[Beowulf] mysterious slow disk

ariel sabiguero yawelak asabigue at fing.edu.uy
Tue Mar 4 02:14:19 PST 2008

I found a situation pretty similar to this a few years ago in a system
with shared video memory.
Whenever you allocate less than 32MB of video memory (even without X
server running) the performance drops incredibly low, without any kind
of error, warning or whatever. System seems to stalls erratically, but
when it continues working, everythig seems ok. The performance problem
was related to every I/O operation we performed, not only HDD related.
We were able to detect the problem because we were "tunning" the
configuration, trying to free as much memory and resources. After we
tunned the system, It just started to crawl and when we rolled back, we
realized the source of the problem: "If it works, don't fix it"

I hope this helps.

best regards


David Mathog escribió:
> One node has developed a "slow disk", although at this point I'm not
> at all sure that the disk is actually at fault.  Have any of you ever
> seen something like this:
> 1.  hdparm -t -T /dev/hda on the slow node is typically:
>  Timing cached reads:   504 MB in  2.00 seconds = 251.61 MB/sec
>  Timing buffered disk reads:  104 MB in  3.55 seconds =  29.29 MB/sec
> but the second line varies A LOT, down to 24Mb and up to over
> 30.  However the same test on the other nodes varies only a little:
>  Timing cached reads:   514 MB in  2.01 seconds = 256.03 MB/sec
>  Timing buffered disk reads:  124 MB in  3.04 seconds =  40.74 MB/sec
> (plus or minus about 1MB/sec on the second line).
> 2.  hdparm -i -v and -i -m are identical on all machines, except
> for serial number.  Here is -i -v on the slow one:
> /dev/hda:
>  multcount    = 16 (on)
>  IO_support   =  1 (32-bit)
>  unmaskirq    =  1 (on)
>  using_dma    =  1 (on)
>  keepsettings =  0 (off)
>  readonly     =  0 (off)
>  readahead    = 256 (on)
>  geometry     = 65535/16/63, sectors = 78165360, start = 0
>  Model=WDC WD400BB-00DEA0, FwRev=05.03E05, SerialNo=WD-WMAD11736294
>  Config={ HardSect NotMFM HdSw>15uSec SpinMotCtl Fixed DTR>5Mbs FmtGapReq }
>  RawCHS=16383/16/63, TrkSize=57600, SectSize=600, ECCbytes=40
>  BuffType=DualPortCache, BuffSize=2048kB, MaxMultSect=16, MultSect=16
>  CurCHS=16383/16/63, CurSects=16514064, LBA=yes, LBAsects=78165360
>  IORDY=on/off, tPIO={min:120,w/IORDY:120}, tDMA={min:120,rec:120}
>  PIO modes:  pio0 pio1 pio2 pio3 pio4 
>  DMA modes:  mdma0 mdma1 mdma2 
>  UDMA modes: udma0 udma1 udma2 udma3 udma4 *udma5 udma3 udma4 *udma5 
>  AdvancedPM=no WriteCache=enabled
>  Drive conforms to: Unspecified:  ATA/ATAPI-1 ATA/ATAPI-2 ATA/ATAPI-3
> 3.  Western Digital diagnostics and smartctl show nothing wrong with
> the disk.  It has no bad sectors or other errors logged.  The smartctl
> tests do take longer to complete than on the other disks.
> 4.  DMA is working (at least partially), since turning that off drops
> the hdparm test down to about 4Mb/sec.
> 5.  Opened the case and all jumpers were as they should be, Power supply
> tested good.
> 6.  dmesg from the slow node and a normal node shows no significant
> differences.  (Changes in the 3rd digit after the decimal of the
> bogoMIPS value, for instance.)
> The only oddity I've found was that the setting "32 bit I/O" in the BIOS
> was disabled for some reason on the slow node.  Changing it to enabled
> made no difference (even after several reboots, cold and warm.)  Is it
> possible that the OS has the earlier setting hidden away somewhere and
> is still using it?  This was particularly weird because hdparm showed
> IO_Support = 1 (32-bit)
> even when this BIOS bit was disabled.
> The speed issue initially turned up in a run where a certain program was
> required to allocate about 1.6 Gb of memory (at least .6GB of which had
> to come out of the 2GB swap, since there was only 1GB of RAM.)  That
> large region was then ordered with qsort().  Bizarrely, this took
> forever on one node (hours longer than on any other node, with similar
> sized data), and when it finished the sort the resulting binary data was
> written to disk at only 0.5 Mb/sec.  Yes, 500kilobytes/sec.  Nothing
> else was using CPU time.  Prior to that one run this node did
> nothing to draw my attention to it as a "slow node".
> This is on one of the notorious Tyan S2466 boards. I'm beginning to
> wonder if perhaps it now has a bit stuck somewhere in the BIOS, in which
> case maybe wiping the BIOS settings and redoing them will fix it.
> I already tried powering it off for 15 minutes unplugged, but that
> did not help.
> Also the whole cluster had to be powered down for about 15 minutes
> in the morning before this started for A/C service.  If the battery
> on that board is iffy it might explain how the "32 bit I/O" became
> disabled.  However, it did not reset again on a subsequent long power down.
> Thanks,
> David Mathog
> mathog at caltech.edu
> Manager, Sequence Analysis Facility, Biology Division, Caltech
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