Space reuse

Neo4j uses logical deletes to remove data from the database to achieve maximum performance and scalability. A logical delete means that all relevant records are marked as deleted, but the space they occupy is not immediately returned to the operating system. Instead, it is subsequently reused by the transactions creating data.

Marking a record as deleted requires writing a record update command to the transaction log files, as when something is created or updated. Therefore, when deleting large amounts of data, this leads to a storage usage growth of that particular database, because Neo4j writes records for all deleted nodes, their properties, and relationships to the transaction log.

Keep in mind that when doing DETACH DELETE on many nodes, those deletes can take up more space in the in-memory transaction state and the transaction log than you might expect.

Transactions are eventually pruned out of the transaction log files, bringing the storage usage of the log back down to the expected level. The store files, on the other hand, do not shrink when data is deleted. The space that the deleted records take up is kept in the store files. Until the space is reused, the store files are sparse and fragmented, but the performance impact of this is usually minimal.

ID files

Neo4j uses .id files for managing the space that can be reused. These files contain the set of IDs for all the deleted records in their respective files. The ID of the record uniquely identifies it within the store file. For instance, depending on the store format, the IDs of all deleted nodes are contained in neostore.nodestore.db.id or block.x1.db.id.

These .id files are maintained as part of the write transactions that interact with them. When a write transaction commits a deletion, the record’s ID is buffered in memory. The buffer keeps track of all overlapping unfinished transactions. When they complete, the ID becomes available for reuse.

The buffered IDs are flushed to the .id files as part of the checkpointing. Concurrently, the .id file changes (the ID additions and removals) are inferred from the transaction commands. This way, the recovery process ensures that the .id files are always in-sync with their store files. The same process also ensures that clustered databases have precise and transactional space reuse.

If you want to shrink the size of your database, do not delete the .id files. The store files must only be modified by the Neo4j database and the neo4j-admin tools.

Reclaim unused space

You can use the neo4j-admin database copy command to create a defragmented copy of your database. The copy command creates and entirely new and independent database. If you want to run that database in a cluster, you have to re-seed the existing cluster, or seed a new cluster from that copy.

Example 1. Example of database compaction using neo4j-admin database copy

The following is a detailed example on how to check your database store usage and how to reclaim space.

Let’s use the Cypher Shell command-line tool to add 100k nodes and then see how much store they occupy.

  1. In a running Neo4j standalone instance, log in to the Cypher Shell command-line tool with your credentials.

    bin/cypher-shell -u neo4j -p <password>
    Connected to Neo4j at neo4j://localhost:7687 as user neo4j.
Type :help for a list of available commands or :exit to exit the shell.
Note that Cypher queries must end with a semicolon.

  2. Add 100k nodes to the neo4j database using the following command:

    neo4j@neo4j> foreach (x in range (1,100000) | create (n:testnode1 {id:x}));
    0 rows available after 1071 ms, consumed after another 0 ms
Added 100000 nodes, Set 100000 properties, Added 100000 labels

  3. Check the allocated ID range:

    neo4j@neo4j> MATCH (n:testnode1) RETURN ID(n) as ID order by ID limit 5;
    +----+
| ID |
+----+
| 0  |
| 1  |
| 2  |
| 3  |
| 4  |
+----+

5 rows available after 171 ms, consumed after another 84 ms

  4. Run call db.checkpoint() procedure to force a checkpoint.

    neo4j@neo4j> call db.checkpoint();
    +-----------------------------------+
| success | message                 |
+-----------------------------------+
| TRUE    | "Checkpoint completed." |
+-----------------------------------+

1 row available after 18 ms, consumed after another 407 ms

  5. In Neo4j Browser, run :sysinfo to check the total store size of neo4j.

    The reported output for the store size is 791.92 KiB, ID Allocation: Node ID 100000, Property ID 100000.

  6. Delete the above created nodes.

    neo4j@neo4j> Match (n) detach delete n;

  7. Run call db.checkpoint() procedure again.

    neo4j@neo4j> call db.checkpoint();
    +-----------------------------------+
| success | message                 |
+-----------------------------------+
| TRUE    | "Checkpoint completed." |
+-----------------------------------+

1 row available after 18 ms, consumed after another 407 ms

  8. In Neo4j Browser, run :sysinfo to check the total store size of neo4j.

    The reported output for the store size is 31.01 MiB, ID Allocation: Node ID 100000, Property ID 100000.

    By default, a checkpoint flushes any cached updates in pagecache to store files. Thus, the allocated IDs remain unchanged, and the store size increases or does not alter (if the instance restarts) despite the deletion. In a production database, where numerous load/deletes are frequently performed, the result is a significant unused space occupied by store files.

To reclaim that unused space, you can use the neo4j-admin database copy command to create a defragmented copy of your database. Use the system database and stop the neo4j database before running the command.

  1. Invoke the neo4j-admin database copy command to create a copy of your neo4j database.

    bin/neo4j-admin database copy neo4j neo4jcopy1 --compact-node-store --verbose
    Starting to copy store, output will be saved to: $neo4j_home/logs/neo4j-admin-copy-2020-11-04.11.30.57.log
2020-10-23 11:40:00.749+0000 INFO [StoreCopy] ### Copy Data ###
2020-10-23 11:40:00.750+0000 INFO [StoreCopy] Source: $neo4j_home/data/databases/neo4j (page cache 8m) (page cache 8m)
2020-10-23 11:40:00.750+0000 INFO [StoreCopy] Target: $neo4j_home/data/databases/neo4jcopy1 (page cache 8m)
2020-10-23 11:40:00.750+0000 INFO [StoreCopy] Empty database created, will start importing readable data from the source.
2020-10-23 11:40:02.397+0000 INFO [o.n.i.b.ImportLogic] Import starting
Nodes, started 2020-11-04 11:31:00.088+0000
[*Nodes:?? 7.969MiB---------------------------------------------------------------------------] 100K ∆ 100K
Done in 632ms
Prepare node index, started 2020-11-04 11:31:00.735+0000
[*DETECT:7.969MiB-----------------------------------------------------------------------------]    0 ∆    0
Done in 79ms
Relationships, started 2020-11-04 11:31:00.819+0000
[*Relationships:?? 7.969MiB-------------------------------------------------------------------]    0 ∆    0
Done in 37ms
Node Degrees, started 2020-11-04 11:31:01.162+0000
[*>:??----------------------------------------------------------------------------------------]    0 ∆    0
Done in 12ms
Relationship --> Relationship 1/1, started 2020-11-04 11:31:01.207+0000
[*>:??----------------------------------------------------------------------------------------]    0 ∆    0
Done in 0ms
RelationshipGroup 1/1, started 2020-11-04 11:31:01.232+0000
[*>:??----------------------------------------------------------------------------------------]    0 ∆    0
Done in 10ms
Node --> Relationship, started 2020-11-04 11:31:01.245+0000
[*>:??----------------------------------------------------------------------------------------]    0 ∆    0
Done in 10ms
Relationship <-- Relationship 1/1, started 2020-11-04 11:31:01.287+0000
[*>:??----------------------------------------------------------------------------------------]    0 ∆    0
Done in 0ms
Count groups, started 2020-11-04 11:31:01.549+0000
[*>:??----------------------------------------------------------------------------------------]    0 ∆    0
Done in 0ms
Node --> Group, started 2020-11-04 11:31:01.579+0000
[*>:??----------------------------------------------------------------------------------------]    0 ∆    0
Done in 1ms
Node counts and label index build, started 2020-11-04 11:31:01.986+0000
[*>:??----------------------------------------------------------------------------------------]    0 ∆    0
Done in 11ms
Relationship counts, started 2020-11-04 11:31:02.034+0000
[*>:??----------------------------------------------------------------------------------------]    0 ∆    0
Done in 0ms

IMPORT DONE in 3s 345ms.
Imported:
  0 nodes
  0 relationships
  0 properties
Peak memory usage: 7.969MiB
2020-11-04 11:31:02.835+0000 INFO [o.n.i.b.ImportLogic] Import completed successfully, took 3s 345ms. Imported:
  0 nodes
  0 relationships
  0 properties
2020-11-04 11:31:03.330+0000 INFO [StoreCopy] Import summary: Copying of 100704 records took 5 seconds (20140 rec/s). Unused Records 100704 (100%) Removed Records 0 (0%)
2020-11-04 11:31:03.330+0000 INFO [StoreCopy] ### Extracting schema ###
2020-11-04 11:31:03.330+0000 INFO [StoreCopy] Trying to extract schema...
2020-11-04 11:31:03.338+0000 INFO [StoreCopy] ... found 0 schema definitions.

    The example resulted in a compact and consistent store (any inconsistent nodes, properties, relationships are not copied over to the newly created store).

  2. Use the system database and create the neo4jcopy1 database.

    neo4j@system> create database neo4jcopy1;
    0 rows available after 60 ms, consumed after another 0 ms

  3. Verify that the neo4jcopy1 database is online.

    neo4j@system> show databases;
    +-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| name         | type       | aliases | access       | address          | role      | writer | requestedStatus | currentStatus | statusMessage | default | home  | constituents |
+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| "neo4j"      | "standard" | []      | "read-write" | "localhost:7687" | "primary" | TRUE   | "offline"       | "offline"     | ""            | TRUE    | TRUE  | []           |
| "neo4jcopy1" | "standard" | []      | "read-write" | "localhost:7687" | "primary" | TRUE   | "online"        | "online"      | ""            | FALSE   | FALSE | []           |
| "system"     | "system"   | []      | "read-write" | "localhost:7687" | "primary" | TRUE   | "online"        | "online"      | ""            | FALSE   | FALSE | []           |
+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+

3 rows available after 2 ms, consumed after another 1 ms

  4. In Neo4j Browser, run :sysinfo to check the total store size of neo4jcopy1.

    The reported output for the store size after the compaction is 800.68 KiB, ID Allocation: Node ID 0, Property ID 0.