Planning a repository configuration¶

To plan your repository configuration, check out the following sections:

• Sizing guidelines.
• Disk space requirements.
• Configuration parameters.
• How the template works.
• GraphDB data structures.
• Configuring Java heap memory.
• Configuring Entity pool memory.

Configuring a repository through the GraphDB Workbench¶

To configure a new repository through the Workbench, fill in the configuration page that opens when you click the ‘Create Repository’ button. The parameters are described in the Configuration parameters section.

Alternatively, you can create a .ttl configuration file using the template and specify the repository type, ID and configuration parameters. Click the triangle at the edge of the Create repository button and upload it.

Editing a repository

Some of the parameters you specify at repository creation time can be changed at any point. Click the edit icon next to a repository to edit it. Note that you have to restart GraphDB for the changes to take effect.

Configuring a repository programmatically¶

To configure a new repository programmatically, fill in the .ttl configuration template that can be found in the /templates folder of the GraphDB distribution. The parameters are described in the Configuration parameters section.

# Sesame configuration template for a GraphDB Free repository

@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>.
@prefix rep: <http://www.openrdf.org/config/repository#>.
@prefix sr: <http://www.openrdf.org/config/repository/sail#>.
@prefix sail: <http://www.openrdf.org/config/sail#>.
@prefix owlim: <http://www.ontotext.com/trree/owlim#>.

[] a rep:Repository ;
    rep:repositoryID "graphdb-test" ;
    rdfs:label "GraphDB Free repository" ;
    rep:repositoryImpl [
        rep:repositoryType "graphdb:FreeSailRepository" ;
        sr:sailImpl [
            sail:sailType "graphdb:FreeSail" ;

            owlim:base-URL "http://example.org/graphdb#" ;
            owlim:defaultNS "" ;
            owlim:entity-index-size "10000000" ;
            owlim:entity-id-size  "32" ;
            owlim:imports "" ;
            owlim:repository-type "file-repository" ;
            owlim:ruleset "owl-horst-optimized" ;
            owlim:storage-folder "storage" ;

            owlim:enable-context-index "false" ;

            owlim:cache-memory "256m" ;
            owlim:tuple-index-memory "224m" ;
            owlim:enablePredicateList "true" ;
            owlim:predicate-memory "32m" ;

            owlim:in-memory-literal-properties "true" ;
            owlim:enable-literal-index "true" ;

            owlim:check-for-inconsistencies "false" ;
            owlim:disable-sameAs  "false" ;
            owlim:transaction-mode "safe" ;
            owlim:transaction-isolation "true" ;
            owlim:query-timeout  "0" ;
            owlim:query-limit-results  "0" ;
            owlim:throw-QueryEvaluationException-on-timeout "false" ;
            owlim:read-only "false" ;
        ]
    ].

Configuration parameters¶

This is a list of all repository configuration parameters. Some of the parameters can be changed (effective after a restart), some cannot be changed (the change has no effect) and others need special attention once a repository has been created, as changing them will likely lead to inconsistent data (e.g., unsupported inferred statements, missing inferred statements, or inferred statements that can not be deleted).

• base-URL
• defaultNS
• entity-index-size
• entity-id-size
• imports
• repository-type
• ruleset
• storage-folder
• enable-context-index
• cache-memory
• tuple-index-memory
• enablePredicateList
• predicate-memory
• in-memory-literal-properties
• enable-literal-index
• check-for-inconsistencies
• disable-sameAs
• transaction-mode
• transaction-isolation
• query-timeout
• query-limit-results
• throw-QueryEvaluationException-on-timeout
• useShutdownHooks (deprecated)
• index-compression-ratio (deprecated)
• enable-optimization (deprecated)
• read-only

base-URL (Can be changed)

Description: Specifies the default namespace for the main persistence file. Non-empty namespaces are recommended, because their use guarantees the uniqueness of the anonymous nodes that may appear within the repository.

Default value: none

defaultNS (Cannot be changed)

Description: Default namespaces corresponding to each imported schema file separated by semicolon and the number of namespaces must be equal to the number of schema files from the imports parameter.

Default value: <empty>

Example: owlim:defaultNS "http://www.w3.org/2002/07/owl#;http://example.org/owlim#".

Warning

This parameter cannot be set via a command line argument.

entity-index-size (Cannot be changed)

Description: Defines the number of entity hash table index entries. The bigger the size, the less the collisions in the hash table and the faster the entity retrieval. The entity hash table does not rehash, so its index size is constant throughout the life of the repository. The recommended value is *the number of entities x 1,5*.

Default value: 10000000

entity-id-size (Cannot be changed)

Description: Defines the bit size of internal IDs used to index entities (URIs, blank nodes and literals). In most cases, this parameter can be left to its default value. However, if very large datasets containing more than 2 ³² entities are used, set this parameter to 40. Be aware that this can only be set when instantiating a new repository and converting an existing repository from 32 to 40-bit entity widths is not possible.

Default value: 32

Possible values: 32 and 40

imports (Cannot be changed)

Description: A list of schema files that will be imported at start up. All the statements, found in these files, will be loaded in the repository and will be treated as read-only. The serialisation format is determined by the file extension:

• .brf => BinaryRDF
• .n3 => N3
• .nq => N-Quads
• .nt => N-Triples
• .owl => RDF/XML
• .rdf => RDF/XML
• .rdfs => RDF/XML
• .trig => TriG
• .trix => TriX
• .ttl => Turtle
• .xml => TriX

repository-type (Cannot be changed)

Default value: file-repository

Possible values: file-repository, weighted-file-repository.

ruleset (Needs special attention)

Description: Sets of axiomatic triples, consistency checks and entailment rules, which determine the applied semantics.

Default value: owl-horst-optimized

Possible values: empty, rdfs, owl-horst, owl-max and owl2-rl and their optimised counterparts rdfs-optimized, owl-horst-optimized, owl-max-optimized and owl2-rl-optimized. A custom ruleset is chosen by setting the path to its rule file .pie.

Tip

Hints on optimising GraphDB’s rulesets.

storage-folder (Can be changed)

Description: specifies the folder where the index files will be stored.

Default value: none

cache-memory (Can be changed)

Description: Specifies the total amount of memory to be given to all types of cache.

Default value: <none>

tuple-index-memory (Can be changed)

Description: Specifies the amount of memory to be used for statement storage cache.

Default value: 224m

enable-context-index (Can be changed)

Default value: false

Possible value: true, where GraphDB will build and use the context index/indices.

enablePredicateList (Can be changed)

Description: Enables or disables mappings from an entity (subject or object) to its predicates; switching this on can significantly speed up queries that use wildcard predicate patterns.

Default value: false:

predicate-memory (Can be changed)

Description: Specifies the amount of memory to be used for predicate lists cache.

Default value: 32m

in-memory-literal-properties (Can be changed)

Description: Turns caching of the literal languages and data-types on and off. If the caching is on and the entity pool is restored from persistence, but there is no such cache available on disk, it is created after the entity pool initialisation.

Default value: false

enable-literal-index (Can be changed)

Description: Enables or disables the Storage. The literal index is always built as data is loaded/modified. This parameter only affects whether the index is used during query-answering.

Default value: true

check-for-inconsistencies (Can be changed)

Description: Turns the mechanism for consistency checking on and off; consistency checks are defined in the rule file and are applied at the end of every transaction, if this parameter is true. If an inconsistency is detected when committing a transaction, the whole transaction will be rolled back.

Default value: false

disable-sameAs (Needs special attention)

Description: Enables or disables the owl:sameAs optimisation.

Default value: false

transaction-mode (Can be changed)

Description: Specifies the transaction mode. In fast mode, dirty pages are written to disk in the laziest fashion possible, i.e., pages are only swapped when a new page is requested and there is no more memory available. No guarantees about data security are given when operating in this mode. So, in the event of an abnormal termination, the database must be considered corrupted and will need to be recreated from scratch.

Default value: safe; when set to safe, all updates are flushed to disk at the end of each transaction. Commit operations normally take a little longer, but recovery after an abnormal termination is instant. This mode also has much better concurrency characteristics.

transaction-isolation (Can be changed)

Description: This parameter only has an effect when transaction-mode=fast. In fast mode, updates lock the repository preventing concurrent query answering.

Default value: true;

Possible value: false, if set, concurrent queries are permitted with the loss of isolation.

query-timeout (Can be changed)

Description: Sets the number of seconds after which the evaluation of a query will be terminated; values less than or equal to zero mean no limit.

Default value: 0; (no limit);

query-limit-results (Can be changed)

Description: Sets the maximum number of results returned from a query after which the evaluation of a query will be terminated; values less than or equal to zero mean no limit.

Default value: 0; (no limit);

throw-QueryEvaluationException-on-timeout (Can be changed)

Default value: false

Possible value: true; if set, a QueryEvaluationException is thrown when the duration of a query execution exceeds the time-out parameter.

useShutdownHooks (Can be changed) (deprecated)

Default value: true. If set, the method OwlimSchemaRepository.shutdown() is called when the JVM exits (running GraphDB under Tomcat requires this parameter to be true, otherwise it cannot be guaranteed that the shutdown() method will be called at all).

index-compression-ratio (Cannot be changed) (deprecated)

Description: The compression ratio of paged index files as a percentage of their uncompressed size. The value indicates how much smaller the compressed page should be, so a value of 25 (percent) will attempt to make the index files one quarter of their uncompressed size. Any page that can not be compressed to this size will be stored uncompressed in a separate overlay file.

Default value: -1

Possible value: -1 (off) and the range [10-50]

Recommended value: 30

enable-optimization (Can be changed) (deprecated)

Description: Enables or disables query optimisation.

Default value: true

Warning

Disabling query optimisation is rarely needed - usually only for debugging purposes. Also, be aware that disabling query optimisation will also disable the correct behaviour of plugins (Full-text search, Geo-spatial extensions, RDF Rank, etc).

read-only (Can be changed)

Description: In this mode, no modifications are allowed to the data or namespaces.

Default value: false

Possible value: true, puts the repository in to read-only mode.

Configuring GraphDB memory¶

Configuring Java heap memory¶

The following diagram offers a view of the memory use by the GraphDB structures and processes:

To specify the maximum amount of heap space used by a JVM, use the -Xmx virtual machine parameter.

The Xmx value should be about 2/3 of the system memory. For example, if a system has 8GB total of RAM and 1GB is used by the operating system, services, etc. and 1GB by the entity pool and the hash maps, as they are off heap, ideally, the JVM that hosts the application using GraphDB should have a maximum heap size of 6GB and can be set using the JVM argument: -Xmx6g.

-Dgraphdb.epool.onheap=true