I am using the embedded Solr API for my indexing process. I created a brand new 
index with my application without any problem. I then ran my indexer in 
incremental mode. This process copies the working index to a temporary Solr 
location, adds/updates any records, optimizes the index, and then copies it 
back to the working location. There are currently not any instances of Solr 
reading this index. Also, I commit after every 100000 rows. The schema.xml and 
solrconfig.xml files have not changed.

Here is my function call.
protected void optimizeProducts() throws IOException {
        UpdateHandler updateHandler = m_SolrCore.getUpdateHandler();
        CommitUpdateCommand commitCmd = new CommitUpdateCommand(true);
        commitCmd.optimize = true;
        
        updateHandler.commit(commitCmd);
        
        log.info("Optimized index");
    }

So, during the optimize phase, I get the following stack trace:
java.io.IOException: read past EOF
        at 
org.apache.lucene.store.BufferedIndexInput.refill(BufferedIndexInput.java:89)
        at 
org.apache.lucene.store.BufferedIndexInput.readByte(BufferedIndexInput.java:34)
        at org.apache.lucene.store.IndexInput.readChars(IndexInput.java:107)
        at org.apache.lucene.store.IndexInput.readString(IndexInput.java:93)
        at 
org.apache.lucene.index.FieldsReader.addFieldForMerge(FieldsReader.java:211)
        at org.apache.lucene.index.FieldsReader.doc(FieldsReader.java:119)
        at 
org.apache.lucene.index.SegmentReader.document(SegmentReader.java:323)
        at 
org.apache.lucene.index.SegmentMerger.mergeFields(SegmentMerger.java:206)
        at org.apache.lucene.index.SegmentMerger.merge(SegmentMerger.java:96)
        at 
org.apache.lucene.index.IndexWriter.mergeSegments(IndexWriter.java:1835)
        at org.apache.lucene.index.IndexWriter.optimize(IndexWriter.java:1195)
        at 
org.apache.solr.update.DirectUpdateHandler2.commit(DirectUpdateHandler2.java:508)
        at ...

There are no exceptions or anything else that appears to be incorrect during 
the adds or commits. After this, the index files are still non-optimized.

I know there is not a whole lot to go on here. Anything in particular that I 
should look at?

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