The compaction code removes tombstones, and it runs whenever you have enough sstable fragments.
I think I know what is happening -- as an optimization, if there is only one version of a row it will just copy it to the new sstable. This means it won't clean out tombstones. Can you file a bug at https://issues.apache.org/jira/browse/CASSANDRA ? -Jonathan On Wed, Oct 21, 2009 at 2:01 PM, Ramzi Rabah <[email protected]> wrote: > Hi Jonathan I am still running into the timeout issue even after > reducing the GCGraceSeconds to 1 hour (we have tons of deletes > happening in our app). Which part of Cassandra > is responsible for deleting the tombstone records and how often does it run. > > > On Tue, Oct 20, 2009 at 12:02 PM, Ramzi Rabah <[email protected]> wrote: >> Thank you so much Jonathan. >> >> Data is test data so I'll just wipe it out and restart after updating >> GCGraceSeconds. >> Thanks for your help. >> >> Ray >> >> On Tue, Oct 20, 2009 at 11:39 AM, Jonathan Ellis <[email protected]> wrote: >>> The problem is you have a few MB of actual data and a few hundred MB >>> of tombstones (data marked deleted). So what happens is get_key_range >>> spends a long, long time iterating through the tombstoned rows, >>> looking for keys that actually still exist. >>> >>> We're going to redesign this for CASSANDRA-344, but for the 0.4 >>> series, you should restart with GCGraceSeconds much lower (e.g. 3600), >>> delete your old data files, and reload your data fresh. (Instead of >>> reloading, you can use "nodeprobe compact" on each node to force a >>> major compaction but it will take much longer since you have so many >>> tombstones). >>> >>> -Jonathan >>> >>> On Mon, Oct 19, 2009 at 10:45 PM, Ramzi Rabah <[email protected]> wrote: >>>> Hi Jonathan: >>>> >>>> Here is the storage_conf.xml for one of the servers >>>> http://email.slicezero.com/storage-conf.xml >>>> >>>> and here is the zipped data: >>>> http://email.slicezero.com/datastoreDeletion.tgz >>>> >>>> Thanks >>>> Ray >>>> >>>> >>>> >>>> >>>> On Mon, Oct 19, 2009 at 8:30 PM, Jonathan Ellis <[email protected]> wrote: >>>>> Yes, please. You'll probably have to use something like >>>>> http://www.getdropbox.com/ if you don't have a public web server to >>>>> stash it temporarily. >>>>> >>>>> On Mon, Oct 19, 2009 at 10:28 PM, Ramzi Rabah <[email protected]> wrote: >>>>>> Hi Jonathan the data is about 60 MB. Would you like me to send it to you? >>>>>> >>>>>> >>>>>> On Mon, Oct 19, 2009 at 8:20 PM, Jonathan Ellis <[email protected]> >>>>>> wrote: >>>>>>> Is the data on 6, 9, or 10 small enough that you could tar.gz it up >>>>>>> for me to use to reproduce over here? >>>>>>> >>>>>>> On Mon, Oct 19, 2009 at 10:17 PM, Ramzi Rabah <[email protected]> >>>>>>> wrote: >>>>>>>> So my cluster has 4 nodes node6, node8, node9 and node10. I turned >>>>>>>> them all off. >>>>>>>> 1- I started node6 by itself and still got the problem. >>>>>>>> 2- I started node8 by itself and it ran fine (returned no keys) >>>>>>>> 3- I started node9 by itself and still got the problem. >>>>>>>> 4- I started node10 by itself and still got the problem. >>>>>>>> >>>>>>>> Ray >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Mon, Oct 19, 2009 at 7:44 PM, Jonathan Ellis <[email protected]> >>>>>>>> wrote: >>>>>>>>> That's really strange... Can you reproduce on a single-node cluster? >>>>>>>>> >>>>>>>>> On Mon, Oct 19, 2009 at 9:34 PM, Ramzi Rabah <[email protected]> >>>>>>>>> wrote: >>>>>>>>>> The rows are very small. There are a handful of columns per row >>>>>>>>>> (approximately about 4-5 columns per row). >>>>>>>>>> Each column has a name which is a String (20-30 characters long), and >>>>>>>>>> the value is an empty array of bytes (new byte[0]). >>>>>>>>>> I just use the names of the columns, and don't need to store any >>>>>>>>>> values in this Column Family. >>>>>>>>>> >>>>>>>>>> -- Ray >>>>>>>>>> >>>>>>>>>> On Mon, Oct 19, 2009 at 7:24 PM, Jonathan Ellis <[email protected]> >>>>>>>>>> wrote: >>>>>>>>>>> Can you tell me anything about the nature of your rows? Many/few >>>>>>>>>>> columns? Large/small column values? >>>>>>>>>>> >>>>>>>>>>> On Mon, Oct 19, 2009 at 9:17 PM, Ramzi Rabah <[email protected]> >>>>>>>>>>> wrote: >>>>>>>>>>>> Hi Jonathan >>>>>>>>>>>> I actually spoke too early. Now even if I restart the servers it >>>>>>>>>>>> still >>>>>>>>>>>> gives a timeout exception. >>>>>>>>>>>> As far as the sstable files are, not sure which ones are the >>>>>>>>>>>> sstables, >>>>>>>>>>>> but here is the list of files in the data directory that are >>>>>>>>>>>> prepended >>>>>>>>>>>> with the column family name: >>>>>>>>>>>> DatastoreDeletionSchedule-1-Data.db >>>>>>>>>>>> DatastoreDeletionSchedule-1-Filter.db >>>>>>>>>>>> DatastoreDeletionSchedule-1-Index.db >>>>>>>>>>>> DatastoreDeletionSchedule-5-Data.db >>>>>>>>>>>> DatastoreDeletionSchedule-5-Filter.db >>>>>>>>>>>> DatastoreDeletionSchedule-5-Index.db >>>>>>>>>>>> DatastoreDeletionSchedule-7-Data.db >>>>>>>>>>>> DatastoreDeletionSchedule-7-Filter.db >>>>>>>>>>>> DatastoreDeletionSchedule-7-Index.db >>>>>>>>>>>> DatastoreDeletionSchedule-8-Data.db >>>>>>>>>>>> DatastoreDeletionSchedule-8-Filter.db >>>>>>>>>>>> DatastoreDeletionSchedule-8-Index.db >>>>>>>>>>>> >>>>>>>>>>>> I am not currently doing any system stat collection. >>>>>>>>>>>> >>>>>>>>>>>> On Mon, Oct 19, 2009 at 6:41 PM, Jonathan Ellis >>>>>>>>>>>> <[email protected]> wrote: >>>>>>>>>>>>> How many sstable files are in the data directories for the >>>>>>>>>>>>> columnfamily you are querying? >>>>>>>>>>>>> >>>>>>>>>>>>> How many are there after you restart and it is happy? >>>>>>>>>>>>> >>>>>>>>>>>>> Are you doing system stat collection with munin or ganglia or >>>>>>>>>>>>> some such? >>>>>>>>>>>>> >>>>>>>>>>>>> On Mon, Oct 19, 2009 at 8:25 PM, Ramzi Rabah <[email protected]> >>>>>>>>>>>>> wrote: >>>>>>>>>>>>>> Hi Jonathan I updated to 4.1 and I still get the same exception >>>>>>>>>>>>>> when I >>>>>>>>>>>>>> call get_key_range. >>>>>>>>>>>>>> I checked all the server logs, and there is only one exception >>>>>>>>>>>>>> being >>>>>>>>>>>>>> thrown by whichever server I am connecting to. >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>> Ray >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Mon, Oct 19, 2009 at 4:52 PM, Jonathan Ellis >>>>>>>>>>>>>> <[email protected]> wrote: >>>>>>>>>>>>>>> No, it's smart enough to avoid scanning. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Mon, Oct 19, 2009 at 6:49 PM, Ramzi Rabah >>>>>>>>>>>>>>> <[email protected]> wrote: >>>>>>>>>>>>>>>> Hi Jonathan thanks for the reply, I will update the code to >>>>>>>>>>>>>>>> 0.4.1 and >>>>>>>>>>>>>>>> will check all the logs on all the machines. >>>>>>>>>>>>>>>> Just a simple question, when you do a get_key_range and you >>>>>>>>>>>>>>>> specify "" >>>>>>>>>>>>>>>> and "" for start and end, and the limit is 25, if there are >>>>>>>>>>>>>>>> too many >>>>>>>>>>>>>>>> entries, does it do a scan to find out the start or is it >>>>>>>>>>>>>>>> smart enough >>>>>>>>>>>>>>>> to know what the start key is? >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On Mon, Oct 19, 2009 at 4:42 PM, Jonathan Ellis >>>>>>>>>>>>>>>> <[email protected]> wrote: >>>>>>>>>>>>>>>>> You should check the other nodes for potential exceptions >>>>>>>>>>>>>>>>> keeping them >>>>>>>>>>>>>>>>> from replying. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Without seeing that it's hard to say if this is caused by an >>>>>>>>>>>>>>>>> old bug, >>>>>>>>>>>>>>>>> but you should definitely upgrade to 0.4.1 either way :) >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> On Mon, Oct 19, 2009 at 5:51 PM, Ramzi Rabah >>>>>>>>>>>>>>>>> <[email protected]> wrote: >>>>>>>>>>>>>>>>>> Hello all, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> I am running into problems with get_key_range. I have >>>>>>>>>>>>>>>>>> OrderPreservingPartitioner defined in storage-conf.xml and I >>>>>>>>>>>>>>>>>> am using >>>>>>>>>>>>>>>>>> a columnfamily that looks like >>>>>>>>>>>>>>>>>> <ColumnFamily CompareWith="BytesType" >>>>>>>>>>>>>>>>>> Name="DatastoreDeletionSchedule" >>>>>>>>>>>>>>>>>> /> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> My command is client.get_key_range("Keyspace1", >>>>>>>>>>>>>>>>>> "DatastoreDeletionSchedule", >>>>>>>>>>>>>>>>>> "", "", 25, ConsistencyLevel.ONE); >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> It usually works fine but after a day or so from server >>>>>>>>>>>>>>>>>> writes into >>>>>>>>>>>>>>>>>> this column family, I started getting >>>>>>>>>>>>>>>>>> ERROR [pool-1-thread-36] 2009-10-19 17:24:28,223 >>>>>>>>>>>>>>>>>> Cassandra.java (line >>>>>>>>>>>>>>>>>> 770) Internal error processing get_key_range >>>>>>>>>>>>>>>>>> java.lang.RuntimeException: >>>>>>>>>>>>>>>>>> java.util.concurrent.TimeoutException: >>>>>>>>>>>>>>>>>> Operation timed out. >>>>>>>>>>>>>>>>>> at >>>>>>>>>>>>>>>>>> org.apache.cassandra.service.StorageProxy.getKeyRange(StorageProxy.java:560) >>>>>>>>>>>>>>>>>> at >>>>>>>>>>>>>>>>>> org.apache.cassandra.service.CassandraServer.get_key_range(CassandraServer.java:595) >>>>>>>>>>>>>>>>>> at >>>>>>>>>>>>>>>>>> org.apache.cassandra.service.Cassandra$Processor$get_key_range.process(Cassandra.java:766) >>>>>>>>>>>>>>>>>> at >>>>>>>>>>>>>>>>>> org.apache.cassandra.service.Cassandra$Processor.process(Cassandra.java:609) >>>>>>>>>>>>>>>>>> at >>>>>>>>>>>>>>>>>> org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(TThreadPoolServer.java:253) >>>>>>>>>>>>>>>>>> at >>>>>>>>>>>>>>>>>> java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:885) >>>>>>>>>>>>>>>>>> at >>>>>>>>>>>>>>>>>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:907) >>>>>>>>>>>>>>>>>> at java.lang.Thread.run(Thread.java:619) >>>>>>>>>>>>>>>>>> Caused by: java.util.concurrent.TimeoutException: Operation >>>>>>>>>>>>>>>>>> timed out. >>>>>>>>>>>>>>>>>> at >>>>>>>>>>>>>>>>>> org.apache.cassandra.net.AsyncResult.get(AsyncResult.java:97) >>>>>>>>>>>>>>>>>> at >>>>>>>>>>>>>>>>>> org.apache.cassandra.service.StorageProxy.getKeyRange(StorageProxy.java:556) >>>>>>>>>>>>>>>>>> ... 7 more >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> I still get the timeout exceptions even though the servers >>>>>>>>>>>>>>>>>> have been >>>>>>>>>>>>>>>>>> idle for 2 days. When I restart the cassandra servers, it >>>>>>>>>>>>>>>>>> seems to >>>>>>>>>>>>>>>>>> work fine again. Any ideas what could be wrong? >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> By the way, I am using >>>>>>>>>>>>>>>>>> version:apache-cassandra-incubating-0.4.0-rc2 >>>>>>>>>>>>>>>>>> Not sure if this is fixed in the 0.4.1 version >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>> Ray >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> >
