Thanks for the CheckIndex info, that worked!  It looks like only one of the 
segments in that shard has issues:

  1 of 20: name=_1om docCount=216683
    codec=Lucene3x
    compound=false
    numFiles=10
    size (MB)=5,111.421
    diagnostics = {os=Linux, os.version=3.5.7, mergeFactor=7, source=merge, 
lucene.version=3.6.0 1310449 - rmuir - 2012-04-06 11:31:16, os.arch=amd64, 
mergeMaxNumSegments=-1, java.version=1.6.0_26, java.vendor=Sun Microsystems 
Inc.}
    no deletions
    test: open reader.........OK
    test: check integrity.....OK
    test: check live docs.....OK
    test: fields..............OK [31 fields]
    test: field norms.........OK [20 fields]
    test: terms, freq, prox...ERROR: java.lang.AssertionError: 
index=216690, numBits=216683
java.lang.AssertionError: index=216690, numBits=216683
        at org.apache.lucene.util.FixedBitSet.set(FixedBitSet.java:252)
        at 
org.apache.lucene.index.CheckIndex.checkFields(CheckIndex.java:932)
        at 
org.apache.lucene.index.CheckIndex.testPostings(CheckIndex.java:1325)
        at 
org.apache.lucene.index.CheckIndex.checkIndex(CheckIndex.java:631)
        at org.apache.lucene.index.CheckIndex.main(CheckIndex.java:2051)
    test: stored fields.......OK [3033562 total field count; avg 14 fields 
per doc]
    test: term vectors........OK [0 total vector count; avg 0 term/freq 
vector fields per doc]
    test: docvalues...........OK [0 docvalues fields; 0 BINARY; 0 NUMERIC; 
0 SORTED; 0 SORTED_NUMERIC; 0 SORTED_SET]
FAILED
    WARNING: fixIndex() would remove reference to this segment; full 
exception:
java.lang.RuntimeException: Term Index test failed
        at 
org.apache.lucene.index.CheckIndex.checkIndex(CheckIndex.java:646)
        at org.apache.lucene.index.CheckIndex.main(CheckIndex.java:2051)

This is on ES 1.3.4, but the index I was running optimize on was likely 
created back in 0.9 or 1.0.

On Tuesday, March 24, 2015 at 5:27:04 AM UTC-4, Michael McCandless wrote:
>
> Hmm, not good.
>
> Which version of ES?  Do you have a full stack trace for the exception?
>
> To run CheckIndex you need to add all ES jars to the classpath.  It's 
> easiest to just use a wildcard for this, e.g.:
>
>   java -cp "/path/to/es-install/lib/*" org.apache.lucene.index.CheckIndex 
> ...
>
> Make sure you have the double quotes so the shell does not expand that 
> wildcard!
>
> Mike McCandless
>
> On Mon, Mar 23, 2015 at 9:50 PM, <mjd...@gmail.com <javascript:>> wrote:
>
>> I did an optimize on this index and it looks like it caused a shard to 
>> become corrupted.  Or maybe the optimize just brought the shard corruption 
>> to light?
>>
>> On the node that reported the corrupted shard I tried shutting it down, 
>> moving the shard out and then restarting. Unfortunately the next node that 
>> got that shard then started with the same corruption issues.  The errors:
>>
>> Mar 24 01:40:17 localhost elasticsearch: [bma.0][WARN 
>> ][indices.cluster          ] [Meteorite II] [1-2013][0] failed to start 
>> shard
>> Mar 24 01:40:17 localhost 
>> org.elasticsearch.index.gateway.IndexShardGatewayRecoveryException: 
>> [1-2013][0] failed to fetch index version after copying it over
>> Mar 24 01:40:17 localhost elasticsearch: [bma.0][WARN 
>> ][cluster.action.shard     ] [Meteorite II] [1-2013][0] sending failed 
>> shard for [1-2013][0], node[ZzXsIZCsTyWD2emFuU0idg], [P], s[INITIALIZING], 
>> indexUUID [_na_], reason [Failed to start shard, message 
>> [IndexShardGatewayRecoveryException[[1-2013][0] failed to fetch index 
>> version after copying it over]; nested: CorruptIndexException[[1-2013][0] 
>> Corrupted index [corrupted_OahNymObSTyBzCCPu1FuJA] caused by: 
>> CorruptIndexException[docs out of order (1493829 <= 1493874 ) (docOut: 
>> org.apache.lucene.store.RateLimitedIndexOutput@2901a3e1)]]; ]]
>>
>> I tried using CheckIndex, but had this issue:
>>
>> java.lang.IllegalArgumentException: A SPI class of type 
>> org.apache.lucene.codecs.PostingsFormat with name 'es090' does not exist. 
>> You need to add the corresponding JAR file supporting this SPI to your 
>> classpath.The current classpath supports the following names: [Pulsing41, 
>> SimpleText, Memory, BloomFilter, Direct, FSTPulsing41, FSTOrdPulsing41, 
>> FST41, FSTOrd41, Lucene40, Lucene41]
>>
>> When running with:
>>
>> java -cp 
>> /usr/share/elasticsearch/lib/lucene-codecs-4.9.1.jar:/usr/share/elasticsearch/lib/lucene-core-4.9.1.jar
>>  
>> -ea:org.apache.lucene... org.apache.lucene.index.CheckIndex
>>
>> I'm not a java programmer so after I tried other classpath combinations I 
>> was out of ideas.
>>
>>
>> Any tips?  Looking at _cat/shards the replica is currently marked 
>> "unassigned" while the primary is "initializing".  Thanks!
>>
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>
>

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