This was confirmed as a bug in Kopf master 
(https://github.com/lmenezes/elasticsearch-kopf/issues/190)

On Monday, October 27, 2014 3:21:24 PM UTC+1, Magnus Persson wrote:
>
> When using the count API the document count seems to more reasonably match 
> up. Might possibly be that Kopf is counting documents differently on 0.90 
> than on 1.3.. seems far fetched though.
>
> On Monday, October 27, 2014 1:16:40 PM UTC+1, Magnus Persson wrote:
>>
>> https://gist.github.com/magnusp/515a5c3debed12802d1f is the 
>> configuration im running on the new cluster. The old cluster is the default 
>> that came with 0.90.3 (replicas and shards were set via templates I guess)
>>
>> On Monday, October 27, 2014 12:37:48 PM UTC+1, Magnus Persson wrote:
>>>
>>> This is very strange.
>>>
>>> I shut down the old cluster while copying the files. For some reason I'm 
>>> seeing duplicate docs again with ~3.2M docs on the old cluster and ~6.3M 
>>> docs on the new cluster (using Kopf to compare). Am I missing something 
>>> obvious? At one point I _think_ I got the document count to match up but 
>>> obviously I'm not able to reach this state again.
>>>
>>>
>>> On Friday, October 24, 2014 11:42:27 PM UTC+2, Jörg Prante wrote:
>>>>
>>>> The plan to move from a 2 node to a 3 node cluster is as follows
>>>>
>>>> - backup your old data files (in case you want to go back, once 
>>>> upgraded, there is no way back)
>>>>
>>>> - shutdown old cluster
>>>>
>>>> - move the data file folder of the old cluster nodes to the new cluster 
>>>> nodes data folders. One node gets no data folder. No rsync required.
>>>>
>>>> - check minimum_master_nodes = 2. This is essential for 3 nodes.
>>>>
>>>> - start up cluster, all nodes. See the shards rebalancing. No need to 
>>>> worry about primary shards.
>>>>
>>>> Jörg
>>>>
>>>>
>>>>
>>>> On Fri, Oct 24, 2014 at 8:03 PM, Magnus Persson <magnus.e...@gmail.com> 
>>>> wrote:
>>>>
>>>>> Oh, didn't know about optimize so I'll definitely keep that in mind.
>>>>>
>>>>> The reason I was asking about primary shards is that I saw, when 
>>>>> starting from a rsync'd datafolder off of one of the nodes, double the 
>>>>> amount of documents. It wasn't immediatly apparent but when I later on 
>>>>> tried with two rsyncs matching up old node 1 with new node 1 and old node 
>>>>> 2 
>>>>> with new node 2 the "duplicates" went away... and the cluster recovered 
>>>>> significantly faster. But reading this, it seems to be sufficient just to 
>>>>> rsync the data folder from any 1 node in the old cluster and things will 
>>>>> just work? Is there a way to verify the consistency of my cluster? 
>>>>> Something like index checksums, or somesuch?
>>>>>
>>>>> On 24 October 2014 17:54, Ivan Brusic <iv...@brusic.com> wrote:
>>>>>
>>>>>> Unless you are moving to new hardware, there is no need to rsync your 
>>>>>> data. Both Elasticsaerch 0.90.x and 1.3.x are based on Lucene 4, so the 
>>>>>> underlying data is compatible. Of course, you should backup your data 
>>>>>> before such an upgrade.
>>>>>>
>>>>>> After restarting your new cluster with your old data, I would run an 
>>>>>> optimize on your indices so that Lucene can upgrade all your segments 
>>>>>> into 
>>>>>> the new format. There have been some issues with Lucene format 
>>>>>> incompatibilities, but they usually deal with indices with beta Lucene 
>>>>>> versions.
>>>>>>
>>>>>> You cannot bring up a mixed cluster between 0.90 and 1.x, so you 
>>>>>> would need to stop all your VMs. Why are you interested in primary 
>>>>>> shards? 
>>>>>> Elasticsearch is not like most database where the primary node has an 
>>>>>> extra 
>>>>>> special connotation. I have not played around with shard allocation 
>>>>>> much, 
>>>>>> but here is an old article: 
>>>>>> http://blog.sematext.com/2012/05/29/elasticsearch-shard-placement-control/
>>>>>>
>>>>>> Cheers,
>>>>>>
>>>>>> Ivan
>>>>>>
>>>>>> On Thu, Oct 23, 2014 at 4:18 PM, Magnus Persson <
>>>>>> magnus.e...@gmail.com> wrote:
>>>>>>
>>>>>>> Ah, slight typo in regard to the old cluster. It is 1 replica per 
>>>>>>> index.
>>>>>>>
>>>>>>>
>>>>>>> On Thursday, October 23, 2014 10:13:57 PM UTC+2, Magnus Persson 
>>>>>>> wrote:
>>>>>>>>
>>>>>>>> So I'm about to upgrade to 1.3.4, but due to some unfortunate 
>>>>>>>> circumstances I need to migrate my ES cluster to new VMs.
>>>>>>>> The environment is fairly simple. At the top I have logstash agent 
>>>>>>>> pulling messages off of a Redis server and feeding it to my 2 node 
>>>>>>>> cluster 
>>>>>>>> (2 replicas, 2 shards per index). So for what it's worth I can stop 
>>>>>>>> logstash and the cluster will essentially stop indexing data, allowing 
>>>>>>>> me 
>>>>>>>> to shut it down without issue. Once I have the old cluster shut down, 
>>>>>>>> I 
>>>>>>>> intend to rsync it over to the new cluster which is 3 nodes (2 
>>>>>>>> replicas, 3 
>>>>>>>> shards per index).
>>>>>>>> What is the best approach here? I was thinking that I could rsync 
>>>>>>>> the data folder from 1 of my 2 VMs running on the old cluster but then 
>>>>>>>> I 
>>>>>>>> realized that the primary shard for each index might not be on that 
>>>>>>>> VM. Can 
>>>>>>>> I manually set the primary shard somehow?
>>>>>>>>
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