Re: clearing tombstones?
I tried to do this, however the doubling in disk space is not temporary as you state in your note. What am I missing? On Fri, Apr 11, 2014 at 10:44 AM, William Oberman ober...@civicscience.comwrote: So, if I was impatient and just wanted to make this happen now, I could: 1.) Change GCGraceSeconds of the CF to 0 2.) run nodetool compact (*) 3.) Change GCGraceSeconds of the CF back to 10 days Since I have ~900M tombstones, even if I miss a few due to impatience, I don't care *that* much as I could re-run my clean up tool against the now much smaller CF. (*) A long long time ago I seem to recall reading advice about don't ever run nodetool compact, but I can't remember why. Is there any bad long term consequence? Short term there are several: -a heavy operation -temporary 2x disk space -one big SSTable afterwards But moving forward, everything is ok right? CommitLog/MemTable-SStables, minor compactions that merge SSTables, etc... The only flaw I can think of is it will take forever until the SSTable minor compactions build up enough to consider including the big SSTable in a compaction, making it likely I'll have to self manage compactions. On Fri, Apr 11, 2014 at 10:31 AM, Mark Reddy mark.re...@boxever.comwrote: Correct, a tombstone will only be removed after gc_grace period has elapsed. The default value is set to 10 days which allows a great deal of time for consistency to be achieved prior to deletion. If you are operationally confident that you can achieve consistency via anti-entropy repairs within a shorter period you can always reduce that 10 day interval. Mark On Fri, Apr 11, 2014 at 3:16 PM, William Oberman ober...@civicscience.com wrote: I'm seeing a lot of articles about a dependency between removing tombstones and GCGraceSeconds, which might be my problem (I just checked, and this CF has GCGraceSeconds of 10 days). On Fri, Apr 11, 2014 at 10:10 AM, tommaso barbugli tbarbu...@gmail.comwrote: compaction should take care of it; for me it never worked so I run nodetool compaction on every node; that does it. 2014-04-11 16:05 GMT+02:00 William Oberman ober...@civicscience.com: I'm wondering what will clear tombstoned rows? nodetool cleanup, nodetool repair, or time (as in just wait)? I had a CF that was more or less storing session information. After some time, we decided that one piece of this information was pointless to track (and was 90%+ of the columns, and in 99% of those cases was ALL columns for a row). I wrote a process to remove all of those columns (which again in a vast majority of cases had the effect of removing the whole row). This CF had ~1 billion rows, so I expect to be left with ~100m rows. After I did this mass delete, everything was the same size on disk (which I expected, knowing how tombstoning works). It wasn't 100% clear to me what to poke to cause compactions to clear the tombstones. First I tried nodetool cleanup on a candidate node. But, afterwards the disk usage was the same. Then I tried nodetool repair on that same node. But again, disk usage is still the same. The CF has no snapshots. So, am I misunderstanding something? Is there another operation to try? Do I have to just wait? I've only done cleanup/repair on one node. Do I have to run one or the other over all nodes to clear tombstones? Cassandra 1.2.15 if it matters, Thanks! will
Re: clearing tombstones?
Not an expert, just a user of cassandra. For me, before was a cf with a set of files (I forget the official naming system, so I'll make up my own): A0 A1 ... AN During: A0 A1 ... AN B0 Where B0 is the union of Ai. Due to tombstones, mutations, etc. B0 is at most 2x, but also probably close to 2x (unless you are all tombstones, like me). After B0 Since cassandra can clean up Ai. Not sure when this happens. Not sure what state you are in above. Sounds like between during and after. Will On Thursday, May 8, 2014, Ruchir Jha ruchir@gmail.com wrote: I tried to do this, however the doubling in disk space is not temporary as you state in your note. What am I missing? On Fri, Apr 11, 2014 at 10:44 AM, William Oberman ober...@civicscience.comjavascript:_e(%7B%7D,'cvml','ober...@civicscience.com'); wrote: So, if I was impatient and just wanted to make this happen now, I could: 1.) Change GCGraceSeconds of the CF to 0 2.) run nodetool compact (*) 3.) Change GCGraceSeconds of the CF back to 10 days Since I have ~900M tombstones, even if I miss a few due to impatience, I don't care *that* much as I could re-run my clean up tool against the now much smaller CF. (*) A long long time ago I seem to recall reading advice about don't ever run nodetool compact, but I can't remember why. Is there any bad long term consequence? Short term there are several: -a heavy operation -temporary 2x disk space -one big SSTable afterwards But moving forward, everything is ok right? CommitLog/MemTable-SStables, minor compactions that merge SSTables, etc... The only flaw I can think of is it will take forever until the SSTable minor compactions build up enough to consider including the big SSTable in a compaction, making it likely I'll have to self manage compactions. On Fri, Apr 11, 2014 at 10:31 AM, Mark Reddy mark.re...@boxever.comwrote: Correct, a tombstone will only be removed after gc_grace period has elapsed. The default value is set to 10 days which allows a great deal of time for consistency to be achieved prior to deletion. If you are operationally confident that you can achieve consistency via anti-entropy repairs within a shorter period you can always reduce that 10 day interval. Mark On Fri, Apr 11, 2014 at 3:16 PM, William Oberman ober...@civicscience.com wrote: I'm seeing a lot of articles about a dependency between removing tombstones and GCGraceSeconds, which might be my problem (I just checked, and this CF has GCGraceSeconds of 10 days). On Fri, Apr 11, 2014 at 10:10 AM, tommaso barbugli tbarbu...@gmail.comwrote: compaction should take care of it; for me it never worked so I run nodetool compaction on every node; that does it. 2014-04-11 16:05 GMT+02:00 William Oberman ober...@civicscience.com: I'm wondering what will clear tombstoned rows? nodetool cleanup, nodetool repair, or time (as in just wait)? I had a CF that was more or less storing session information. After some time, we decided that one piece of this information was pointless to track (and was 90%+ of the columns, and in 99% of those cases was ALL columns for a row). I wrote a process to remove all of those columns (which again in a vast majority of cases had the effect of removing the whole row). This CF had ~1 billion rows, so I expect to be left with ~100m rows. After I did this mass delete, everything was the same size on disk (which I expected, knowing how tombstoning works). It wasn't 100% clear to me what to poke to cause compactions to clear the tombstones. First I tried nodetool cleanup on a candidate node. But, afterwards the disk usage was the same. Then I tried nodetool repair on that same node. But again, disk usage is still the same. The CF has no snapshots. So, am I misunderstanding something? Is there another operation to try? Do I have to just wait? I've only done cleanup/re -- Will Oberman Civic Science, Inc. 6101 Penn Avenue, Fifth Floor Pittsburgh, PA 15206 (M) 412-480-7835 (E) ober...@civicscience.com
Re: clearing tombstones?
I'm still somewhat in the middle of the process, but it's far enough along to report back. 1.) I changed GCGraceSeconds of the CF to 0 using cassandra-cli 2.) I ran nodetool compact on a single node of the nine (I'll call it 1). It took 5-7 hours, and reduced the CF from ~450 to ~75GG (*). 3.) I ran nodetool compact on nodes 2, 3, while watching write/read latency averages in OpsCenter. I got all of the way to 9 without any ill effect 4.) 2-9 all completed with similar results (*) So, I left one one detail that changed the math (I said above I expected to clear down to at most 50GB). I found a small bug in my delete code mid-last week. Basically, it deleted all of the rows I wanted, but due to a race condition, there was a chance I'd delete rows in the middle of doing new inserts. Luckily, even in this case, it wasn't end of the world, but I stopped the cleanup anyways and added a time check (as all of the rows I wanted to delete were older than 30 days). I *thought* I'd restarted the cleanup threads on a smaller dataset due to all of the deletes, but instead I saw millions millions of empty rows (the tombstones). Thus the start of this clear the tombstones subtask to the original goal, and the reason I didn't see a 90%+ reduction in size. In any case, now I'm running the cleanup process again, which will be followed by ANOTHER round of compactions, and then I'll finally turn GCGraceSeconds back on. On the read/write production side, you'd never know anything happened. Good job on the distributed system! :-) Thanks again, will On Fri, Apr 11, 2014 at 1:02 PM, Mark Reddy mark.re...@boxever.com wrote: Thats great Will, if you could update the thread with the actions you decide to take and the results that would be great. Mark On Fri, Apr 11, 2014 at 5:53 PM, William Oberman ober...@civicscience.com wrote: I've learned a *lot* from this thread. My thanks to all of the contributors! Paulo: Good luck with LCS. I wish I could help there, but all of my CF's are SizeTiered (mostly as I'm on the same schema/same settings since 0.7...) will On Fri, Apr 11, 2014 at 12:14 PM, Mina Naguib mina.nag...@adgear.comwrote: Levelled Compaction is a wholly different beast when it comes to tombstones. The tombstones are inserted, like any other write really, at the lower levels in the leveldb hierarchy. They are only removed after they have had the chance to naturally migrate upwards in the leveldb hierarchy to the highest level in your data store. How long that takes depends on: 1. The amount of data in your store and the number of levels your LCS strategy has 2. The amount of new writes entering the bottom funnel of your leveldb, forcing upwards compaction and combining To give you an idea, I had a similar scenario and ran a (slow, throttled) delete job on my cluster around December-January. Here's a graph of the disk space usage on one node. Notice the still-diclining usage long after the cleanup job has finished (sometime in January). I tend to think of tombstones in LCS as little bombs that get to explode much later in time: http://mina.naguib.ca/images/tombstones-cassandra-LCS.jpg On 2014-04-11, at 11:20 AM, Paulo Ricardo Motta Gomes paulo.mo...@chaordicsystems.com wrote: I have a similar problem here, I deleted about 30% of a very large CF using LCS (about 80GB per node), but still my data hasn't shrinked, even if I used 1 day for gc_grace_seconds. Would nodetool scrub help? Does nodetool scrub forces a minor compaction? Cheers, Paulo On Fri, Apr 11, 2014 at 12:12 PM, Mark Reddy mark.re...@boxever.comwrote: Yes, running nodetool compact (major compaction) creates one large SSTable. This will mess up the heuristics of the SizeTiered strategy (is this the compaction strategy you are using?) leading to multiple 'small' SSTables alongside the single large SSTable, which results in increased read latency. You will incur the operational overhead of having to manage compactions if you wish to compact these smaller SSTables. For all these reasons it is generally advised to stay away from running compactions manually. Assuming that this is a production environment and you want to keep everything running as smoothly as possible I would reduce the gc_grace on the CF, allow automatic minor compactions to kick in and then increase the gc_grace once again after the tombstones have been removed. On Fri, Apr 11, 2014 at 3:44 PM, William Oberman ober...@civicscience.com wrote: So, if I was impatient and just wanted to make this happen now, I could: 1.) Change GCGraceSeconds of the CF to 0 2.) run nodetool compact (*) 3.) Change GCGraceSeconds of the CF back to 10 days Since I have ~900M tombstones, even if I miss a few due to impatience, I don't care *that* much as I could re-run my clean up tool against the now much smaller CF. (*) A long long time ago I seem to recall reading advice about don't ever run
Re: clearing tombstones?
compaction should take care of it; for me it never worked so I run nodetool compaction on every node; that does it. 2014-04-11 16:05 GMT+02:00 William Oberman ober...@civicscience.com: I'm wondering what will clear tombstoned rows? nodetool cleanup, nodetool repair, or time (as in just wait)? I had a CF that was more or less storing session information. After some time, we decided that one piece of this information was pointless to track (and was 90%+ of the columns, and in 99% of those cases was ALL columns for a row). I wrote a process to remove all of those columns (which again in a vast majority of cases had the effect of removing the whole row). This CF had ~1 billion rows, so I expect to be left with ~100m rows. After I did this mass delete, everything was the same size on disk (which I expected, knowing how tombstoning works). It wasn't 100% clear to me what to poke to cause compactions to clear the tombstones. First I tried nodetool cleanup on a candidate node. But, afterwards the disk usage was the same. Then I tried nodetool repair on that same node. But again, disk usage is still the same. The CF has no snapshots. So, am I misunderstanding something? Is there another operation to try? Do I have to just wait? I've only done cleanup/repair on one node. Do I have to run one or the other over all nodes to clear tombstones? Cassandra 1.2.15 if it matters, Thanks! will
Re: clearing tombstones?
I'm seeing a lot of articles about a dependency between removing tombstones and GCGraceSeconds, which might be my problem (I just checked, and this CF has GCGraceSeconds of 10 days). On Fri, Apr 11, 2014 at 10:10 AM, tommaso barbugli tbarbu...@gmail.comwrote: compaction should take care of it; for me it never worked so I run nodetool compaction on every node; that does it. 2014-04-11 16:05 GMT+02:00 William Oberman ober...@civicscience.com: I'm wondering what will clear tombstoned rows? nodetool cleanup, nodetool repair, or time (as in just wait)? I had a CF that was more or less storing session information. After some time, we decided that one piece of this information was pointless to track (and was 90%+ of the columns, and in 99% of those cases was ALL columns for a row). I wrote a process to remove all of those columns (which again in a vast majority of cases had the effect of removing the whole row). This CF had ~1 billion rows, so I expect to be left with ~100m rows. After I did this mass delete, everything was the same size on disk (which I expected, knowing how tombstoning works). It wasn't 100% clear to me what to poke to cause compactions to clear the tombstones. First I tried nodetool cleanup on a candidate node. But, afterwards the disk usage was the same. Then I tried nodetool repair on that same node. But again, disk usage is still the same. The CF has no snapshots. So, am I misunderstanding something? Is there another operation to try? Do I have to just wait? I've only done cleanup/repair on one node. Do I have to run one or the other over all nodes to clear tombstones? Cassandra 1.2.15 if it matters, Thanks! will
Re: clearing tombstones?
Correct, a tombstone will only be removed after gc_grace period has elapsed. The default value is set to 10 days which allows a great deal of time for consistency to be achieved prior to deletion. If you are operationally confident that you can achieve consistency via anti-entropy repairs within a shorter period you can always reduce that 10 day interval. Mark On Fri, Apr 11, 2014 at 3:16 PM, William Oberman ober...@civicscience.comwrote: I'm seeing a lot of articles about a dependency between removing tombstones and GCGraceSeconds, which might be my problem (I just checked, and this CF has GCGraceSeconds of 10 days). On Fri, Apr 11, 2014 at 10:10 AM, tommaso barbugli tbarbu...@gmail.comwrote: compaction should take care of it; for me it never worked so I run nodetool compaction on every node; that does it. 2014-04-11 16:05 GMT+02:00 William Oberman ober...@civicscience.com: I'm wondering what will clear tombstoned rows? nodetool cleanup, nodetool repair, or time (as in just wait)? I had a CF that was more or less storing session information. After some time, we decided that one piece of this information was pointless to track (and was 90%+ of the columns, and in 99% of those cases was ALL columns for a row). I wrote a process to remove all of those columns (which again in a vast majority of cases had the effect of removing the whole row). This CF had ~1 billion rows, so I expect to be left with ~100m rows. After I did this mass delete, everything was the same size on disk (which I expected, knowing how tombstoning works). It wasn't 100% clear to me what to poke to cause compactions to clear the tombstones. First I tried nodetool cleanup on a candidate node. But, afterwards the disk usage was the same. Then I tried nodetool repair on that same node. But again, disk usage is still the same. The CF has no snapshots. So, am I misunderstanding something? Is there another operation to try? Do I have to just wait? I've only done cleanup/repair on one node. Do I have to run one or the other over all nodes to clear tombstones? Cassandra 1.2.15 if it matters, Thanks! will
Re: clearing tombstones?
In my experience even after the gc_grace period tombstones remains stored on disk (at least using cassandra 2.0.5) ; only a full compaction clears them. Perhaps that is because my application never reads tombstones? 2014-04-11 16:31 GMT+02:00 Mark Reddy mark.re...@boxever.com: Correct, a tombstone will only be removed after gc_grace period has elapsed. The default value is set to 10 days which allows a great deal of time for consistency to be achieved prior to deletion. If you are operationally confident that you can achieve consistency via anti-entropy repairs within a shorter period you can always reduce that 10 day interval. Mark On Fri, Apr 11, 2014 at 3:16 PM, William Oberman ober...@civicscience.com wrote: I'm seeing a lot of articles about a dependency between removing tombstones and GCGraceSeconds, which might be my problem (I just checked, and this CF has GCGraceSeconds of 10 days). On Fri, Apr 11, 2014 at 10:10 AM, tommaso barbugli tbarbu...@gmail.comwrote: compaction should take care of it; for me it never worked so I run nodetool compaction on every node; that does it. 2014-04-11 16:05 GMT+02:00 William Oberman ober...@civicscience.com: I'm wondering what will clear tombstoned rows? nodetool cleanup, nodetool repair, or time (as in just wait)? I had a CF that was more or less storing session information. After some time, we decided that one piece of this information was pointless to track (and was 90%+ of the columns, and in 99% of those cases was ALL columns for a row). I wrote a process to remove all of those columns (which again in a vast majority of cases had the effect of removing the whole row). This CF had ~1 billion rows, so I expect to be left with ~100m rows. After I did this mass delete, everything was the same size on disk (which I expected, knowing how tombstoning works). It wasn't 100% clear to me what to poke to cause compactions to clear the tombstones. First I tried nodetool cleanup on a candidate node. But, afterwards the disk usage was the same. Then I tried nodetool repair on that same node. But again, disk usage is still the same. The CF has no snapshots. So, am I misunderstanding something? Is there another operation to try? Do I have to just wait? I've only done cleanup/repair on one node. Do I have to run one or the other over all nodes to clear tombstones? Cassandra 1.2.15 if it matters, Thanks! will
Re: clearing tombstones?
So, if I was impatient and just wanted to make this happen now, I could: 1.) Change GCGraceSeconds of the CF to 0 2.) run nodetool compact (*) 3.) Change GCGraceSeconds of the CF back to 10 days Since I have ~900M tombstones, even if I miss a few due to impatience, I don't care *that* much as I could re-run my clean up tool against the now much smaller CF. (*) A long long time ago I seem to recall reading advice about don't ever run nodetool compact, but I can't remember why. Is there any bad long term consequence? Short term there are several: -a heavy operation -temporary 2x disk space -one big SSTable afterwards But moving forward, everything is ok right? CommitLog/MemTable-SStables, minor compactions that merge SSTables, etc... The only flaw I can think of is it will take forever until the SSTable minor compactions build up enough to consider including the big SSTable in a compaction, making it likely I'll have to self manage compactions. On Fri, Apr 11, 2014 at 10:31 AM, Mark Reddy mark.re...@boxever.com wrote: Correct, a tombstone will only be removed after gc_grace period has elapsed. The default value is set to 10 days which allows a great deal of time for consistency to be achieved prior to deletion. If you are operationally confident that you can achieve consistency via anti-entropy repairs within a shorter period you can always reduce that 10 day interval. Mark On Fri, Apr 11, 2014 at 3:16 PM, William Oberman ober...@civicscience.com wrote: I'm seeing a lot of articles about a dependency between removing tombstones and GCGraceSeconds, which might be my problem (I just checked, and this CF has GCGraceSeconds of 10 days). On Fri, Apr 11, 2014 at 10:10 AM, tommaso barbugli tbarbu...@gmail.comwrote: compaction should take care of it; for me it never worked so I run nodetool compaction on every node; that does it. 2014-04-11 16:05 GMT+02:00 William Oberman ober...@civicscience.com: I'm wondering what will clear tombstoned rows? nodetool cleanup, nodetool repair, or time (as in just wait)? I had a CF that was more or less storing session information. After some time, we decided that one piece of this information was pointless to track (and was 90%+ of the columns, and in 99% of those cases was ALL columns for a row). I wrote a process to remove all of those columns (which again in a vast majority of cases had the effect of removing the whole row). This CF had ~1 billion rows, so I expect to be left with ~100m rows. After I did this mass delete, everything was the same size on disk (which I expected, knowing how tombstoning works). It wasn't 100% clear to me what to poke to cause compactions to clear the tombstones. First I tried nodetool cleanup on a candidate node. But, afterwards the disk usage was the same. Then I tried nodetool repair on that same node. But again, disk usage is still the same. The CF has no snapshots. So, am I misunderstanding something? Is there another operation to try? Do I have to just wait? I've only done cleanup/repair on one node. Do I have to run one or the other over all nodes to clear tombstones? Cassandra 1.2.15 if it matters, Thanks! will
Re: clearing tombstones?
Answered my own question. Good writeup here of the pros/cons of compact: http://www.datastax.com/documentation/cassandra/1.2/cassandra/operations/ops_about_config_compact_c.html And I was thinking of bad information that used to float in this forum about major compactions (with respect to the impact to minor compactions). I'm hesitant to write the offending sentence again :-) On Fri, Apr 11, 2014 at 10:44 AM, William Oberman ober...@civicscience.comwrote: So, if I was impatient and just wanted to make this happen now, I could: 1.) Change GCGraceSeconds of the CF to 0 2.) run nodetool compact (*) 3.) Change GCGraceSeconds of the CF back to 10 days Since I have ~900M tombstones, even if I miss a few due to impatience, I don't care *that* much as I could re-run my clean up tool against the now much smaller CF. (*) A long long time ago I seem to recall reading advice about don't ever run nodetool compact, but I can't remember why. Is there any bad long term consequence? Short term there are several: -a heavy operation -temporary 2x disk space -one big SSTable afterwards But moving forward, everything is ok right? CommitLog/MemTable-SStables, minor compactions that merge SSTables, etc... The only flaw I can think of is it will take forever until the SSTable minor compactions build up enough to consider including the big SSTable in a compaction, making it likely I'll have to self manage compactions. On Fri, Apr 11, 2014 at 10:31 AM, Mark Reddy mark.re...@boxever.comwrote: Correct, a tombstone will only be removed after gc_grace period has elapsed. The default value is set to 10 days which allows a great deal of time for consistency to be achieved prior to deletion. If you are operationally confident that you can achieve consistency via anti-entropy repairs within a shorter period you can always reduce that 10 day interval. Mark On Fri, Apr 11, 2014 at 3:16 PM, William Oberman ober...@civicscience.com wrote: I'm seeing a lot of articles about a dependency between removing tombstones and GCGraceSeconds, which might be my problem (I just checked, and this CF has GCGraceSeconds of 10 days). On Fri, Apr 11, 2014 at 10:10 AM, tommaso barbugli tbarbu...@gmail.comwrote: compaction should take care of it; for me it never worked so I run nodetool compaction on every node; that does it. 2014-04-11 16:05 GMT+02:00 William Oberman ober...@civicscience.com: I'm wondering what will clear tombstoned rows? nodetool cleanup, nodetool repair, or time (as in just wait)? I had a CF that was more or less storing session information. After some time, we decided that one piece of this information was pointless to track (and was 90%+ of the columns, and in 99% of those cases was ALL columns for a row). I wrote a process to remove all of those columns (which again in a vast majority of cases had the effect of removing the whole row). This CF had ~1 billion rows, so I expect to be left with ~100m rows. After I did this mass delete, everything was the same size on disk (which I expected, knowing how tombstoning works). It wasn't 100% clear to me what to poke to cause compactions to clear the tombstones. First I tried nodetool cleanup on a candidate node. But, afterwards the disk usage was the same. Then I tried nodetool repair on that same node. But again, disk usage is still the same. The CF has no snapshots. So, am I misunderstanding something? Is there another operation to try? Do I have to just wait? I've only done cleanup/repair on one node. Do I have to run one or the other over all nodes to clear tombstones? Cassandra 1.2.15 if it matters, Thanks! will
Re: clearing tombstones?
Yes, running nodetool compact (major compaction) creates one large SSTable. This will mess up the heuristics of the SizeTiered strategy (is this the compaction strategy you are using?) leading to multiple 'small' SSTables alongside the single large SSTable, which results in increased read latency. You will incur the operational overhead of having to manage compactions if you wish to compact these smaller SSTables. For all these reasons it is generally advised to stay away from running compactions manually. Assuming that this is a production environment and you want to keep everything running as smoothly as possible I would reduce the gc_grace on the CF, allow automatic minor compactions to kick in and then increase the gc_grace once again after the tombstones have been removed. On Fri, Apr 11, 2014 at 3:44 PM, William Oberman ober...@civicscience.comwrote: So, if I was impatient and just wanted to make this happen now, I could: 1.) Change GCGraceSeconds of the CF to 0 2.) run nodetool compact (*) 3.) Change GCGraceSeconds of the CF back to 10 days Since I have ~900M tombstones, even if I miss a few due to impatience, I don't care *that* much as I could re-run my clean up tool against the now much smaller CF. (*) A long long time ago I seem to recall reading advice about don't ever run nodetool compact, but I can't remember why. Is there any bad long term consequence? Short term there are several: -a heavy operation -temporary 2x disk space -one big SSTable afterwards But moving forward, everything is ok right? CommitLog/MemTable-SStables, minor compactions that merge SSTables, etc... The only flaw I can think of is it will take forever until the SSTable minor compactions build up enough to consider including the big SSTable in a compaction, making it likely I'll have to self manage compactions. On Fri, Apr 11, 2014 at 10:31 AM, Mark Reddy mark.re...@boxever.comwrote: Correct, a tombstone will only be removed after gc_grace period has elapsed. The default value is set to 10 days which allows a great deal of time for consistency to be achieved prior to deletion. If you are operationally confident that you can achieve consistency via anti-entropy repairs within a shorter period you can always reduce that 10 day interval. Mark On Fri, Apr 11, 2014 at 3:16 PM, William Oberman ober...@civicscience.com wrote: I'm seeing a lot of articles about a dependency between removing tombstones and GCGraceSeconds, which might be my problem (I just checked, and this CF has GCGraceSeconds of 10 days). On Fri, Apr 11, 2014 at 10:10 AM, tommaso barbugli tbarbu...@gmail.comwrote: compaction should take care of it; for me it never worked so I run nodetool compaction on every node; that does it. 2014-04-11 16:05 GMT+02:00 William Oberman ober...@civicscience.com: I'm wondering what will clear tombstoned rows? nodetool cleanup, nodetool repair, or time (as in just wait)? I had a CF that was more or less storing session information. After some time, we decided that one piece of this information was pointless to track (and was 90%+ of the columns, and in 99% of those cases was ALL columns for a row). I wrote a process to remove all of those columns (which again in a vast majority of cases had the effect of removing the whole row). This CF had ~1 billion rows, so I expect to be left with ~100m rows. After I did this mass delete, everything was the same size on disk (which I expected, knowing how tombstoning works). It wasn't 100% clear to me what to poke to cause compactions to clear the tombstones. First I tried nodetool cleanup on a candidate node. But, afterwards the disk usage was the same. Then I tried nodetool repair on that same node. But again, disk usage is still the same. The CF has no snapshots. So, am I misunderstanding something? Is there another operation to try? Do I have to just wait? I've only done cleanup/repair on one node. Do I have to run one or the other over all nodes to clear tombstones? Cassandra 1.2.15 if it matters, Thanks! will
Re: clearing tombstones?
I have a similar problem here, I deleted about 30% of a very large CF using LCS (about 80GB per node), but still my data hasn't shrinked, even if I used 1 day for gc_grace_seconds. Would nodetool scrub help? Does nodetool scrub forces a minor compaction? Cheers, Paulo On Fri, Apr 11, 2014 at 12:12 PM, Mark Reddy mark.re...@boxever.com wrote: Yes, running nodetool compact (major compaction) creates one large SSTable. This will mess up the heuristics of the SizeTiered strategy (is this the compaction strategy you are using?) leading to multiple 'small' SSTables alongside the single large SSTable, which results in increased read latency. You will incur the operational overhead of having to manage compactions if you wish to compact these smaller SSTables. For all these reasons it is generally advised to stay away from running compactions manually. Assuming that this is a production environment and you want to keep everything running as smoothly as possible I would reduce the gc_grace on the CF, allow automatic minor compactions to kick in and then increase the gc_grace once again after the tombstones have been removed. On Fri, Apr 11, 2014 at 3:44 PM, William Oberman ober...@civicscience.com wrote: So, if I was impatient and just wanted to make this happen now, I could: 1.) Change GCGraceSeconds of the CF to 0 2.) run nodetool compact (*) 3.) Change GCGraceSeconds of the CF back to 10 days Since I have ~900M tombstones, even if I miss a few due to impatience, I don't care *that* much as I could re-run my clean up tool against the now much smaller CF. (*) A long long time ago I seem to recall reading advice about don't ever run nodetool compact, but I can't remember why. Is there any bad long term consequence? Short term there are several: -a heavy operation -temporary 2x disk space -one big SSTable afterwards But moving forward, everything is ok right? CommitLog/MemTable-SStables, minor compactions that merge SSTables, etc... The only flaw I can think of is it will take forever until the SSTable minor compactions build up enough to consider including the big SSTable in a compaction, making it likely I'll have to self manage compactions. On Fri, Apr 11, 2014 at 10:31 AM, Mark Reddy mark.re...@boxever.comwrote: Correct, a tombstone will only be removed after gc_grace period has elapsed. The default value is set to 10 days which allows a great deal of time for consistency to be achieved prior to deletion. If you are operationally confident that you can achieve consistency via anti-entropy repairs within a shorter period you can always reduce that 10 day interval. Mark On Fri, Apr 11, 2014 at 3:16 PM, William Oberman ober...@civicscience.com wrote: I'm seeing a lot of articles about a dependency between removing tombstones and GCGraceSeconds, which might be my problem (I just checked, and this CF has GCGraceSeconds of 10 days). On Fri, Apr 11, 2014 at 10:10 AM, tommaso barbugli tbarbu...@gmail.com wrote: compaction should take care of it; for me it never worked so I run nodetool compaction on every node; that does it. 2014-04-11 16:05 GMT+02:00 William Oberman ober...@civicscience.com: I'm wondering what will clear tombstoned rows? nodetool cleanup, nodetool repair, or time (as in just wait)? I had a CF that was more or less storing session information. After some time, we decided that one piece of this information was pointless to track (and was 90%+ of the columns, and in 99% of those cases was ALL columns for a row). I wrote a process to remove all of those columns (which again in a vast majority of cases had the effect of removing the whole row). This CF had ~1 billion rows, so I expect to be left with ~100m rows. After I did this mass delete, everything was the same size on disk (which I expected, knowing how tombstoning works). It wasn't 100% clear to me what to poke to cause compactions to clear the tombstones. First I tried nodetool cleanup on a candidate node. But, afterwards the disk usage was the same. Then I tried nodetool repair on that same node. But again, disk usage is still the same. The CF has no snapshots. So, am I misunderstanding something? Is there another operation to try? Do I have to just wait? I've only done cleanup/repair on one node. Do I have to run one or the other over all nodes to clear tombstones? Cassandra 1.2.15 if it matters, Thanks! will -- *Paulo Motta* Chaordic | *Platform* *www.chaordic.com.br http://www.chaordic.com.br/* +55 48 3232.3200
Re: clearing tombstones?
Yes, I'm using SizeTiered. I totally understand the mess up the heuristics issue. But, I don't understand You will incur the operational overhead of having to manage compactions if you wish to compact these smaller SSTables. My understanding is the small tables will still compact. The problem is that until I have 3 other (by default) tables of the same size as the big table, it won't be compacted. In my case, this might not be terrible though, right? To get into the trees, I have 9 nodes with RF=3 and this CF is ~500GB/node. I deleted like 90-95% of the data, so I expect the data to be 25-50GB after the tombstones are cleared, but call it 50GB. That means I won't compact this 50GB file until I gather another 150GB (50,50,50,50-200). But, that's not *horrible*. Now, if I only deleted 10% of the data, waiting to compact 450GB until I had another 1.3TB would be rough... I think your advice is great for people looking for normal answers in the forum, but I don't think my use case is very normal :-) will On Fri, Apr 11, 2014 at 11:12 AM, Mark Reddy mark.re...@boxever.com wrote: Yes, running nodetool compact (major compaction) creates one large SSTable. This will mess up the heuristics of the SizeTiered strategy (is this the compaction strategy you are using?) leading to multiple 'small' SSTables alongside the single large SSTable, which results in increased read latency. You will incur the operational overhead of having to manage compactions if you wish to compact these smaller SSTables. For all these reasons it is generally advised to stay away from running compactions manually. Assuming that this is a production environment and you want to keep everything running as smoothly as possible I would reduce the gc_grace on the CF, allow automatic minor compactions to kick in and then increase the gc_grace once again after the tombstones have been removed. On Fri, Apr 11, 2014 at 3:44 PM, William Oberman ober...@civicscience.com wrote: So, if I was impatient and just wanted to make this happen now, I could: 1.) Change GCGraceSeconds of the CF to 0 2.) run nodetool compact (*) 3.) Change GCGraceSeconds of the CF back to 10 days Since I have ~900M tombstones, even if I miss a few due to impatience, I don't care *that* much as I could re-run my clean up tool against the now much smaller CF. (*) A long long time ago I seem to recall reading advice about don't ever run nodetool compact, but I can't remember why. Is there any bad long term consequence? Short term there are several: -a heavy operation -temporary 2x disk space -one big SSTable afterwards But moving forward, everything is ok right? CommitLog/MemTable-SStables, minor compactions that merge SSTables, etc... The only flaw I can think of is it will take forever until the SSTable minor compactions build up enough to consider including the big SSTable in a compaction, making it likely I'll have to self manage compactions. On Fri, Apr 11, 2014 at 10:31 AM, Mark Reddy mark.re...@boxever.comwrote: Correct, a tombstone will only be removed after gc_grace period has elapsed. The default value is set to 10 days which allows a great deal of time for consistency to be achieved prior to deletion. If you are operationally confident that you can achieve consistency via anti-entropy repairs within a shorter period you can always reduce that 10 day interval. Mark On Fri, Apr 11, 2014 at 3:16 PM, William Oberman ober...@civicscience.com wrote: I'm seeing a lot of articles about a dependency between removing tombstones and GCGraceSeconds, which might be my problem (I just checked, and this CF has GCGraceSeconds of 10 days). On Fri, Apr 11, 2014 at 10:10 AM, tommaso barbugli tbarbu...@gmail.com wrote: compaction should take care of it; for me it never worked so I run nodetool compaction on every node; that does it. 2014-04-11 16:05 GMT+02:00 William Oberman ober...@civicscience.com: I'm wondering what will clear tombstoned rows? nodetool cleanup, nodetool repair, or time (as in just wait)? I had a CF that was more or less storing session information. After some time, we decided that one piece of this information was pointless to track (and was 90%+ of the columns, and in 99% of those cases was ALL columns for a row). I wrote a process to remove all of those columns (which again in a vast majority of cases had the effect of removing the whole row). This CF had ~1 billion rows, so I expect to be left with ~100m rows. After I did this mass delete, everything was the same size on disk (which I expected, knowing how tombstoning works). It wasn't 100% clear to me what to poke to cause compactions to clear the tombstones. First I tried nodetool cleanup on a candidate node. But, afterwards the disk usage was the same. Then I tried nodetool repair on that same node. But again, disk usage is still the same. The CF has no snapshots. So, am I misunderstanding
Re: clearing tombstones?
I have played with this quite a bit and recommend you set gc_grace_seconds to 0 and use 'nodetool compact [keyspace] [cfname]' on your table. A caveat I have is that we use C* 2.0.6 - but the space we expect to recover is in fact recovered. Actually, since we never delete explicitly (just ttl) we always have gc_grace_seconds set to 0. Another important caveat is to be careful with repair: having set gc to 0 and compacted on a node, if you then repair it, data may come streaming in from the other nodes. We don't run into this, as our gc is always 0, but others may be able to comment. ml On Fri, Apr 11, 2014 at 11:26 AM, William Oberman ober...@civicscience.comwrote: Yes, I'm using SizeTiered. I totally understand the mess up the heuristics issue. But, I don't understand You will incur the operational overhead of having to manage compactions if you wish to compact these smaller SSTables. My understanding is the small tables will still compact. The problem is that until I have 3 other (by default) tables of the same size as the big table, it won't be compacted. In my case, this might not be terrible though, right? To get into the trees, I have 9 nodes with RF=3 and this CF is ~500GB/node. I deleted like 90-95% of the data, so I expect the data to be 25-50GB after the tombstones are cleared, but call it 50GB. That means I won't compact this 50GB file until I gather another 150GB (50,50,50,50-200). But, that's not *horrible*. Now, if I only deleted 10% of the data, waiting to compact 450GB until I had another 1.3TB would be rough... I think your advice is great for people looking for normal answers in the forum, but I don't think my use case is very normal :-) will On Fri, Apr 11, 2014 at 11:12 AM, Mark Reddy mark.re...@boxever.comwrote: Yes, running nodetool compact (major compaction) creates one large SSTable. This will mess up the heuristics of the SizeTiered strategy (is this the compaction strategy you are using?) leading to multiple 'small' SSTables alongside the single large SSTable, which results in increased read latency. You will incur the operational overhead of having to manage compactions if you wish to compact these smaller SSTables. For all these reasons it is generally advised to stay away from running compactions manually. Assuming that this is a production environment and you want to keep everything running as smoothly as possible I would reduce the gc_grace on the CF, allow automatic minor compactions to kick in and then increase the gc_grace once again after the tombstones have been removed. On Fri, Apr 11, 2014 at 3:44 PM, William Oberman ober...@civicscience.com wrote: So, if I was impatient and just wanted to make this happen now, I could: 1.) Change GCGraceSeconds of the CF to 0 2.) run nodetool compact (*) 3.) Change GCGraceSeconds of the CF back to 10 days Since I have ~900M tombstones, even if I miss a few due to impatience, I don't care *that* much as I could re-run my clean up tool against the now much smaller CF. (*) A long long time ago I seem to recall reading advice about don't ever run nodetool compact, but I can't remember why. Is there any bad long term consequence? Short term there are several: -a heavy operation -temporary 2x disk space -one big SSTable afterwards But moving forward, everything is ok right? CommitLog/MemTable-SStables, minor compactions that merge SSTables, etc... The only flaw I can think of is it will take forever until the SSTable minor compactions build up enough to consider including the big SSTable in a compaction, making it likely I'll have to self manage compactions. On Fri, Apr 11, 2014 at 10:31 AM, Mark Reddy mark.re...@boxever.comwrote: Correct, a tombstone will only be removed after gc_grace period has elapsed. The default value is set to 10 days which allows a great deal of time for consistency to be achieved prior to deletion. If you are operationally confident that you can achieve consistency via anti-entropy repairs within a shorter period you can always reduce that 10 day interval. Mark On Fri, Apr 11, 2014 at 3:16 PM, William Oberman ober...@civicscience.com wrote: I'm seeing a lot of articles about a dependency between removing tombstones and GCGraceSeconds, which might be my problem (I just checked, and this CF has GCGraceSeconds of 10 days). On Fri, Apr 11, 2014 at 10:10 AM, tommaso barbugli tbarbu...@gmail.com wrote: compaction should take care of it; for me it never worked so I run nodetool compaction on every node; that does it. 2014-04-11 16:05 GMT+02:00 William Oberman ober...@civicscience.com : I'm wondering what will clear tombstoned rows? nodetool cleanup, nodetool repair, or time (as in just wait)? I had a CF that was more or less storing session information. After some time, we decided that one piece of this information was pointless to track (and was 90%+ of the columns, and in 99% of those cases
Re: clearing tombstones?
To clarify, you would want to manage compactions only if you were concerned about read latency. If you update rows, those rows may become spread across an increasing number of SSTables leading to increased read latency. Thanks for providing some insight into your use case as it does differ from the norm. If you would consider 50GB a small CF and your data ingestion sufficient enough to result in more SSTables of similar size soon, yes you could run a major compaction will little operational overhead and the compaction strategies heuristics would level out after some time. On Fri, Apr 11, 2014 at 4:52 PM, Laing, Michael michael.la...@nytimes.comwrote: I have played with this quite a bit and recommend you set gc_grace_seconds to 0 and use 'nodetool compact [keyspace] [cfname]' on your table. A caveat I have is that we use C* 2.0.6 - but the space we expect to recover is in fact recovered. Actually, since we never delete explicitly (just ttl) we always have gc_grace_seconds set to 0. Another important caveat is to be careful with repair: having set gc to 0 and compacted on a node, if you then repair it, data may come streaming in from the other nodes. We don't run into this, as our gc is always 0, but others may be able to comment. ml On Fri, Apr 11, 2014 at 11:26 AM, William Oberman ober...@civicscience.com wrote: Yes, I'm using SizeTiered. I totally understand the mess up the heuristics issue. But, I don't understand You will incur the operational overhead of having to manage compactions if you wish to compact these smaller SSTables. My understanding is the small tables will still compact. The problem is that until I have 3 other (by default) tables of the same size as the big table, it won't be compacted. In my case, this might not be terrible though, right? To get into the trees, I have 9 nodes with RF=3 and this CF is ~500GB/node. I deleted like 90-95% of the data, so I expect the data to be 25-50GB after the tombstones are cleared, but call it 50GB. That means I won't compact this 50GB file until I gather another 150GB (50,50,50,50-200). But, that's not *horrible*. Now, if I only deleted 10% of the data, waiting to compact 450GB until I had another 1.3TB would be rough... I think your advice is great for people looking for normal answers in the forum, but I don't think my use case is very normal :-) will On Fri, Apr 11, 2014 at 11:12 AM, Mark Reddy mark.re...@boxever.comwrote: Yes, running nodetool compact (major compaction) creates one large SSTable. This will mess up the heuristics of the SizeTiered strategy (is this the compaction strategy you are using?) leading to multiple 'small' SSTables alongside the single large SSTable, which results in increased read latency. You will incur the operational overhead of having to manage compactions if you wish to compact these smaller SSTables. For all these reasons it is generally advised to stay away from running compactions manually. Assuming that this is a production environment and you want to keep everything running as smoothly as possible I would reduce the gc_grace on the CF, allow automatic minor compactions to kick in and then increase the gc_grace once again after the tombstones have been removed. On Fri, Apr 11, 2014 at 3:44 PM, William Oberman ober...@civicscience.com wrote: So, if I was impatient and just wanted to make this happen now, I could: 1.) Change GCGraceSeconds of the CF to 0 2.) run nodetool compact (*) 3.) Change GCGraceSeconds of the CF back to 10 days Since I have ~900M tombstones, even if I miss a few due to impatience, I don't care *that* much as I could re-run my clean up tool against the now much smaller CF. (*) A long long time ago I seem to recall reading advice about don't ever run nodetool compact, but I can't remember why. Is there any bad long term consequence? Short term there are several: -a heavy operation -temporary 2x disk space -one big SSTable afterwards But moving forward, everything is ok right? CommitLog/MemTable-SStables, minor compactions that merge SSTables, etc... The only flaw I can think of is it will take forever until the SSTable minor compactions build up enough to consider including the big SSTable in a compaction, making it likely I'll have to self manage compactions. On Fri, Apr 11, 2014 at 10:31 AM, Mark Reddy mark.re...@boxever.comwrote: Correct, a tombstone will only be removed after gc_grace period has elapsed. The default value is set to 10 days which allows a great deal of time for consistency to be achieved prior to deletion. If you are operationally confident that you can achieve consistency via anti-entropy repairs within a shorter period you can always reduce that 10 day interval. Mark On Fri, Apr 11, 2014 at 3:16 PM, William Oberman ober...@civicscience.com wrote: I'm seeing a lot of articles about a dependency between removing tombstones and GCGraceSeconds, which
Re: clearing tombstones?
Thats great Will, if you could update the thread with the actions you decide to take and the results that would be great. Mark On Fri, Apr 11, 2014 at 5:53 PM, William Oberman ober...@civicscience.comwrote: I've learned a *lot* from this thread. My thanks to all of the contributors! Paulo: Good luck with LCS. I wish I could help there, but all of my CF's are SizeTiered (mostly as I'm on the same schema/same settings since 0.7...) will On Fri, Apr 11, 2014 at 12:14 PM, Mina Naguib mina.nag...@adgear.comwrote: Levelled Compaction is a wholly different beast when it comes to tombstones. The tombstones are inserted, like any other write really, at the lower levels in the leveldb hierarchy. They are only removed after they have had the chance to naturally migrate upwards in the leveldb hierarchy to the highest level in your data store. How long that takes depends on: 1. The amount of data in your store and the number of levels your LCS strategy has 2. The amount of new writes entering the bottom funnel of your leveldb, forcing upwards compaction and combining To give you an idea, I had a similar scenario and ran a (slow, throttled) delete job on my cluster around December-January. Here's a graph of the disk space usage on one node. Notice the still-diclining usage long after the cleanup job has finished (sometime in January). I tend to think of tombstones in LCS as little bombs that get to explode much later in time: http://mina.naguib.ca/images/tombstones-cassandra-LCS.jpg On 2014-04-11, at 11:20 AM, Paulo Ricardo Motta Gomes paulo.mo...@chaordicsystems.com wrote: I have a similar problem here, I deleted about 30% of a very large CF using LCS (about 80GB per node), but still my data hasn't shrinked, even if I used 1 day for gc_grace_seconds. Would nodetool scrub help? Does nodetool scrub forces a minor compaction? Cheers, Paulo On Fri, Apr 11, 2014 at 12:12 PM, Mark Reddy mark.re...@boxever.comwrote: Yes, running nodetool compact (major compaction) creates one large SSTable. This will mess up the heuristics of the SizeTiered strategy (is this the compaction strategy you are using?) leading to multiple 'small' SSTables alongside the single large SSTable, which results in increased read latency. You will incur the operational overhead of having to manage compactions if you wish to compact these smaller SSTables. For all these reasons it is generally advised to stay away from running compactions manually. Assuming that this is a production environment and you want to keep everything running as smoothly as possible I would reduce the gc_grace on the CF, allow automatic minor compactions to kick in and then increase the gc_grace once again after the tombstones have been removed. On Fri, Apr 11, 2014 at 3:44 PM, William Oberman ober...@civicscience.com wrote: So, if I was impatient and just wanted to make this happen now, I could: 1.) Change GCGraceSeconds of the CF to 0 2.) run nodetool compact (*) 3.) Change GCGraceSeconds of the CF back to 10 days Since I have ~900M tombstones, even if I miss a few due to impatience, I don't care *that* much as I could re-run my clean up tool against the now much smaller CF. (*) A long long time ago I seem to recall reading advice about don't ever run nodetool compact, but I can't remember why. Is there any bad long term consequence? Short term there are several: -a heavy operation -temporary 2x disk space -one big SSTable afterwards But moving forward, everything is ok right? CommitLog/MemTable-SStables, minor compactions that merge SSTables, etc... The only flaw I can think of is it will take forever until the SSTable minor compactions build up enough to consider including the big SSTable in a compaction, making it likely I'll have to self manage compactions. On Fri, Apr 11, 2014 at 10:31 AM, Mark Reddy mark.re...@boxever.comwrote: Correct, a tombstone will only be removed after gc_grace period has elapsed. The default value is set to 10 days which allows a great deal of time for consistency to be achieved prior to deletion. If you are operationally confident that you can achieve consistency via anti-entropy repairs within a shorter period you can always reduce that 10 day interval. Mark On Fri, Apr 11, 2014 at 3:16 PM, William Oberman ober...@civicscience.com wrote: I'm seeing a lot of articles about a dependency between removing tombstones and GCGraceSeconds, which might be my problem (I just checked, and this CF has GCGraceSeconds of 10 days). On Fri, Apr 11, 2014 at 10:10 AM, tommaso barbugli tbarbu...@gmail.com wrote: compaction should take care of it; for me it never worked so I run nodetool compaction on every node; that does it. 2014-04-11 16:05 GMT+02:00 William Oberman ober...@civicscience.com : I'm wondering what will clear tombstoned rows? nodetool cleanup, nodetool repair, or time (as in just wait)? I had a CF
Re: clearing tombstones?
This thread is really informative, thanks for the good feedback. My question is : Is there a way to force tombstones to be clared with LCS? Does scrub help in any case? Or the only solution would be to create a new CF and migrate all the data if you intend to do a large CF cleanup? Cheers, On Fri, Apr 11, 2014 at 2:02 PM, Mark Reddy mark.re...@boxever.com wrote: Thats great Will, if you could update the thread with the actions you decide to take and the results that would be great. Mark On Fri, Apr 11, 2014 at 5:53 PM, William Oberman ober...@civicscience.com wrote: I've learned a *lot* from this thread. My thanks to all of the contributors! Paulo: Good luck with LCS. I wish I could help there, but all of my CF's are SizeTiered (mostly as I'm on the same schema/same settings since 0.7...) will On Fri, Apr 11, 2014 at 12:14 PM, Mina Naguib mina.nag...@adgear.comwrote: Levelled Compaction is a wholly different beast when it comes to tombstones. The tombstones are inserted, like any other write really, at the lower levels in the leveldb hierarchy. They are only removed after they have had the chance to naturally migrate upwards in the leveldb hierarchy to the highest level in your data store. How long that takes depends on: 1. The amount of data in your store and the number of levels your LCS strategy has 2. The amount of new writes entering the bottom funnel of your leveldb, forcing upwards compaction and combining To give you an idea, I had a similar scenario and ran a (slow, throttled) delete job on my cluster around December-January. Here's a graph of the disk space usage on one node. Notice the still-diclining usage long after the cleanup job has finished (sometime in January). I tend to think of tombstones in LCS as little bombs that get to explode much later in time: http://mina.naguib.ca/images/tombstones-cassandra-LCS.jpg On 2014-04-11, at 11:20 AM, Paulo Ricardo Motta Gomes paulo.mo...@chaordicsystems.com wrote: I have a similar problem here, I deleted about 30% of a very large CF using LCS (about 80GB per node), but still my data hasn't shrinked, even if I used 1 day for gc_grace_seconds. Would nodetool scrub help? Does nodetool scrub forces a minor compaction? Cheers, Paulo On Fri, Apr 11, 2014 at 12:12 PM, Mark Reddy mark.re...@boxever.comwrote: Yes, running nodetool compact (major compaction) creates one large SSTable. This will mess up the heuristics of the SizeTiered strategy (is this the compaction strategy you are using?) leading to multiple 'small' SSTables alongside the single large SSTable, which results in increased read latency. You will incur the operational overhead of having to manage compactions if you wish to compact these smaller SSTables. For all these reasons it is generally advised to stay away from running compactions manually. Assuming that this is a production environment and you want to keep everything running as smoothly as possible I would reduce the gc_grace on the CF, allow automatic minor compactions to kick in and then increase the gc_grace once again after the tombstones have been removed. On Fri, Apr 11, 2014 at 3:44 PM, William Oberman ober...@civicscience.com wrote: So, if I was impatient and just wanted to make this happen now, I could: 1.) Change GCGraceSeconds of the CF to 0 2.) run nodetool compact (*) 3.) Change GCGraceSeconds of the CF back to 10 days Since I have ~900M tombstones, even if I miss a few due to impatience, I don't care *that* much as I could re-run my clean up tool against the now much smaller CF. (*) A long long time ago I seem to recall reading advice about don't ever run nodetool compact, but I can't remember why. Is there any bad long term consequence? Short term there are several: -a heavy operation -temporary 2x disk space -one big SSTable afterwards But moving forward, everything is ok right? CommitLog/MemTable-SStables, minor compactions that merge SSTables, etc... The only flaw I can think of is it will take forever until the SSTable minor compactions build up enough to consider including the big SSTable in a compaction, making it likely I'll have to self manage compactions. On Fri, Apr 11, 2014 at 10:31 AM, Mark Reddy mark.re...@boxever.comwrote: Correct, a tombstone will only be removed after gc_grace period has elapsed. The default value is set to 10 days which allows a great deal of time for consistency to be achieved prior to deletion. If you are operationally confident that you can achieve consistency via anti-entropy repairs within a shorter period you can always reduce that 10 day interval. Mark On Fri, Apr 11, 2014 at 3:16 PM, William Oberman ober...@civicscience.com wrote: I'm seeing a lot of articles about a dependency between removing tombstones and GCGraceSeconds, which might be my problem (I just checked, and this CF has GCGraceSeconds of 10 days). On Fri, Apr 11,
Re: clearing tombstones?
At the cost of really quite a lot of compaction, you can temporarily switch to SizeTiered, and when that is completely done (check each node), switch back to Leveled. it's like doing the laundry twice :) I've done this on CFs that were about 5GB but I don't see why it wouldn't work on larger ones. ml On Fri, Apr 11, 2014 at 1:33 PM, Paulo Ricardo Motta Gomes paulo.mo...@chaordicsystems.com wrote: This thread is really informative, thanks for the good feedback. My question is : Is there a way to force tombstones to be clared with LCS? Does scrub help in any case? Or the only solution would be to create a new CF and migrate all the data if you intend to do a large CF cleanup? Cheers, On Fri, Apr 11, 2014 at 2:02 PM, Mark Reddy mark.re...@boxever.comwrote: Thats great Will, if you could update the thread with the actions you decide to take and the results that would be great. Mark On Fri, Apr 11, 2014 at 5:53 PM, William Oberman ober...@civicscience.com wrote: I've learned a *lot* from this thread. My thanks to all of the contributors! Paulo: Good luck with LCS. I wish I could help there, but all of my CF's are SizeTiered (mostly as I'm on the same schema/same settings since 0.7...) will On Fri, Apr 11, 2014 at 12:14 PM, Mina Naguib mina.nag...@adgear.comwrote: Levelled Compaction is a wholly different beast when it comes to tombstones. The tombstones are inserted, like any other write really, at the lower levels in the leveldb hierarchy. They are only removed after they have had the chance to naturally migrate upwards in the leveldb hierarchy to the highest level in your data store. How long that takes depends on: 1. The amount of data in your store and the number of levels your LCS strategy has 2. The amount of new writes entering the bottom funnel of your leveldb, forcing upwards compaction and combining To give you an idea, I had a similar scenario and ran a (slow, throttled) delete job on my cluster around December-January. Here's a graph of the disk space usage on one node. Notice the still-diclining usage long after the cleanup job has finished (sometime in January). I tend to think of tombstones in LCS as little bombs that get to explode much later in time: http://mina.naguib.ca/images/tombstones-cassandra-LCS.jpg On 2014-04-11, at 11:20 AM, Paulo Ricardo Motta Gomes paulo.mo...@chaordicsystems.com wrote: I have a similar problem here, I deleted about 30% of a very large CF using LCS (about 80GB per node), but still my data hasn't shrinked, even if I used 1 day for gc_grace_seconds. Would nodetool scrub help? Does nodetool scrub forces a minor compaction? Cheers, Paulo On Fri, Apr 11, 2014 at 12:12 PM, Mark Reddy mark.re...@boxever.comwrote: Yes, running nodetool compact (major compaction) creates one large SSTable. This will mess up the heuristics of the SizeTiered strategy (is this the compaction strategy you are using?) leading to multiple 'small' SSTables alongside the single large SSTable, which results in increased read latency. You will incur the operational overhead of having to manage compactions if you wish to compact these smaller SSTables. For all these reasons it is generally advised to stay away from running compactions manually. Assuming that this is a production environment and you want to keep everything running as smoothly as possible I would reduce the gc_grace on the CF, allow automatic minor compactions to kick in and then increase the gc_grace once again after the tombstones have been removed. On Fri, Apr 11, 2014 at 3:44 PM, William Oberman ober...@civicscience.com wrote: So, if I was impatient and just wanted to make this happen now, I could: 1.) Change GCGraceSeconds of the CF to 0 2.) run nodetool compact (*) 3.) Change GCGraceSeconds of the CF back to 10 days Since I have ~900M tombstones, even if I miss a few due to impatience, I don't care *that* much as I could re-run my clean up tool against the now much smaller CF. (*) A long long time ago I seem to recall reading advice about don't ever run nodetool compact, but I can't remember why. Is there any bad long term consequence? Short term there are several: -a heavy operation -temporary 2x disk space -one big SSTable afterwards But moving forward, everything is ok right? CommitLog/MemTable-SStables, minor compactions that merge SSTables, etc... The only flaw I can think of is it will take forever until the SSTable minor compactions build up enough to consider including the big SSTable in a compaction, making it likely I'll have to self manage compactions. On Fri, Apr 11, 2014 at 10:31 AM, Mark Reddy mark.re...@boxever.comwrote: Correct, a tombstone will only be removed after gc_grace period has elapsed. The default value is set to 10 days which allows a great deal of time for consistency to be achieved prior to deletion. If you are operationally confident that you can achieve
Re: clearing tombstones?
(probably should have read downthread before writing my reply.. briefly, +1 most of the thread's commentary regarding major compaction, but don't listen to the FUD about major compaction, unless you have a really large amount of data you'll probably be fine..) On Fri, Apr 11, 2014 at 7:05 AM, William Oberman ober...@civicscience.comwrote: I'm wondering what will clear tombstoned rows? nodetool cleanup, nodetool repair, or time (as in just wait)? The only operation guaranteed to collect 100% of tombstones is major compaction. gc_grace_seconds duration is also involved, so be sure to understand its value. I had a CF that was more or less storing session information. After some time, we decided that one piece of this information was pointless to track (and was 90%+ of the columns, and in 99% of those cases was ALL columns for a row). I wrote a process to remove all of those columns (which again in a vast majority of cases had the effect of removing the whole row). https://issues.apache.org/jira/browse/CASSANDRA-1581 Describes a tool which filtered sstables to remove rows. In a future case like this one, you might want to consider this approach. It wasn't 100% clear to me what to poke to cause compactions to clear the tombstones. In order to delete a tombstone, all fragments of the row must be in a sstable involved in the current compaction. Some discussion here : https://issues.apache.org/jira/browse/CASSANDRA-1074 First I tried nodetool cleanup on a candidate node. But, afterwards the disk usage was the same. Cleanup writes out sstables 1:1, removing data which no belongs to a range if the node cleaning up no longer owns that range. It is meant for use when ranges are split, in order to clean up the data from the range being given up. Then I tried nodetool repair on that same node. But again, disk usage is still the same. The CF has no snapshots. Repair is unrelated to the purging of tombstones. So, am I misunderstanding something? Is there another operation to try? Do I have to just wait? I've only done cleanup/repair on one node. Do I have to run one or the other over all nodes to clear tombstones? If you are using size tiered compaction, run a major compaction. (nodetool compact). If you aren't, I believe that there is nothing you can do. =Rob
Re: clearing tombstones?
I was wondering, to remove the tombstones from Sstables created by LCS, why don't we just set the tombstone_threshold table property to a very small value (say 0.01)..? As the doc said ( www.datastax.com/documentation/cql/3.0/cql/cql_reference/compactSubprop.html) this will force compaction on the sstable itself for the purpose of cleaning tombstones, no merging with other sstables is done. In addition this property applies to both compaction strategies :-) Isn't a little bit lighter than changing strategy and hoping for the best? Regards Duy Hai DOAN Le 11 avr. 2014 20:16, Robert Coli rc...@eventbrite.com a écrit : On Fri, Apr 11, 2014 at 10:33 AM, Paulo Ricardo Motta Gomes paulo.mo...@chaordicsystems.com wrote: My question is : Is there a way to force tombstones to be clared with LCS? Does scrub help in any case? 1) Switch to size tiered compaction, compact, and switch back. Not only with LCS, but... 2) scrub does a 1:1 rewrite of sstables, watching for corruption. I believe it does throw away tombstones if it is able to, but that is not the purpose of it. =Rob
Re: clearing tombstones?
I've never noticed that that setting tombstone_threshold has any effect... at least in 2.0.6. What gets written to the log? On Fri, Apr 11, 2014 at 3:31 PM, DuyHai Doan doanduy...@gmail.com wrote: I was wondering, to remove the tombstones from Sstables created by LCS, why don't we just set the tombstone_threshold table property to a very small value (say 0.01)..? As the doc said ( www.datastax.com/documentation/cql/3.0/cql/cql_reference/compactSubprop.html) this will force compaction on the sstable itself for the purpose of cleaning tombstones, no merging with other sstables is done. In addition this property applies to both compaction strategies :-) Isn't a little bit lighter than changing strategy and hoping for the best? Regards Duy Hai DOAN Le 11 avr. 2014 20:16, Robert Coli rc...@eventbrite.com a écrit : On Fri, Apr 11, 2014 at 10:33 AM, Paulo Ricardo Motta Gomes paulo.mo...@chaordicsystems.com wrote: My question is : Is there a way to force tombstones to be clared with LCS? Does scrub help in any case? 1) Switch to size tiered compaction, compact, and switch back. Not only with LCS, but... 2) scrub does a 1:1 rewrite of sstables, watching for corruption. I believe it does throw away tombstones if it is able to, but that is not the purpose of it. =Rob
Re: Clearing tombstones
Yeah, I didn't mean normal as in what most people use. I meant that they are not strange like Tyler mentions. 2013/3/28 aaron morton aa...@thelastpickle.com The cleanup operation took several minutes though. This doesn't seem normal then It read all the data and made sure the node was a replica for it. Since a single node cluster replicas all data, there was not a lot to throw away. My replication settings should be very normal (simple strategy and replication factor 1). Most people use the Network Topology Strategy and RF 3, even if they dont have multiple DC's. Cheers - Aaron Morton Freelance Cassandra Consultant New Zealand @aaronmorton http://www.thelastpickle.com On 28/03/2013, at 3:34 AM, Joel Samuelsson samuelsson.j...@gmail.com wrote: I see. The cleanup operation took several minutes though. This doesn't seem normal then? My replication settings should be very normal (simple strategy and replication factor 1). 2013/3/26 Tyler Hobbs ty...@datastax.com On Tue, Mar 26, 2013 at 5:39 AM, Joel Samuelsson samuelsson.j...@gmail.com wrote: Sorry. I failed to mention that all my CFs had a gc_grace_seconds of 0 since it's a 1 node cluster. I managed to accomplish what I wanted by first running cleanup and then compact. Is there any logic to this or should my tombstones be cleared by just running compact? There's nothing for cleanup to do on a single node cluster (unless you've changed your replication settings in a strange way, like setting no replicas for a keyspace). Just doing a major compaction will take care of tombstones that are gc_grace_seconds old. -- Tyler Hobbs DataStax http://datastax.com/
Re: Clearing tombstones
I see. The cleanup operation took several minutes though. This doesn't seem normal then? My replication settings should be very normal (simple strategy and replication factor 1). 2013/3/26 Tyler Hobbs ty...@datastax.com On Tue, Mar 26, 2013 at 5:39 AM, Joel Samuelsson samuelsson.j...@gmail.com wrote: Sorry. I failed to mention that all my CFs had a gc_grace_seconds of 0 since it's a 1 node cluster. I managed to accomplish what I wanted by first running cleanup and then compact. Is there any logic to this or should my tombstones be cleared by just running compact? There's nothing for cleanup to do on a single node cluster (unless you've changed your replication settings in a strange way, like setting no replicas for a keyspace). Just doing a major compaction will take care of tombstones that are gc_grace_seconds old. -- Tyler Hobbs DataStax http://datastax.com/
Re: Clearing tombstones
The cleanup operation took several minutes though. This doesn't seem normal then It read all the data and made sure the node was a replica for it. Since a single node cluster replicas all data, there was not a lot to throw away. My replication settings should be very normal (simple strategy and replication factor 1). Most people use the Network Topology Strategy and RF 3, even if they dont have multiple DC's. Cheers - Aaron Morton Freelance Cassandra Consultant New Zealand @aaronmorton http://www.thelastpickle.com On 28/03/2013, at 3:34 AM, Joel Samuelsson samuelsson.j...@gmail.com wrote: I see. The cleanup operation took several minutes though. This doesn't seem normal then? My replication settings should be very normal (simple strategy and replication factor 1). 2013/3/26 Tyler Hobbs ty...@datastax.com On Tue, Mar 26, 2013 at 5:39 AM, Joel Samuelsson samuelsson.j...@gmail.com wrote: Sorry. I failed to mention that all my CFs had a gc_grace_seconds of 0 since it's a 1 node cluster. I managed to accomplish what I wanted by first running cleanup and then compact. Is there any logic to this or should my tombstones be cleared by just running compact? There's nothing for cleanup to do on a single node cluster (unless you've changed your replication settings in a strange way, like setting no replicas for a keyspace). Just doing a major compaction will take care of tombstones that are gc_grace_seconds old. -- Tyler Hobbs DataStax
Re: Clearing tombstones
Sorry. I failed to mention that all my CFs had a gc_grace_seconds of 0 since it's a 1 node cluster. I managed to accomplish what I wanted by first running cleanup and then compact. Is there any logic to this or should my tombstones be cleared by just running compact? 2013/3/25 Tyler Hobbs ty...@datastax.com You'll need to temporarily lower gc_grace_seconds for that column family, run compaction, and then restore gc_grace_seconds to its original value. See http://wiki.apache.org/cassandra/DistributedDeletes for more info. On Mon, Mar 25, 2013 at 7:40 AM, Joel Samuelsson samuelsson.j...@gmail.com wrote: Hi, I've deleted a range of keys in my one node test-cluster and want to re-add them with an older creation time. How can I make sure all tombstones are gone so that they can be re-added properly? I've tried nodetool compact but it seems some tombstones remain. Best regards, Joel Samuelsson -- Tyler Hobbs DataStax http://datastax.com/
Re: Clearing tombstones
You'll need to temporarily lower gc_grace_seconds for that column family, run compaction, and then restore gc_grace_seconds to its original value. See http://wiki.apache.org/cassandra/DistributedDeletes for more info. On Mon, Mar 25, 2013 at 7:40 AM, Joel Samuelsson samuelsson.j...@gmail.comwrote: Hi, I've deleted a range of keys in my one node test-cluster and want to re-add them with an older creation time. How can I make sure all tombstones are gone so that they can be re-added properly? I've tried nodetool compact but it seems some tombstones remain. Best regards, Joel Samuelsson -- Tyler Hobbs DataStax http://datastax.com/
