Will do. I'll build off 1.1.4 with the patch, apply it to the region servers, and capture logs and let you know if I see the exception occur.
--Jacob -----Original Message----- From: Ted Yu [mailto:[email protected]] Sent: Wednesday, May 24, 2017 11:57 AM To: [email protected] Subject: Re: Missing data in snapshot - possible flush timing issue? I attached tentative fix to HBASE-18099. If you have a bandwidth, you can try it out. On Wed, May 24, 2017 at 8:53 AM, LeBlanc, Jacob <[email protected]> wrote: > Great! I see the JIRA bug you just opened. I'll enable debug logging > on FlushSnapshotSubprocedure and HRegion on the region servers in the > cluster to see if I can capture log messages as better evidence. Since > it's a timing issue I'm not sure when we might see it again, but I'll > keep an eye out. > > Thanks so much for your help, > > --Jacob > > -----Original Message----- > From: Ted Yu [mailto:[email protected]] > Sent: Wednesday, May 24, 2017 11:29 AM > To: [email protected] > Subject: Re: Missing data in snapshot - possible flush timing issue? > > In FlushSnapshotSubprocedure (running on region server), there is > debug > log: > > LOG.debug("... Flush Snapshotting region " + > region.toString() + " > completed."); > > If you enable debug log, we would know whether the underlying region > is considered having completed the flush. > > Higher in call() method there is this: > > region.flush(true); > > The return value is not checked. > > In HRegion#flushcache(), Result.CANNOT_FLUSH may be returned due to: > > String msg = "Not flushing since " > > + (writestate.flushing ? "already flushing" > > : "writes not enabled"); > > The above seems to correlate with your description. > > Let me log a JIRA referring to this thread. > > On Wed, May 24, 2017 at 8:08 AM, LeBlanc, Jacob > <[email protected]> > wrote: > > > Thanks for looking Ted! > > > > My understanding of the log messages is that the last line of the > > pastebin is the end of the flush of the memstore for the region > > where we missed data, but that line is tagged with "[MemStoreFlusher.1]" > > whereas the other regions that were getting flushed as part of > > snapshot are tagged with "[rs( > > a1-qa-hbr31416d.lab.lynx-connected.com > ,16020,1494432106955)-snapshot-pool81-thread-1]". > > With only a superficial understanding, it seems like the flush of > > that region where messages were tagged with "[MemStoreFlusher.1]", > > while happening at the same time, wasn't really part of the snapshot > > process. For example, line 3 in the pastebin shows the flush of one > > region starting and tagged with snapshot-pool81-thread-1, line 4 > > shows the flush starting for the region we missed data and tagged > > with MemStoreFlusher.1, and line 5 continues with the flush of > > region as part of snapshot. So it definitely looks like multiple > > flushes were occurring at the same time whereas elsewhere in the > > logs it seems like the flushes are always done sequentially as part > > of snapshot. So I came to the theory that perhaps there is a timing > > issue where the flushed data for a region is missed as part of a > > snapshot because the flush is occurring on another thread as part of > > normal, periodic > flushing of memstore. > > > > The last line I see in the full region server log that has anything > > to do with the snapshot is line 11 in the pastebin at 2017-05-12 > > 02:06:05,577 where it's processing events from zookeeper. Again with > > only a superficial understanding, I was assuming this had something > > to do with the master signaling that the snapshot was complete. > > We'll be sure to capture the master log next time. > > > > And thanks for also checking JIRA for me. If there is a bug here it > > seems as though we don't have an option to upgrade to fix it and > > we'll have to plan on coding around it for now. > > > > Thanks, > > > > --Jacob > > > > -----Original Message----- > > From: Ted Yu [mailto:[email protected]] > > Sent: Wednesday, May 24, 2017 8:47 AM > > To: [email protected] > > Subject: Re: Missing data in snapshot - possible flush timing issue? > > > > bq. the snapshot finishes before the flush of that last region > > finishes > > > > According to the last line in the pastebin, flush finished at > > 2017-05-12 > > 02:06:06,063 > > Did you find something in master log which indicated that snapshot > > finished before the above time ? > > > > I went thru snapshot bug fixes in branch-1.1 backward until seeing > > HBASE-15430 which was in 1.1.4 Among more recent snapshot fixes, > > there was none matching your description. > > > > Next time this happens to your cluster, can you capture master log > > (hopefully with DEBUG logging) ? We would get more clue from master log. > > > > Thanks > > > > On Wed, May 24, 2017 at 1:21 AM, LeBlanc, Jacob > > <[email protected]> > > wrote: > > > > > Hi all, > > > > > > We've recently been testing a Spark job that takes a snapshot of > > > an HBase table and then creates an RDD using > > > TableSnapshotInputFormat class, and we've run into an interesting > > > issue. It appears that the snapshot, and therefore resulting RDD, > > > was missing some data that was recently written to the table. > > > After some digging, it looks like the missing data was limited to > > > a particular region as if the memstore for the region failed to flush > > > before the snapshot was taken. > > > > > > For our testing the job was scheduled in Oozie to run hourly and > > > we are missing data from the region for exactly the last hour, > > > indicating that when the job ran at 1:05 and took the snapshot > > > everything was flushed and worked fine, but at 2:05 when the job > > > ran we missed everything written to the region since the flush at 1:05. > > > > > > Here is an excerpt from the region server at that time: > > > > > > https://pastebin.com/1ECXjhRp > > > > > > Of the three regions for the table owned by this region server, > > > two of them have messages from "snapshot-pool81-thread-1" saying > > > it's flushing the memstore. But at "2017-05-12 02:06:03,229" > > > before the flush of region with rowkey starting with ";uP\xE1" > > > finishes, there is a message from "MemStoreFlusher.1" saying it's > > > starting the flush of memstore for region with rowkey starting > > > with "\xC0\x8F". Then it appears that the snapshot finishes before > > > the flush of that last region finishes, and that is the exact > > > region from which we are missing > > data. > > > > > > So it kind of looks like some timing issue where a normal > > > scheduled flush of the region's memstore kicked in on one thread > > > while the regions were being flushed for the snapshot by another > > > thread causing us to miss the flushed data for that one region in > > > the snapshot. Out of something like > > > 50-100 times this job was run we saw this occur twice. > > > > > > We are running HBase 1.1.4. Is this a known problem? I've tried > > > looking around JIRA but didn't find anything obvious. Anyone > > > familiar with the code could see how this might happen? > > > > > > We can code defensively against this, but wanted to understand > > > what we are dealing with. > > > > > > BTW, I don't have the logs from the master at that time as they've > > > been rolled since then. > > > > > > Thanks! > > > > > > --Jacob LeBlanc > > > > > >
