Hi Zhenya, Thanks for the pointers - I will look into them.
I have been doing some additional reading into this and discovered we are using a 4.0 NFS client, which seems to be the first 'no-no'; we will look at updating to use the 41 NFS client. We have modified our default timer cadence for checkpointing from 3 minutes to 1 minutes, which seems to be giving us better performance. We will continue to measure the impact that has. Lastly, I'm planning to merge our two data regions into a single region to reduce 'too many dirty pages' checkpoints due to high write activity in a small region. Would using larger pages sizes (eg: 16kb) be useful with EFS? Raymond. On Tue, Jan 12, 2021 at 8:27 PM Zhenya Stanilovsky <arzamas...@mail.ru> wrote: > hope it would be helpful too: > > https://www.jeffgeerling.com/blog/2018/getting-best-performance-out-amazon-efs > https://docs.aws.amazon.com/efs/latest/ug/storage-classes.html > > > Hi Zhenya, > > The matching checkpoint finished log is this: > > 2020-12-15 19:07:39,253 [106] INF [MutableCacheComputeServer] Checkpoint > finished [cpId=e2c31b43-44df-43f1-b162-6b6cefa24e28, pages=33421, > markPos=FileWALPointer [idx=6339, fileOff=243287334, len=196573], > walSegmentsCleared=0, walSegmentsCovered=[], markDuration=218ms, > pagesWrite=1150ms, fsync=37104ms, total=38571ms] > > Regards your comment that 3/4 of pages in whole data region need to be > dirty to trigger this, can you confirm this is 3/4 of the maximum size of > the data region, or of the currently used size (eg: if Min is 1Gb, and Max > is 4Gb, and used is 2Gb, would 1.5Gb of dirty pages trigger this?) > > Are data regions independently checkpointed, or are they checkpointed as a > whole, so that a 'too many dirty pages' condition affects all data regions > in terms of write blocking? > > Can you comment on my query regarding should we set Min and Max size of > the data region to be the same? Ie: Don't bother with growing the data > region memory use on demand, just allocate the maximum? > > In terms of the checkpoint lock hold time metric, of the checkpoints > quoting 'too many dirty pages' there is one instance apart from the one I > have provided earlier violating this limit, ie: > > 2020-12-17 18:56:39,086 [104] INF [MutableCacheComputeServer] Checkpoint > started [checkpointId=e9ccf0ca-f813-4f91-ac93-5483350fdf66, > startPtr=FileWALPointer [idx=7164, fileOff=389224517, len=196573], > checkpointBeforeLockTime=276ms, checkpointLockWait=0ms, > checkpointListenersExecuteTime=16ms, checkpointLockHoldTime=39ms, > walCpRecordFsyncDuration=254ms, writeCheckpointEntryDuration=32ms, > splitAndSortCpPagesDuration=276ms, pages=77774, reason='too many dirty > pages'] > > This is out of a population of 16 instances I can find. The remainder have > lock times of 16-17ms. > > Regarding writes of pages to the persistent store, does the check pointing > system parallelise writes across partitions ro maximise throughput? > > Thanks, > Raymond. > > > > On Thu, Dec 31, 2020 at 1:17 AM Zhenya Stanilovsky <arzamas...@mail.ru > <//e.mail.ru/compose/?mailto=mailto%3aarzamas...@mail.ru>> wrote: > > > All write operations will be blocked for this timeout : > checkpointLockHoldTime=32ms > (Write Lock holding) If you observe huge amount of such messages : > reason='too many dirty pages' may be you need to store some data in not > persisted regions for example or reduce indexes (if you use them). And > please attach other part of cp message starting with : Checkpoint finished. > > > > > In ( > https://cwiki.apache.org/confluence/display/IGNITE/Ignite+Persistent+Store+-+under+the+hood), > there is a mention of a dirty pages limit that is a factor that can trigger > check points. > > I also found this issue: > http://apache-ignite-users.70518.x6.nabble.com/too-many-dirty-pages-td28572.html > where "too many dirty pages" is a reason given for initiating a checkpoint. > > After reviewing our logs I found this: (one example) > > 2020-12-15 19:07:00,999 [106] INF [MutableCacheComputeServer] Checkpoint > started [checkpointId=e2c31b43-44df-43f1-b162-6b6cefa24e28, > startPtr=FileWALPointer [idx=6339, fileOff=243287334, len=196573], > checkpointBeforeLockTime=99ms, checkpointLockWait=0ms, > checkpointListenersExecuteTime=16ms, checkpointLockHoldTime=32ms, > walCpRecordFsyncDuration=113ms, writeCheckpointEntryDuration=27ms, > splitAndSortCpPagesDuration=45ms, pages=33421, reason='too many dirty > pages'] > > Which suggests we may have the issue where writes are frozen until the > check point is completed. > > Looking at the AI 2.8.1 source code, the dirty page limit fraction appears > to be 0.1 (10%), via this entry in GridCacheDatabaseSharedManager.java: > > /** > * Threshold to calculate limit for pages list on-heap caches. > * <p> > > * Note: When a checkpoint is triggered, we need some amount of page > memory to store pages list on-heap cache. > > * If a checkpoint is triggered by "too many dirty pages" reason and > pages list cache is rather big, we can get > > * {@code IgniteOutOfMemoryException}. To prevent this, we can limit the total > amount of cached page list buckets, > > * assuming that checkpoint will be triggered if no more then 3/4 of > pages will be marked as dirty (there will be > > * at least 1/4 of clean pages) and each cached page list bucket can be > stored to up to 2 pages (this value is not > > * static, but depends on PagesCache.MAX_SIZE, so if PagesCache.MAX_SIZE > > PagesListNodeIO#getCapacity it can take > > * more than 2 pages). Also some amount of page memory needed to store > page list metadata. > */ > private static final double PAGE_LIST_CACHE_LIMIT_THRESHOLD = 0.1; > > This raises two questions: > > 1. The data region where most writes are occurring has 4Gb allocated to > it, though it is permitted to start at a much lower level. 4Gb should be > 1,000,000 pages, 10% of which should be 100,000 dirty pages. > > The 'limit holder' is calculated like this: > > /** > * @return Holder for page list cache limit for given data region. > */ > public AtomicLong pageListCacheLimitHolder(DataRegion dataRegion) { > if (dataRegion.config().isPersistenceEnabled()) { > return pageListCacheLimits.computeIfAbsent(dataRegion.config > ().getName(), name -> new AtomicLong( > (long)(((PageMemoryEx)dataRegion.pageMemory()).totalPages > () * PAGE_LIST_CACHE_LIMIT_THRESHOLD))); > } > > return null; > } > > ... but I am unsure if totalPages() is referring to the current size of > the data region, or the size it is permitted to grow to. ie: Could the > 'dirty page limit' be a sliding limit based on the growth of the data > region? Is it better to set the initial and maximum sizes of data regions > to be the same number? > > 2. We have two data regions, one supporting inbound arrival of data (with > low numbers of writes), and one supporting storage of processed results > from the arriving data (with many more writes). > > The block on writes due to the number of dirty pages appears to affect all > data regions, not just the one which has violated the dirty page limit. Is > that correct? If so, is this something that can be improved? > > Thanks, > Raymond. > > > On Wed, Dec 30, 2020 at 9:17 PM Raymond Wilson <raymond_wil...@trimble.com > <http://e.mail.ru/compose/?mailto=mailto%3araymond_wil...@trimble.com>> > wrote: > > I'm working on getting automatic JVM thread stack dumping occurring if we > detect long delays in put (PutIfAbsent) operations. Hopefully this will > provide more information. > > On Wed, Dec 30, 2020 at 7:48 PM Zhenya Stanilovsky <arzamas...@mail.ru > <http://e.mail.ru/compose/?mailto=mailto%3aarzamas...@mail.ru>> wrote: > > > Don`t think so, checkpointing work perfectly well already before this fix. > Need additional info for start digging your problem, can you share ignite > logs somewhere? > > > > I noticed an entry in the Ignite 2.9.1 changelog: > > - Improved checkpoint concurrent behaviour > > I am having trouble finding the relevant Jira ticket for this in the 2.9.1 > Jira area at > https://issues.apache.org/jira/browse/IGNITE-13876?jql=project%20%3D%20IGNITE%20AND%20fixVersion%20%3D%202.9.1%20and%20status%20%3D%20Resolved > > Perhaps this change may improve the checkpointing issue we are seeing? > > Raymond. > > > On Tue, Dec 29, 2020 at 8:35 PM Raymond Wilson <raymond_wil...@trimble.com > <http://e.mail.ru/compose/?mailto=mailto%3araymond_wil...@trimble.com>> > wrote: > > Hi Zhenya, > > 1. We currently use AWS EFS for primary storage, with provisioned IOPS to > provide sufficient IO. Our Ignite cluster currently tops out at ~10% usage > (with at least 5 nodes writing to it, including WAL and WAL archive), so we > are not saturating the EFS interface. We use the default page size > (experiments with larger page sizes showed instability when checkpointing > due to free page starvation, so we reverted to the default size). > > 2. Thanks for the detail, we will look for that in thread dumps when we > can create them. > > 3. We are using the default CP buffer size, which is max(256Mb, > DataRagionSize / 4) according to the Ignite documentation, so this should > have more than enough checkpoint buffer space to cope with writes. As > additional information, the cache which is displaying very slow writes is > in a data region with relatively slow write traffic. There is a primary > (default) data region with large write traffic, and the vast majority of > pages being written in a checkpoint will be for that default data region. > > 4. Yes, this is very surprising. Anecdotally from our logs it appears > write traffic into the low write traffic cache is blocked during > checkpoints. > > Thanks, > Raymond. > > > > On Tue, Dec 29, 2020 at 7:31 PM Zhenya Stanilovsky <arzamas...@mail.ru > <http://e.mail.ru/compose/?mailto=mailto%3aarzamas...@mail.ru>> wrote: > > > 1. Additionally to Ilya reply you can check vendors page for > additional info, all in this page are applicable for ignite too [1]. > Increasing threads number leads to concurrent io usage, thus if your have > something like nvme — it`s up to you but in case of sas possibly better > would be to reduce this param. > 2. Log will shows you something like : > > Parking thread=%Thread name% for timeout(ms)= %time% > > and appropriate : > > Unparking thread= > > 3. No additional looging with cp buffer usage are provided. cp buffer > need to be more than 10% of overall persistent DataRegions size. > 4. 90 seconds or longer — Seems like problems in io or system tuning, > it`s very bad score i hope. > > [1] > https://www.gridgain.com/docs/latest/perf-troubleshooting-guide/persistence-tuning > > > > > > Hi, > > We have been investigating some issues which appear to be related to > checkpointing. We currently use the IA 2.8.1 with the C# client. > > I have been trying to gain clarity on how certain aspects of the Ignite > configuration relate to the checkpointing process: > > 1. Number of check pointing threads. This defaults to 4, but I don't > understand how it applies to the checkpointing process. Are more threads > generally better (eg: because it makes the disk IO parallel across the > threads), or does it only have a positive effect if you have many data > storage regions? Or something else? If this could be clarified in the > documentation (or a pointer to it which Google has not yet found), that > would be good. > > 2. Checkpoint frequency. This is defaulted to 180 seconds. I was thinking > that reducing this time would result in smaller less disruptive check > points. Setting it to 60 seconds seems pretty safe, but is there a > practical lower limit that should be used for use cases with new data > constantly being added, eg: 5 seconds, 10 seconds? > > 3. Write exclusivity constraints during checkpointing. I understand that > while a checkpoint is occurring ongoing writes will be supported into the > caches being check pointed, and if those are writes to existing pages then > those will be duplicated into the checkpoint buffer. If this buffer becomes > full or stressed then Ignite will throttle, and perhaps block, writes until > the checkpoint is complete. If this is the case then Ignite will emit > logging (warning or informational?) that writes are being throttled. > > We have cases where simple puts to caches (a few requests per second) are > taking up to 90 seconds to execute when there is an active check point > occurring, where the check point has been triggered by the checkpoint > timer. When a checkpoint is not occurring the time to do this is usually in > the milliseconds. The checkpoints themselves can take 90 seconds or longer, > and are updating up to 30,000-40,000 pages, across a pair of data storage > regions, one with 4Gb in-memory space allocated (which should be 1,000,000 > pages at the standard 4kb page size), and one small region with 128Mb. > There is no 'throttling' logging being emitted that we can tell, so the > checkpoint buffer (which should be 1Gb for the first data region and 256 Mb > for the second smaller region in this case) does not look like it can fill > up during the checkpoint. > > It seems like the checkpoint is affecting the put operations, but I don't > understand why that may be given the documented checkpointing process, and > the checkpoint itself (at least via Informational logging) is not > advertising any restrictions. > > Thanks, > Raymond. > > -- > <http://www.trimble.com/> > Raymond Wilson > Solution Architect, Civil Construction Software Systems (CCSS) > > > > > > > > > > -- > <http://www.trimble.com/> > Raymond Wilson > Solution Architect, Civil Construction Software Systems (CCSS) > 11 Birmingham Drive | Christchurch, New Zealand > +64-21-2013317 Mobile > raymond_wil...@trimble.com > <http://e.mail.ru/compose/?mailto=mailto%3araymond_wil...@trimble.com> > > > > <https://worksos.trimble.com/?utm_source=Trimble&utm_medium=emailsign&utm_campaign=Launch> > > > > -- > <http://www.trimble.com/> > Raymond Wilson > Solution Architect, Civil Construction Software Systems (CCSS) > 11 Birmingham Drive | Christchurch, New Zealand > +64-21-2013317 Mobile > raymond_wil...@trimble.com > <http://e.mail.ru/compose/?mailto=mailto%3araymond_wil...@trimble.com> > > > > <https://worksos.trimble.com/?utm_source=Trimble&utm_medium=emailsign&utm_campaign=Launch> > > > > > > > > > -- > <http://www.trimble.com/> > Raymond Wilson > Solution Architect, Civil Construction Software Systems (CCSS) > 11 Birmingham Drive | Christchurch, New Zealand > +64-21-2013317 Mobile > raymond_wil...@trimble.com > <http://e.mail.ru/compose/?mailto=mailto%3araymond_wil...@trimble.com> > > > > <https://worksos.trimble.com/?utm_source=Trimble&utm_medium=emailsign&utm_campaign=Launch> > > > > -- > <http://www.trimble.com/> > Raymond Wilson > Solution Architect, Civil Construction Software Systems (CCSS) > 11 Birmingham Drive | Christchurch, New Zealand > +64-21-2013317 Mobile > raymond_wil...@trimble.com > <http://e.mail.ru/compose/?mailto=mailto%3araymond_wil...@trimble.com> > > > > <https://worksos.trimble.com/?utm_source=Trimble&utm_medium=emailsign&utm_campaign=Launch> > > > > > > > > > -- > <http://www.trimble.com/> > Raymond Wilson > Solution Architect, Civil Construction Software Systems (CCSS) > 11 Birmingham Drive | Christchurch, New Zealand > +64-21-2013317 Mobile > raymond_wil...@trimble.com > <//e.mail.ru/compose/?mailto=mailto%3araymond_wil...@trimble.com> > > > > <https://worksos.trimble.com/?utm_source=Trimble&utm_medium=emailsign&utm_campaign=Launch> > > > > > > > > > -- <http://www.trimble.com/> Raymond Wilson Solution Architect, Civil Construction Software Systems (CCSS) 11 Birmingham Drive | Christchurch, New Zealand raymond_wil...@trimble.com <https://worksos.trimble.com/?utm_source=Trimble&utm_medium=emailsign&utm_campaign=Launch>
