You should consider upgrading to 0.7.6 to get a fix to Gossip. Earlier 0.7 
releases were prone to marking nodes up and down when they should not have 
been. See https://github.com/apache/cassandra/blob/cassandra-0.7/CHANGES.txt#L22

Are the TimedOutExceptions to the client for read or write requests ? During 
the burst times which stages are backing up  nodetool tpstats ? Compaction 
should not affect writes too much (assuming different log and data spindles). 

You could also take a look at the read and write latency stats for a particular 
CF using nodetool cfstats or JConsole. These will give you the stats for the 
local operations. You could also take a look at the iostats on the box 
http://spyced.blogspot.com/2010/01/linux-performance-basics.html

Hope that helps.

-----------------
Aaron Morton
Freelance Cassandra Developer
@aaronmorton
http://www.thelastpickle.com

On 7 Jun 2011, at 00:30, David Boxenhorn wrote:

> Version 0.7.3.
> 
> Yes, I am talking about minor compactions. I have three nodes, RF=3.
> 3G data (before replication). Not many users (yet). It seems like 3
> nodes should be plenty. But when all 3 nodes are compacting, I
> sometimes get timeouts on the client, and I see in my logs that each
> one is full of notifications that the other nodes have died (and come
> back to life after about a second). My cluster can tolerate one node
> being out of commission, so I would rather have longer compactions one
> at a time than shorter compactions all at the same time.
> 
> I think that our usage pattern of bursty writes causes the three nodes
> to decide to compact at the same time. These bursts are followed by
> periods of relative quiet, so there should be time for the other two
> nodes to compact one at a time.
> 
> 
> On Mon, Jun 6, 2011 at 3:27 PM, David Boxenhorn <da...@citypath.com> wrote:
>> 
>> Version 0.7.3.
>> 
>> Yes, I am talking about minor compactions. I have three nodes, RF=3. 3G data 
>> (before replication). Not many users (yet). It seems like 3 nodes should be 
>> plenty. But when all 3 nodes are compacting, I sometimes get timeouts on the 
>> client, and I see in my logs that each one is full of notifications that the 
>> other nodes have died (and come back to life after about a second). My 
>> cluster can tolerate one node being out of commission, so I would rather 
>> have longer compactions one at a time than shorter compactions all at the 
>> same time.
>> 
>> I think that our usage pattern of bursty writes causes the three nodes to 
>> decide to compact at the same time. These bursts are followed by periods of 
>> relative quiet, so there should be time for the other two nodes to compact 
>> one at a time.
>> 
>> 
>> On Mon, Jun 6, 2011 at 2:36 PM, aaron morton <aa...@thelastpickle.com> wrote:
>>> 
>>> Are you talking about minor (automatic) compactions ? Can you provide some 
>>> more information on what's happening to make the node unusable and what 
>>> version you are using? It's not lightweight process, but it should not hurt 
>>> the node that badly. It is considered an online operation.
>>> 
>>> Delaying compaction will only make it run for longer and take more 
>>> resources.
>>> 
>>> Cheers
>>> 
>>> -----------------
>>> Aaron Morton
>>> Freelance Cassandra Developer
>>> @aaronmorton
>>> http://www.thelastpickle.com
>>> 
>>> On 6 Jun 2011, at 20:14, David Boxenhorn wrote:
>>> 
>>>> Is there some deep architectural reason why compaction can't be
>>>> replication-aware?
>>>> 
>>>> What I mean is, if one node is doing compaction, its replicas
>>>> shouldn't be doing compaction at the same time. Or, at least a quorum
>>>> of nodes should be available at all times.
>>>> 
>>>> For example, if RF=3, and one node is doing compaction, the nodes to
>>>> its right and left in the ring should wait on compaction until that
>>>> node is done.
>>>> 
>>>> Of course, my real problem is that compaction makes a node pretty much
>>>> unavailable. If we can fix that problem then this is not necessary.
>>> 
>> 

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