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From Tom Brown <tombrow...@gmail.com>
Subject Re: Why is this region compacting?
Date Tue, 24 Sep 2013 18:35:25 GMT
/usr/lib/hbase/bin/hbase org.apache.hadoop.hbase.io.hfile.HFile -m -s -v -f
/hbase/compound3/5ab5fdfcf2aff2633e1d6d5089c96aa2/d/fca0882dc7624342a8f4fce4b89420ff
13/09/24 12:33:40 INFO util.ChecksumType: Checksum using
org.apache.hadoop.util.PureJavaCrc32
Scanning ->
/hbase/compound3/5ab5fdfcf2aff2633e1d6d5089c96aa2/d/fca0882dc7624342a8f4fce4b89420ff
13/09/24 12:33:41 INFO hfile.CacheConfig: Allocating LruBlockCache with
maximum size 2.9g
13/09/24 12:33:41 ERROR metrics.SchemaMetrics: Inconsistent configuration.
Previous configuration for using table name in metrics: true, new
configuration: false
13/09/24 12:33:41 WARN snappy.LoadSnappy: Snappy native library is available
13/09/24 12:33:41 INFO util.NativeCodeLoader: Loaded the native-hadoop
library
13/09/24 12:33:41 INFO snappy.LoadSnappy: Snappy native library loaded
13/09/24 12:33:41 INFO compress.CodecPool: Got brand-new decompressor
Block index size as per heapsize: 336
Exception in thread "main" java.lang.NullPointerException
        at org.apache.hadoop.hbase.KeyValue.keyToString(KeyValue.java:716)
        at
org.apache.hadoop.hbase.io.hfile.AbstractHFileReader.toStringFirstKey(AbstractHFileReader.java:138)
        at
org.apache.hadoop.hbase.io.hfile.AbstractHFileReader.toString(AbstractHFileReader.java:149)
        at
org.apache.hadoop.hbase.io.hfile.HFilePrettyPrinter.printMeta(HFilePrettyPrinter.java:318)
        at
org.apache.hadoop.hbase.io.hfile.HFilePrettyPrinter.processFile(HFilePrettyPrinter.java:234)
        at
org.apache.hadoop.hbase.io.hfile.HFilePrettyPrinter.run(HFilePrettyPrinter.java:189)
        at org.apache.hadoop.hbase.io.hfile.HFile.main(HFile.java:756)


Does this mean the problem might have been caused by a corrupted file(s)?

--Tom


On Tue, Sep 24, 2013 at 12:21 PM, Jean-Marc Spaggiari <
jean-marc@spaggiari.org> wrote:

> One more Tom,
>
> When you will have been able capture de HFile locally, please run run the
> HFile class on it to see the number of keys (is it empty?) and the other
> specific information.
>
> bin/hbase org.apache.hadoop.hbase.io.hfile.HFile -m -s -v -f HFILENAME
>
> Thanks,
>
> JM
>
>
> 2013/9/24 Jean-Marc Spaggiari <jean-marc@spaggiari.org>
>
> > We get -1 because of this:
> >
> >       byte [] timerangeBytes = metadataMap.get(TIMERANGE_KEY);
> >       if (timerangeBytes != null) {
> >         this.reader.timeRangeTracker = new TimeRangeTracker();
> >         Writables.copyWritable(timerangeBytes,
> > this.reader.timeRangeTracker);
> >       }
> > this.reader.timeRangeTracker will return -1 for the maximumTimestamp
> > value. So now, we need to figure if it's normal or not to have
> > TIMERANGE_KEY not null here.
> >
> > I have created the same table locally on 0,94.10 with the same attributes
> > and I'm not facing this issue.
> >
> > We need to look at the related HFile, but files are rolled VERY quickly,
> > so might be difficult to get one.
> >
> > Maybe something like
> > hadoop fs -get hdfs://
> >
> hdpmgr001.pse.movenetworks.com:8020/hbase/compound3/5ab5fdfcf2aff2633e1d6d5089c96aa2/d/*
> > .
> >
> > might help to get the file? Then we can start to look at it and see what
> > exactly trigger this behaviour?
> >
> > JM
> >
> >
> > 2013/9/24 Sergey Shelukhin <sergey@hortonworks.com>
> >
> >> Yeah, I think c3580bdb62d64e42a9eeac50f1c582d2 store file is a good
> >> example.
> >> Can you grep for c3580bdb62d64e42a9eeac50f1c582d2 and post the log just
> to
> >> be sure? Thanks.
> >> It looks like an interaction of deleting expired files and
> >>           // Create the writer even if no kv(Empty store file is also
> ok),
> >>           // because we need record the max seq id for the store file,
> see
> >>           // HBASE-6059
> >> in compactor.
> >> The newly created file is immediately collected the same way and
> replaced
> >> by another file, which seems like not an intended behavior, even though
> >> both pieces of code are technically correct (the empty file is expired,
> >> and
> >> the new file is generally needed).
> >>
> >> I filed HBASE-9648
> >>
> >>
> >> On Tue, Sep 24, 2013 at 10:55 AM, Sergey Shelukhin
> >> <sergey@hortonworks.com>wrote:
> >>
> >> > To mitigate, you can change hbase.store.delete.expired.storefile to
> >> false
> >> > on one region server, or for entire table, and restart this RS.
> >> > This will trigger a different compaction, hopefully.
> >> > We'd need to find what the bug is. My gut feeling (which is known to
> be
> >> > wrong often) is that it has to do with it selecting one file, probably
> >> > invalid check somewhere, or interaction with the code that ensures
> that
> >> at
> >> > least one file needs to be written to preserve metadata, it might be
> >> just
> >> > cycling thru such files.
> >> >
> >> >
> >> > On Tue, Sep 24, 2013 at 10:20 AM, Jean-Marc Spaggiari <
> >> > jean-marc@spaggiari.org> wrote:
> >> >
> >> >> So. Looking at the code, this, for me, sound like a bug.
> >> >>
> >> >> I will try to reproduce it locally. Seems to be related to the
> >> combination
> >> >> of TTL + BLOOM.
> >> >>
> >> >> Creating a table for that right now, will keep you posted very
> shortly.
> >> >>
> >> >> JM
> >> >>
> >> >>
> >> >> 2013/9/24 Tom Brown <tombrown52@gmail.com>
> >> >>
> >> >> > -rw-------   1 hadoop supergroup       2194 2013-09-21 14:32
> >> >> >
> >> >> >
> >> >>
> >>
> /hbase/compound3/5ab5fdfcf2aff2633e1d6d5089c96aa2/d/014ead47a9484d67b55205be16802ff1
> >> >> > -rw-------   1 hadoop supergroup      31321 2013-09-24 05:49
> >> >> >
> >> >> >
> >> >>
> >>
> /hbase/compound3/5ab5fdfcf2aff2633e1d6d5089c96aa2/d/1305d625bd4a4be39a98ae4d91a66140
> >> >> > -rw-------   1 hadoop supergroup       1350 2013-09-24 10:31
> >> >> >
> >> >> >
> >> >>
> >>
> /hbase/compound3/5ab5fdfcf2aff2633e1d6d5089c96aa2/d/1352e0828f974f08b1f3d7a9dff04abd
> >> >> > -rw-------   1 hadoop supergroup       4194 2013-09-21 10:38
> >> >> >
> >> >> >
> >> >>
> >>
> /hbase/compound3/5ab5fdfcf2aff2633e1d6d5089c96aa2/d/17a546064bd840619816809ae0fc4c49
> >> >> > -rw-------   1 hadoop supergroup       1061 2013-09-20 22:55
> >> >> >
> >> >> >
> >> >>
> >>
> /hbase/compound3/5ab5fdfcf2aff2633e1d6d5089c96aa2/d/1cb3df115da244288bd076968ab4ccf6
> >> >> > -rw-------   1 hadoop supergroup       1375 2013-08-24 10:17
> >> >> >
> >> >> >
> >> >>
> >>
> /hbase/compound3/5ab5fdfcf2aff2633e1d6d5089c96aa2/d/1e41a96c49fc4e5ab59392d26935978d
> >> >> > -rw-------   1 hadoop supergroup      96296 2013-08-26 15:48
> >> >> >
> >> >> >
> >> >>
> >>
> /hbase/compound3/5ab5fdfcf2aff2633e1d6d5089c96aa2/d/22d72fd897e34424b5420a96483a571e
> >> >> > -rw-------   1 hadoop supergroup       1356 2013-08-26 15:23
> >> >> >
> >> >> >
> >> >>
> >>
> /hbase/compound3/5ab5fdfcf2aff2633e1d6d5089c96aa2/d/25fee1ffadbe42549bd0b7b13d782b72
> >> >> > -rw-------   1 hadoop supergroup       6229 2013-09-21 11:14
> >> >> >
> >> >> >
> >> >>
> >>
> /hbase/compound3/5ab5fdfcf2aff2633e1d6d5089c96aa2/d/26289c777ec14dc5b7021b4d6b1050c5
> >> >> > -rw-------   1 hadoop supergroup       1223 2013-09-21 02:42
> >> >> >
> >> >> >
> >> >>
> >>
> /hbase/compound3/5ab5fdfcf2aff2633e1d6d5089c96aa2/d/2757d7ba9c8448d6a3d5d46bd4d59758
> >> >> > -rw-------   1 hadoop supergroup    5302248 2013-08-24 02:22
> >> >> >
> >> >> >
> >> >>
> >>
> /hbase/compound3/5ab5fdfcf2aff2633e1d6d5089c96aa2/d/2ec40943787246ea983608dd6591db24
> >> >> > -rw-------   1 hadoop supergroup       1596 2013-08-24 03:37
> >> >> >
> >> >> >
> >> >>
> >>
> /hbase/compound3/5ab5fdfcf2aff2633e1d6d5089c96aa2/d/3157fd1cabe4483aaa4d9a21f75e4d88
> >> >> > -rw-------   1 hadoop supergroup       1338 2013-09-22 04:25
> >> >> >
> >> >> >
> >> >>
> >>
> /hbase/compound3/5ab5fdfcf2aff2633e1d6d5089c96aa2/d/36b0f80a4a7b492f97358b64d879a2df
> >> >> > -rw-------   1 hadoop supergroup       3264 2013-09-21 12:05
> >> >> >
> >> >> >
> >> >>
> >>
> /hbase/compound3/5ab5fdfcf2aff2633e1d6d5089c96aa2/d/39e249fcb532400daed73aed6689ceeb
> >> >> > -rw-------   1 hadoop supergroup       4549 2013-09-21 08:56
> >> >> >
> >> >> >
> >> >>
> >>
> /hbase/compound3/5ab5fdfcf2aff2633e1d6d5089c96aa2/d/3bc9e2a566ad460a9b0ed336b2fb5ed9
> >> >> > -rw-------   1 hadoop supergroup       1630 2013-09-22 03:22
> >> >> >
> >> >> >
> >> >>
> >>
> /hbase/compound3/5ab5fdfcf2aff2633e1d6d5089c96aa2/d/48026d08aae748f08aad59e4eea903be
> >> >> > -rw-------   1 hadoop supergroup     105395 2013-09-20 21:12
> >> >> >
> >> >> >
> >> >>
> >>
> /hbase/compound3/5ab5fdfcf2aff2633e1d6d5089c96aa2/d/53198825f085401cbbd4322faa0e3aae
> >> >> > -rw-------   1 hadoop supergroup       3859 2013-09-21 09:09
> >> >> >
> >> >> >
> >> >>
> >>
> /hbase/compound3/5ab5fdfcf2aff2633e1d6d5089c96aa2/d/71c2f9b2a8ff4c049fcc5a9a22af5cfe
> >> >> > -rw-------   1 hadoop supergroup     311688 2013-09-20 21:12
> >> >> >
> >> >> >
> >> >>
> >>
> /hbase/compound3/5ab5fdfcf2aff2633e1d6d5089c96aa2/d/97ff16d6da974c30835c6e0acc7c737a
> >> >> > -rw-------   1 hadoop supergroup       1897 2013-08-24 08:43
> >> >> >
> >> >> >
> >> >>
> >>
> /hbase/compound3/5ab5fdfcf2aff2633e1d6d5089c96aa2/d/a172d7577641434d82abcce88a433213
> >> >> > -rw-------   1 hadoop supergroup       3380 2013-09-21 13:04
> >> >> >
> >> >> >
> >> >>
> >>
> /hbase/compound3/5ab5fdfcf2aff2633e1d6d5089c96aa2/d/be678e5c60534c65a012a798fbc7e284
> >> >> > -rw-------   1 hadoop supergroup      43710 2013-09-22 02:15
> >> >> >
> >> >> >
> >> >>
> >>
> /hbase/compound3/5ab5fdfcf2aff2633e1d6d5089c96aa2/d/e2508a23acf1491f9d38b9a8594e41e8
> >> >> > -rw-------   1 hadoop supergroup       5409 2013-09-21 10:10
> >> >> >
> >> >> >
> >> >>
> >>
> /hbase/compound3/5ab5fdfcf2aff2633e1d6d5089c96aa2/d/f432846182714b93a1c3df0f5835c09b
> >> >> > -rw-------   1 hadoop supergroup        491 2013-09-24 11:18
> >> >> >
> >> >> >
> >> >>
> >>
> /hbase/compound3/5ab5fdfcf2aff2633e1d6d5089c96aa2/d/f7d8669cf7a047b98c1d3b13c16cfaec
> >> >> > -rw-------   1 hadoop supergroup        491 2013-09-24 11:18
> >> >> >
> >> >> >
> >> >>
> >>
> /hbase/compound3/5ab5fdfcf2aff2633e1d6d5089c96aa2/d/fa1b8f6cc9584eb28365dcd8f10d3f0a
> >> >> > -rw-------   1 hadoop supergroup        491 2013-09-13 11:28
> >> >> >
> >> >> >
> >> >>
> >>
> /hbase/compound3/5ab5fdfcf2aff2633e1d6d5089c96aa2/d/fca0882dc7624342a8f4fce4b89420ff
> >> >> >
> >> >> >
> >> >> >
> >> >> > On Tue, Sep 24, 2013 at 11:14 AM, Jean-Marc Spaggiari <
> >> >> > jean-marc@spaggiari.org> wrote:
> >> >> >
> >> >> > > TTL seems to be fine.
> >> >> > >
> >> >> > > -1 is the default value for TimeRangeTracker.maximumTimestamp.
> >> >> > >
> >> >> > > Can you run:
> >> >> > > hadoop fs -lsr hdfs://
> >> >> > >
> >> >> > >
> >> >> >
> >> >>
> >>
> hdpmgr001.pse.movenetworks.com:8020/hbase/compound3/5ab5fdfcf2aff2633e1d6d5089c96aa2/d/
> >> >> > >
> >> >> > > Thanks,
> >> >> > >
> >> >> > > JM
> >> >> > >
> >> >> > >
> >> >> > > 2013/9/24 Tom Brown <tombrown52@gmail.com>
> >> >> > >
> >> >> > > > 1. Hadoop version is 1.1.2.
> >> >> > > > 2. All servers are synched with NTP.
> >> >> > > > 3. Table definition is: 'compound0', {
> >> >> > > > NAME => 'd',
> >> >> > > > DATA_BLOCK_ENCODING => 'NONE',
> >> >> > > > BLOOMFILTER => 'ROW',
> >> >> > > > REPLICATION_SCOPE => '0',
> >> >> > > > VERSIONS => '1',
> >> >> > > > COMPRESSION => 'SNAPPY',
> >> >> > > > MIN_VERSIONS => '0',
> >> >> > > > TTL => '8640000',
> >> >> > > > KEEP_DELETED_CELLS => 'false',
> >> >> > > > BLOCKSIZE => '65536',
> >> >> > > > IN_MEMORY => 'false',
> >> >> > > > ENCODE_ON_DISK => 'true',
> >> >> > > > BLOCKCACHE => 'true'
> >> >> > > > }
> >> >> > > >
> >> >> > > > The TTL is supposed to be 100 days.
> >> >> > > >
> >> >> > > > --Tom
> >> >> > > >
> >> >> > > >
> >> >> > > > On Tue, Sep 24, 2013 at 10:53 AM, Jean-Marc Spaggiari
<
> >> >> > > > jean-marc@spaggiari.org> wrote:
> >> >> > > >
> >> >> > > > > Another important information why might be the
root cause of
> >> this
> >> >> > > > issue...
> >> >> > > > >
> >> >> > > > > Do you have any TTL defines for this table?
> >> >> > > > >
> >> >> > > > > JM
> >> >> > > > >
> >> >> > > > >
> >> >> > > > > 2013/9/24 Jean-Marc Spaggiari <jean-marc@spaggiari.org>
> >> >> > > > >
> >> >> > > > > > Strange.
> >> >> > > > > >
> >> >> > > > > > Few questions then.
> >> >> > > > > > 1) What is your hadoop version?
> >> >> > > > > > 2) Is the clock on all your severs synched
with NTP?
> >> >> > > > > > 3) What is you table definition? Bloom filters,
etc.?
> >> >> > > > > >
> >> >> > > > > > This is the reason why it keep compacting:
> >> >> > > > > >
> >> >> > > > > > 2013-09-24 10:04:00,548 INFO
> >> >> > > > >
> >> org.apache.hadoop.hbase.regionserver.compactions.CompactSelection:
> >> >> > > > Deleting
> >> >> > > > > the expired store file by compaction: hdfs://
> >> >> > > > >
> >> >> > > >
> >> >> > >
> >> >> >
> >> >>
> >>
> hdpmgr001.pse.movenetworks.com:8020/hbase/compound3/5ab5fdfcf2aff2633e1d6d5089c96aa2/d/7426f128469242ec8ee09f3965fd5a1awhosemaxTimeStampis-1whilethemax
expired timestamp is 1371398640548
> >> >> > > > > >
> >> >> > > > > > maxTimeStamp = -1
> >> >> > > > > >
> >> >> > > > > >
> >> >> > > > > > Each time there is a comparison between maxTimeStamp
for
> this
> >> >> store
> >> >> > > > file
> >> >> > > > > > and the configured maxExpiredTimeStamp and
since
> maxTimeStamp
> >> >> > returns
> >> >> > > > -1,
> >> >> > > > > > it's always elected for a compaction. Now,
we need to find
> >> >> why...
> >> >> > > > > >
> >> >> > > > > > JM
> >> >> > > > > >
> >> >> > > > > >
> >> >> > > > > > 2013/9/24 Tom Brown <tombrown52@gmail.com>
> >> >> > > > > >
> >> >> > > > > >> My cluster is fully distributed (2 regionserver
nodes).
> >> >> > > > > >>
> >> >> > > > > >> Here is a snippet of log entries that
may explain why it
> >> >> started:
> >> >> > > > > >> http://pastebin.com/wQECif8k. I had to
go back 2 days to
> >> find
> >> >> > when
> >> >> > > it
> >> >> > > > > >> started for this region.
> >> >> > > > > >>
> >> >> > > > > >> This is not the only region experiencing
this issue (but
> >> this
> >> >> is
> >> >> > the
> >> >> > > > > >> smallest one it's happened to).
> >> >> > > > > >>
> >> >> > > > > >> --Tom
> >> >> > > > > >>
> >> >> > > > > >>
> >> >> > > > > >> On Tue, Sep 24, 2013 at 10:13 AM, Jean-Marc
Spaggiari <
> >> >> > > > > >> jean-marc@spaggiari.org> wrote:
> >> >> > > > > >>
> >> >> > > > > >> > Can you past logs a bit before that?
To see if anything
> >> >> > triggered
> >> >> > > > the
> >> >> > > > > >> > compaction?
> >> >> > > > > >> > Before the 1M compactions entries.
> >> >> > > > > >> >
> >> >> > > > > >> > Also, what is your setup? Are you
running in Standalone?
> >> >> > > > Pseudo-Dist?
> >> >> > > > > >> > Fully-Dist?
> >> >> > > > > >> >
> >> >> > > > > >> > Thanks,
> >> >> > > > > >> >
> >> >> > > > > >> > JM
> >> >> > > > > >> >
> >> >> > > > > >> >
> >> >> > > > > >> > 2013/9/24 Tom Brown <tombrown52@gmail.com>
> >> >> > > > > >> >
> >> >> > > > > >> > > There is one column family,
d. Each row has about 10
> >> >> columns,
> >> >> > > and
> >> >> > > > > each
> >> >> > > > > >> > > row's total data size is less
than 2K.
> >> >> > > > > >> > >
> >> >> > > > > >> > > Here is a small snippet of logs
from the region
> server:
> >> >> > > > > >> > > http://pastebin.com/S2jE4ZAx
> >> >> > > > > >> > >
> >> >> > > > > >> > > --Tom
> >> >> > > > > >> > >
> >> >> > > > > >> > >
> >> >> > > > > >> > > On Tue, Sep 24, 2013 at 9:59
AM, Bharath Vissapragada
> <
> >> >> > > > > >> > > bharathv@cloudera.com
> >> >> > > > > >> > > > wrote:
> >> >> > > > > >> > >
> >> >> > > > > >> > > > It would help if you can
show your RS log (via
> >> >> pastebin?) .
> >> >> > > Are
> >> >> > > > > >> there
> >> >> > > > > >> > > > frequent flushes for this
region too?
> >> >> > > > > >> > > >
> >> >> > > > > >> > > >
> >> >> > > > > >> > > > On Tue, Sep 24, 2013 at
9:20 PM, Tom Brown <
> >> >> > > > tombrown52@gmail.com>
> >> >> > > > > >> > wrote:
> >> >> > > > > >> > > >
> >> >> > > > > >> > > > > I have a region that
is very small, only 5MB.
> >> Despite
> >> >> it's
> >> >> > > > size,
> >> >> > > > > >> it
> >> >> > > > > >> > has
> >> >> > > > > >> > > > 24
> >> >> > > > > >> > > > > store files. The logs
show that it's compacting
> >> (over
> >> >> and
> >> >> > > over
> >> >> > > > > >> > again).
> >> >> > > > > >> > > > >
> >> >> > > > > >> > > > > The odd thing is that
even though there are 24
> store
> >> >> > files,
> >> >> > > it
> >> >> > > > > >> only
> >> >> > > > > >> > > does
> >> >> > > > > >> > > > > one at a time. Even
more strange is that my logs
> are
> >> >> > filling
> >> >> > > > up
> >> >> > > > > >> with
> >> >> > > > > >> > > > > compacting this one
region. In the last 10 hours,
> >> there
> >> >> > have
> >> >> > > > > been
> >> >> > > > > >> > > > 1,876,200
> >> >> > > > > >> > > > > log entries corresponding
to compacting this
> region
> >> >> alone.
> >> >> > > > > >> > > > >
> >> >> > > > > >> > > > > My cluster is 0.94.10,
and using almost all
> default
> >> >> > > settings.
> >> >> > > > > >> Only a
> >> >> > > > > >> > > few
> >> >> > > > > >> > > > > are not default:
> >> >> > > > > >> > > > > hbase.hregion.max.filesize
= 4294967296
> >> >> > > > > >> > > > > hbase.hstore.compaction.min
= 6
> >> >> > > > > >> > > > >
> >> >> > > > > >> > > > > I am at a total loss
as to why this behavior is
> >> >> occurring.
> >> >> > > Any
> >> >> > > > > >> help
> >> >> > > > > >> > is
> >> >> > > > > >> > > > > appreciated.
> >> >> > > > > >> > > > >
> >> >> > > > > >> > > > > --Tom
> >> >> > > > > >> > > > >
> >> >> > > > > >> > > >
> >> >> > > > > >> > > >
> >> >> > > > > >> > > >
> >> >> > > > > >> > > > --
> >> >> > > > > >> > > > Bharath Vissapragada
> >> >> > > > > >> > > > <http://www.cloudera.com>
> >> >> > > > > >> > > >
> >> >> > > > > >> > >
> >> >> > > > > >> >
> >> >> > > > > >>
> >> >> > > > > >
> >> >> > > > > >
> >> >> > > > >
> >> >> > > >
> >> >> > >
> >> >> >
> >> >>
> >> >
> >> >
> >>
> >> --
> >> CONFIDENTIALITY NOTICE
> >> NOTICE: This message is intended for the use of the individual or entity
> >> to
> >> which it is addressed and may contain information that is confidential,
> >> privileged and exempt from disclosure under applicable law. If the
> reader
> >> of this message is not the intended recipient, you are hereby notified
> >> that
> >> any printing, copying, dissemination, distribution, disclosure or
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