[Beowulf] LSI Megaraid stalls system on very high IO?

[mathog]

Any pointers on why a system might appear to "stall" on very high IO 
through an LSI megaraid adapter?  (dm_raid45, on RHEL 5.10.)

I have been working on another group's big Dell server, which has 16 
CPUs, 82 GB of memory, and 5 1TB disks which go through an LSI Megaraid 
(not sure of the exact configuration and their system admin is out sick) 
and show up as /dev/sda[abc], where the first two are just under 2 TB 
and the third is /boot and is about 133 Gb.  sda and sdb are then 
combined through lvm into one big volume and that is what is mounted.

Yesterday on this system when I ran 14 copies of this simultaneously:

   # X is 0-13
   gunzip -c bigfile${X}.gz > resultfile${X}

the first time, part way through, all of my terminals locked up for 
several minutes, and then recovered.  Another similar command had the 
same issue about half an hour later, but others between and since did 
not stall.  The size of the files unpacked is only about 0.5Gb, so even 
if the entire file was stored in memory in the pipes all 14 should have 
fit in main memory.  Nothing else was running (at least that I noticed 
before or after, something might have started up during the run and 
ended before I could look for it.)  During this period the system would 
still answer pings.  Nothing showed up in /var/log/messages or dmesg, 
"last" showed nobody else had logged in, and overnight runs of "smartctl 
-t long" on the 5 disks were clean - nothing pending, no reallocation 
events.

Today ran the first set of commands again with "nice 10" and had "top" 
going and nothing untoward was observed and there were no stalls. On 
that run iostat showed:

Device:            tps   Blk_read/s   Blk_wrtn/s   Blk_read   Blk_wrtn
sda            6034.00         0.00    529504.00          0     529504
sda5           6034.00         0.00    529504.00          0     529504
dm-0          68260.00      2056.00    546008.00       2056     546008


So why the apparent stalls yesterday?  It felt like either my 
interactive processes were swapped out or they had a much lower priority 
than enough other processes so that they were not getting any CPU time. 
Is there some sort of housekeeping that the Megaraid, LVM, or anything 
normally installed with RHEL 5.10, might need to do, from time to time, 
that would account for these stalls?

Thanks,

David Mathog
mathog at caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech