[Beowulf] Help: Raspberry Pi Cluster

Hearns, John john.hearns at mclaren.com
Mon Dec 17 02:33:55 PST 2012


On 2012/12/17 12:30, Mark Hahn wrote:
>> Thanks for the information. I would like to set up RPi cluster for some
>> bioinformatics jobs like sequences alignment and sequences operations.
>
> you really need to look at where your code is spending its time.
> the seq stuff I see is quite IO-intensive, sometimes memory-intensive.
How do I know if the application is IO-intensive or memory-intensive? 
Any tools to measure that?


That's a good question.

I think often in HPC these are shorthand for:

"Heck - this application writes some huge files. Every time I run it my RAID array lights
Up like a Christmas tree"

"Darn it to heck - every time I run this application the machine runs of of memory.
I need lots of fat nodes to run it"


Seriously though - for measuring memory    vmstat    or    'watch cat /proc/meminfo'

Ganglia also produces some pretty graphs of memory usage, as does sysstat/sar in combination with kSar


For measuring IO rates   iostat   and   iotop

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