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

Gregory Matthews greg.matthews at diamond.ac.uk
Mon Aug 18 05:19:29 PDT 2014

On 16/08/14 08:46, Jörg Saßmannshausen wrote:
> My problem: I got some old PCI-X LSI SCSI cards which are connected to some
> Infortrend storage boxes. We recently had a power-dip (lights went off and came
> back within 2 sec) and now the 10 year old frontend is playing up. So I need a
> new frontend and it seems very difficutl to get a PCI-e to PCI-X riser card so I
> can get a newer motherboard with more cores and more memory.

good luck with that! Those technologies are pretty incompatible. There 
are one or two PCIe (x1) to PCI (maybe compatible with PCI-X - check 
voltages etc.) converters but I wouldn't trust them with my storage.

The last server we bought that was still compatible with PCI-X was a 
Dell Poweredge R200, you needed to specify PCI-X riser when buying. 
Maybe ebay is your best bet at this point?


> Hence the thread was good for me to read as I hopefully can configure the
> frontend a bit better.
> If somebody got any comments on my problem feel free to reply.
> David: By the looks of it you will compress larger files on a regular base.
> Have you considered using the parallel version of gzip? Per default it is
> using all available cores but you can change that in the command line. That
> way you might avoid the problem with disc I/O and simply use the available
> cores. You also could do a 'nice' to make sure the machine does not become
> unresponsive due to high CPU load. Just an idea to speed up your
> decompressions.
> All the best from a sunny London
> Jörg
> On Freitag 15 August 2014 Dimitris Zilaskos wrote:
>> Hi,
>> I hope your issue has been resolved meanwhile. I had a somehow similar
>> mixed experience with Dell branded LSI controllers. It would appear
>> that some models are just not fit for particular workloads. I have put
>> some information in our blog at
>> http://www.gridpp.rl.ac.uk/blog/2013/06/14/lsi-1068e-issues-understood-and-
>> resolved/
>> Cheers,
>> Dimitris
>> On Thu, Jul 31, 2014 at 7:37 PM, mathog <mathog at caltech.edu> wrote:
>>> 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
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Greg Matthews        01235 778658
Scientific Computing Group Leader
Diamond Light Source Ltd. OXON UK

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