How To Solve Issues Related to Log – Corrupt file detected source merge but is set to

Prevent Your Next ELK Incident

Try our free Check Up to test if your ES issues are caused from misconfigured settings

Fix Issue

Updated: Feb-20

In-Page Navigation (click to jump) :

Opster Offer’s World-Class Elasticsearch Expertise In One Powerful Product
Try Our Free ES Check-Up   Prevent Incident

Troubleshooting background

To troubleshoot Elasticsearch log “Corrupt file detected source merge but is set to” it’s important to understand common problems related to Elasticsearch concepts: discovery-file, index. See detailed explanations below complete with common problems, examples and useful tips.

Index in Elasticsearch

What it is

In Elasticsearch, an index (indices in plural) can be thought of as a table inside a database that has a schema and can have one or more shards and replicas. An Elasticsearch index is divided into shards and each shard is an instance of a Lucene index.

Indices are used to store the documents in dedicated data structures corresponding to the data type of fields. For example, text fields are stored inside an inverted index whereas numeric and geo fields are stored inside BKD trees.

Examples
Create Index

The following example is based on Elasticsearch version 5.x onwards. An index with two shards, each having one replica will be created with the name test_index1

PUT /test_index1?pretty
{
    "settings" : {
        "number_of_shards" : 2,
        "number_of_replicas" : 1
    },
    "mappings" : {
        "properties" : {
            "tags" : { "type" : "keyword" },
            "updated_at" : { "type" : "date" }
        }
    }
}
List Indices

All the index names and their basic information can be retrieved using the following command:

GET _cat/indices?v
Index a document

Let’s add a document in the index with below command:

PUT test_index1/_doc/1
{
  "tags": [
    "opster",
    "elasticsearch"
  ],
  "date": "01-01-2020"
}
Query an index
GET test_index1/_search
{
  "query": {
    "match_all": {}
  }
}
Query Multiple Indices

It is possible to search multiple indices with a single request. If it is a raw HTTP request, Index names should be sent in comma-separated format, as shown in the example below, and in the case of a query via a programming language client such as python or Java, index names are to be sent in a list format.

GET test_index1,test_index2/_search
Delete Indices
DELETE test_index1
Common Problems
  • It is good practice to define the settings and mapping of an Index wherever possible because if this is not done, Elasticsearch tries to automatically guess the data type of fields at the time of indexing. This automatic process may have disadvantages, such as mapping conflicts, duplicate data and incorrect data types being set in the index. If the fields are not known in advance, it’s better to use dynamic index templates.
  • Elasticsearch supports wildcard patterns in Index names, which sometimes aids with querying multiple indices, but can also be very destructive too. For example, It is possible to delete all the indices in a single command using the following commands:
DELETE /*

To disable this, you can add the following lines in the elasticsearch.yml:

action.destructive_requires_name: true

Source in Elasticsearch

What it is

When a document is sent to for indexing, Elasticsearch indexes all the fields in the format of inverted index but it also keeps the original json document in a special field called _source. 

Examples

Disabling source field in the index

PUT /api-logs?pretty
{
  "mappings": {
    "_source": {
      "enabled": false
    }
  }
}

Store only selected fields as a part of _source field

PUT api-logs
{
  "mappings": {
    "_source": {
      "includes": [
        "*.count",
        "error_info.*"
      ],
      "excludes": [
        "error_info.traceback_message"
      ]
    }
  }
}

Including only selected fields using source filtering

GET api-logs/_search
{
  "query": {
    "match_all": {}
  },
  "_source": {
       "includes": ["api_name","status_code", "*id"]
  }
}

Notes

The source field brings an overhead of extra storage space but serves special purposes such as:

  • Return as a part of the response when a search query is executed.
  • Used for reindexing purpose, update and update_by_query operations.
  • Used for highlighting, if the field is not stored, it means  the field is not set as “store to true” inside the mapping.
  • Allows selection of fields to be returned.

The only concern with source field is the extra storage usage on disk. But this storage space used by source field can be optimized by changing compression level to best_compression. This setting is done using index.codec parameter.


To help troubleshoot related issues we have gathered selected Q&A from the community and issues from Github , please review the following for further information :

1 Indexoutofbound Exception And Merge  

2Github Issue Number 7238  


Log Context

Log ”corrupt file detected source: [merge] but [{}] is set to [{}]” classname is InternalEngine.java
We have extracted the following from Elasticsearch source code to get an in-depth context :

         public void onFailedMerge(MergePolicy.MergeException e) {
            if (Lucene.isCorruptionException(e)) {
                if (engineConfig.isFailEngineOnCorruption()) {
                    failEngine("corrupt file detected source: [merge]"; e);
                } else {
                    logger.warn("corrupt file detected source: [merge] but [{}] is set to [{}]"; e; EngineConfig.INDEX_FAIL_ON_CORRUPTION_SETTING; engineConfig.isFailEngineOnCorruption());
                }
            } else if (engineConfig.isFailOnMergeFailure()) {
                failEngine("merge exception"; e);
            }
        }






About Opster

Incorporating deep knowledge and broad history of Elasticsearch issues. Opster’s solution identifies and predicts root causes of Elasticsearch problems, provides recommendations and can automatically perform various actions to manage, troubleshoot and prevent issues.

Learn more: Glossary | Blog| Troubleshooting guides | Error Repository

Need help with any Elasticsearch issue ? Contact Opster