Steps¶

To configure a GraphDB repository, follow the steps:

1. Check the Sizing guidelines section.
2. Check the Disk space requirements section.
3. Use the configuration spreadsheet from the doc folder of your distribution to calculate what you need for your setup.
4. Check all GraphDB Configuration parameters - their descriptions as well as their default and allowed values.
5. Check the Configuring memory section.
6. Change the default values of the repository properties, when creating it.

For creating repositories, see Creating a repository.

A repository configuration template - how it works¶

The diagram below provides an illustration of an RDF graph that describes a repository configuration:

Often, it is helpful to ensure that a repository starts with a predefined set of RDF statements - usually one or more schema graphs. This is possible by using the owlim:imports property. After start up, these files are parsed and their contents are permanently added to the repository.

In short, the configuration is an RDF graph, where the root node is of rdf:type rep:Repository, and it must be connected through the rep:RepositoryID property to a Literal that contains the human readable name of the repository. The root node must be connected via the rep:repositoryImpl property to a node that describes the configuration.

The type of the repository is defined via the rep:repositoryType property and its value must be graphdb:FreeSailRepository to allow for custom Sail implementations (such as GraphDB) to be used in Sesame 2.0. Then, a node that specifies the Sail implementation to be instantiated must be connected through the sr:sailImpl property. To instantiate GraphDB, this last node must have a property sail:sailType with the value graphdb:FreeSail - the Sesame framework will locate the correct SailFactory within the application classpath that will be used to instantiate the Java implementation class.

The namespaces corresponding to the prefixes used in the above paragraph are as follows:

rep:   <http://www.openrdf.org/config/repository#>
sr:    <http://www.openrdf.org/config/repository/sail#>
sail:  <http://www.openrdf.org/config/sail#>
owlim: <http://www.ontotext.com/trree/owlim#>

All properties used to specify the GraphDB configuration parameters use the owlim:prefix and the local names match up with the Configuration parameters, e.g., the value of the ruleset parameter can be specified using the http://www.ontotext.com/trree/owlim#ruleset property.

Sample configuration¶

The following is an example configuration (in Turtle RDF format) of a Sesame 2 repository that uses a GraphDB Sail implementation:

# 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:index-compression-ratio "-1" ;

            owlim:check-for-inconsistencies "false" ;
            owlim:disable-sameAs  "false" ;
            owlim:enable-optimization  "true" ;
            owlim:transaction-mode "safe" ;
            owlim:transaction-isolation "true" ;
            owlim:query-timeout  "0" ;
            owlim:query-limit-results  "0" ;
            owlim:throw-QueryEvaluationException-on-timeout "false" ;
            owlim:useShutdownHooks  "true" ;
            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 must NOT be changed once a repository has been created as doing so will likely lead to inconsistent data (e.g., unsupported inferred statements, missing inferred statements, or inferred statements that can not be deleted).

repository-type (Cannot be changed)

Default value: file-repository

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

storage-folder (Can be changed)

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

Default value: none

ruleset (Must NOT be changed)

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.

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

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.

Default value: 10000000

cache-memory (Can be changed)

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

Default value: <none>

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

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.

disable-sameAs (Must NOT be changed)

Description: Enables or disables the owl:sameAs optimisation.

Default value: false

enable-context-index (Can be changed)

Default value: false

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

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

enable-optimization (Can be changed)

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).

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:

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 between 32 and 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

Default value: none

Example: owlim:imports "./ont/owl.rdfs;./ont/ex.rdfs".

Tip

Schema files can be either a local path name, e.g., ./ontology/myfile.rdf or a URL, e.g., http://www.w3.org/2002/07/owl.rdf. If this parameter is used, the default namespace for each imported schema file must be provided using the defaultNS parameter.

index-compression-ratio (Cannot be changed)

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

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

predicate-memory (Can be changed)

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

Default value: 32m

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);

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);

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.

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.

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.

tuple-index-memory (Can be changed)

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

Default value: 224m

useShutdownHooks (Can be changed)

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).

Configuring memory¶

Configuring the memory used by GraphDB is the single most important factor for optimal performance - the more memory available, the better the performance. The available JAVA heap memory is used by:

• the JVM, the application and the GraphDB workspace (byte code, stacks, etc.);
• data structures for storing entities affected by specifying entity-index-size;
• data structures for indexing statements specified using cache-memory.

The following diagram offers a view of the memory use in GraphDB:

The challenge is how to divide up the available memory between the various GraphDB data structures in order to achieve the best overall behaviour.

cache-memory = tuple-index-memory + predicate-memory