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 The contents of this email are confidential and for the exclusive use of the intended recipient. If you receive this email in error you should not copy it, retransmit it, use it or disclose its contents but should return it to the sender immediately and delete your copy. _______________________________________________ Beowulf mailing list, Beowulf@beowulf.org sponsored by Penguin Computing To change your subscription (digest mode or unsubscribe) visit http://www.beowulf.org/mailman/listinfo/beowulf
