Reboot – Is There A Timeout On Filesystem Flush?

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I’ve had a few systems with a lot of RAM and very busy filesystems come up with filesystem errors that took a manual ‘fsck -y’ after what should have been a clean reboot. This is particularly annoying on remote systems where I have to talk someone else through the recovery.

Is there some time limit on the cache write with a ‘reboot’ (no options) command or is ext4 that fragile?

23 thoughts on - Reboot – Is There A Timeout On Filesystem Flush?

  • I’d say there’s no limit in the amount of time the kernel waits until the blocks have been written to disk; driven by there parameters:

    vm.dirty_background_bytes = 0
    vm.dirty_background_ratio = 10
    vm.dirty_bytes = 0
    vm.dirty_expire_centisecs = 3000
    vm.dirty_ratio = 20
    vm.dirty_writeback_centisecs = 500

    ie, if the data cached on RAM is older than 30s or larger than 10%
    available RAM, the kernel will try to flush it to disk. Depending how much data needs to be flushed at poweroff/reboot time, this could have a significant effect on the time taken.

    Regarding systems with lots of RAM, I’ve never seen such a behaviour on a few 192 GB RAM servers I administer. Granted, your system could be tuned in a different way or have some other configuration.

    TBH I’m not confident to give a definitive answer re the data not been totally flushed before reboot. I’d investigate:

    – Whether this happens on every reboot or just on some.
    – Whether your RAM is OK (the FS errors could come from that!).
    – Whether your disks/SAN are caching writes. (Maybe they are and the OS thinks the data has been flushed to disk, but they haven’t)
    – filesystem mount options that might interfere (nobarrier, commit, data…)

    HTH

    ~f

  • This has been discussed to death on various lists, including the LKML…

    Almost every controller and drive out there now lies about what is and isn’t flushed to disk, making it nigh on impossible for the Kernel to reliably know 100% of the time that the data HAS been flushed to disk. This is part of the reason why it is always a Good Idea™ to have some sort of pause in the shut down to ensure that it IS flushed.

    This is also why server grade gear uses battery backed buffers, etc. which are supposed to allow drives to properly flush the data to disk. There is still a slim chance in these cases that the data still will not reach the platter before power off or reboot, especially in catastrophic cases.

  • That’s pretty much entirely irrelevant to the original question.

    (Feel free to correct me if I’m wrong in the following)

    A filesystem has three states: Clean, Dirty, and Dirty with errors.

    When a filesystem is unmounted, the cache is flushed and it is marked clean last. This is the expected state when a filesystem is mounted.

    Once a filesystem is mounted read/write, then it is marked dirty. If a filesystem is dirty when it is mounted, then it wasn’t unmounted properly. In the case of a journaled filesystem, typically the journal will be replayed and the filesystem will then be mounted.

    The last case, dirty with errors indicates that the kernel found invalid data while the filesystem was mounted, and recorded that fact in the filesystem metadata. This will normally be the only condition that will force an fsck on boot. It will also normally result in logs being generated when the errors are encountered. If your filesystems are force-checked on boot, then the logs should usually tell you why. It’s not a matter of a timeout or some device not flushing its cache.

    Of course, the other possibility is simply that you’ve formatted your own filesystems, and they have a maximum mount count or a check interval. Use ‘tune2fs -l’ to check those two values. If either of them are set, then there is no problem with your system. It is behaving as designed, and forcing a periodic check because that is the default behavior.

  • If Les is having to run fsck manually, as he wrote in his OP, then this is unlikely to be the cause of the issues he described in that post. There must be some sort of errors on the filesystem that caused the unattended fsck to exit nonzero.

    –keith

  • Yes – the unattended fsck fails. Personally, I’d prefer for the default run to use ‘-y’ in the first place. It’s not like I’m more likely than fsck to know how to fix it and it is very inconvenient on remote machines. The recent case was an opennms system updating a lot of rrd files, but I’ve also seen it on BackupPC archives with lots of files and lots of hard links. Some of these have been on VMware ESXi hosts where the physical host wasn’t rebooted and the controller/power not involved at all. Eventually these will be replaced with CentOS7 systems, probably using XFS but I don’t know if that will be better or worse. It is mostly on aging hardware, so it is possible that there are underlying controller issues. I also see some rare cases on similar machines where a filesystem will go read-only with some scsi errors logged, but didn’t look for that yet in this case.

  • In that case, there should be logs indicating the cause of the error when it was detected by the kernel. There’s probably something wrong with your controller or other hardware.

    Every regular file’s directory entry on your system is a hard link. There’s nothing particular about links (files) that make a filesystem fragile.

    It’s probably a similar cause in all cases. I don’t know how many times I’ve seen you on this list defending running old hardware / obsolete hardware. Corruption and failure are more or less what I’d expect if your hardware is junk.

  • I know that I have seen it take 10 ot 15 minutes to sync a 7200 rpm 3 TB WD drive that had over
    2 million rrd files being updated by ntopng when the system had 32GB of ram. The system is a Intel(R) Core(TM) i7-3770 CPU @ 3.40GHz but one cpu will in in constant IO wait state until the sync finishes. I have never tried shutting it down when it was syncing though.

  • Agreed, although when there are millions, the fsck fixing it is somewhat slow.

    Not junk – these are mostly IBM 3550/3650 boxes – pretty much top of the line in their day (before the M2/3/4 versions), They have Adaptec raid contollers, SAS drives, mostly configured as RAID1
    mirrors. I realize that hardware isn’t perfect and this is not happening on a large percentage of them. But, I don’t see anything that looks like scsi errors in this log and I’m surprised that after running apparently error-free there would be problems detected after a software reboot.

    I think the newer M2 and later models went to a different RAID
    controller, though. Maybe there was a reason.

  • I never had Adaptec in _my_ list of good RAID hardware… But certainly I
    can note be the one to offer judgement on hardware I avoid to the best of my ability. If you can afford, I would do the test: replace Adaptec with something else (in my list it would be either 3ware or LSI or areca), leaving the rest of hardware as it is. And see it the problems continue. I
    do realize that there is more to it than just pulling one card and sticking another in its place (that’s why I said if you can “afford” it meaning in more general sense, not just monetary).

    Valeri

    ++++++++++++++++++++++++++++++++++++++++
    Valeri Galtsev Sr System Administrator Department of Astronomy and Astrophysics Kavli Institute for Cosmological Physics University of Chicago Phone: 773-702-4247
    ++++++++++++++++++++++++++++++++++++++++

  • It’s not something happening as a repeatable thing or that I could consider better/worse after replacing something. Maybe 3 times a year across a few hundred machines and generally not repeating on the same ones. But if there is anything in common it is on very ‘active’
    filesystems.

  • Seems random to me – not repeating on the same box, and rare enough that it is hard to make any generalization except that it is painful to talk some remote helper through the recovery process – usually involving emailing some cell phone photos of the console to figure out which partition has the problem.

  • Too bad… Reminds me one of my 32 node clusters in which one of the nodes crashed in a crashed once a month (always different node, so probability of run is 32 Month before crash ;-( Too bad for troubleshooting. Only after 6 Months I pinpointed particular brand of RAM mixed in into each node – when I got rid of it, the trouble ended… I would bet on Adaptec cards in your case… though ideally I shouldn’t be offering judgement on hardware of the brand I almost never use. Good luck!

    Valeri

    ++++++++++++++++++++++++++++++++++++++++
    Valeri Galtsev Sr System Administrator Department of Astronomy and Astrophysics Kavli Institute for Cosmological Physics University of Chicago Phone: 773-702-4247
    ++++++++++++++++++++++++++++++++++++++++

  • In most cases intentional reboots _shouldn’t_ trigger this, but I cannot say that with a 100% certainty since, again, controllers CAN and DO lie. If the controller is not battery backed, the certainty is even more shaky, since the card’s firmware can be in the process of lazy writing the content to disk when the main board drops power to the card’s slot on the main board during the reboot, which without the extra battery would cause the data to be lost.

    During the reboot, most card’s drivers on init, will invalidate the cache on the card to ensure dirty pages of data don’t get flushed to disk, to prevent scribbling junk data to the platters. From what I recall, this is true of both the megaraid and adaptec based cards.

  • Problem is, Gordon, the layer I’m talking about is _below_ the logical layer that filesystems live at, in the block layer, at the mercy of drivers, and firmware that the kernel has zero control over. While in a perfect world, the controller would do strictly only what the Kernel tells it, that just isn’t true for a while now with the large caches that drives and controllers have now.

    In most cases, this should never trigger, however in some buggy drivers, or controllers that have buggy firmware, the writes can be seriously delayed to disk, which can cause data to never make it to the platter.

  • I’d have to shut one down and get into the bios config to see, but I
    think these default to write-through if they aren’t battery backed –
    caching may not even be an option. This one might have a battery going bad, though.

    I see a bunch of entries like:
    ioatdma 0000:00:08.0: Channel halted, chanerr = 2
    ioatdma 0000:00:08.0: Channel halted, chanerr = 0
    in the logs and one of these:
    hrtimer: interrupt took 258633 ns

    Not sure what those mean. We do have considerably more systems running windows than linux on this hardware and I don’t think anyone has noticed a systemic problem there.


    Les Mikesell
    lesmikesell@gmail.com

  • Presumably, this cache invalidation is only on cards that don’t have battery (or flash) backed write cache? Doing that on a BB/FBWC
    system would negate the usefulness of said battery backed cache entirely.

    IMHO, an even bigger problem is using cheap desktop class SATA drives for server storage. These FREQUENTLY lie about write commits. This sort of behavior is a VERY good reason to stick with vendor qualified and branded server drives that have been tested to work with the specific controller + backplane configurations they are sold with. And yes, those drives cost 2-3X more than your Newegg/Amazon elcheapo desktop stuff.

    All of this controller and drive behavior is a VERY good argument for the use of end to end checksumming like ZFS does… a ZFS ‘scrub’
    operation WILL detect any data corruption on the file system and raid, whatever the source, and many inconsistencies can be corrected, such as one disk of a mirror having a stale block.


    john r pierce 37N 122W
    somewhere on the middle of the left coast

  • well, those $$$ drives are likely SAS rather than SATA, and that has other advantages… 10k or 15k RPM gives you up to double the IOPS per spindle of a 7200rpm SATA drive (and WD Reds are only 5900 RPM, I
    believe?)… 2.5″ enterprise disks let you have more smaller spindles in the same space (24-25 per 2U vs 12 for 3.5″) for higher IO
    concurrency, and SAS supports multipathing (dual porting) for higher IO
    bandwidth, also SAS has tagged command queueing which often performs better than SATA NCQ under high IO concurrency workloads, like database servers.

  • The ones with batteries will try to properly write the content of the cache to the disk right before the cache invalidate occurs. This is one of the few times when they aren’t lazy in their write patterns.

    Regarding cheap vs. enterprise drives, agreed. You should absolutely never trust the disks to do the “right” thing with cheap models.

  • Was this resolved? The ioatdma messages are from ioat_dma.c, a driver for Intel’s I/OAT DMA engine typically used on high-end server hardware to accelerate network I/O. chanerr = 2 might be an issue with the DMA channel being in a suspended state when the driver isn’t expecting it to be. Maybe a network driver bug.

  • No, reboots are rare on these servers and file corruption is rare even within those, so I don’t anticipate seeing enough instances to find a pattern.

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