfunds.com] 
Sent: Wednesday, April 21, 2004 3:14 PM
To: Huntsinger, Reid
Cc: r-help at stat.math.ethz.ch; openmosix-general at lists.sourceforge.net
Subject: Re: [openMosix-general] openMosix and R: File I/O issues?

Memory could be an issue. The three nodes in the cluster we are using 
only have 512 MB. The machines are otherwise identical in terms of 
hardware. They are dual PIIIs (purchased from Penguin Computing in 
2001). (If you need specs on motherboard etc, we can get that info 

The installed operating system is RHEL-3, standard workstation with some 
additional libraries (e.g., all of the development ones) and packages 
(e.g., tarball-based installs of R & Octave).

Swap was set to twice the RAM.

Not sure about how big the R processes are. Under Matlab and using a 
network version of LVQ, the processes were under 256 MB. It could be a 
lot larger in R, given that KNN is explicitly used in certain stages of 
LVQ and that should consume a lot of memory.

oMFS is not currently being used, nor any other network filesystem... do 
you think this would be helpful by allowing the large processes to 
remain on the nodes to which they migrated when writing files.  The 
actual file I/O is very small.... only approximately 5 - 50 results are 
being written into a file that remains under 2k in size.  However, I 
believe that these results are not derived until LVQ finishes so there's 
no way to write a few resluts periodically.

Thanks for your help!


Huntsinger, Reid wrote:

>Can you have the R processes open the file, write, and close periodically?
>Just to see where they die? Is it that the file never gets flushed to disk
>before the process dies for some reason? Maybe processes migrate back for
>file i/o and the total required memory is just too large? R processes can
>easily have large memory requirements.
>More details on your setup would probably help: are you using omfs? other
>network file systems? How is the cluster set up? How much RAM and swap? How
>big are the R processes?
>Reid Huntsinger
>-----Original Message-----
>From: openmosix-general-admin at lists.sourceforge.net
>[mailto:openmosix-general-admin at lists.sourceforge.net] On Behalf Of Jim
>Sent: Tuesday, April 20, 2004 11:16 AM
>To: r-help at stat.math.ethz.ch; openmosix-general at lists.sourceforge.net
>Subject: [openMosix-general] 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?
>openMosix kernel 2.4.21
>R 1.8.1
>RedHat Enterprise Edition
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