=Paper=
{{Paper
|id=None
|storemode=property
|title=GRID-DL - Semantic GRID Information Service
|pdfUrl=https://ceur-ws.org/Vol-849/paper_29.pdf
|volume=Vol-849
|dblpUrl=https://dblp.org/rec/conf/owled/PospishniyS12
}}
==GRID-DL - Semantic GRID Information Service==
https://ceur-ws.org/Vol-849/paper_29.pdf
GRID-DL – Semantic GRID Information Service
Olexandr Pospishniy1, Sergii Stirenko1
1
National Technical University of Ukraine “Kyiv Polytechnic Institute”, Kiev, Ukraine
pospishniy@kpi.in.ua, stirenko@ugrid.org
Abstract. The effectiveness of modern complex Grid systems strongly depends
on the availability, accuracy and relevance of information on all connected re-
sources, their characteristics and state. An access to this information plays a
very important role in any Grid system, providing necessary information for
other Grid components and users. We set a goal for "intellectualization" of key
Grid systems to promote it to a larger audience of users that sometimes have
difficulties adjusting to way Grid is operated. We believe that application of
semantic technologies opens up many new possibilities and prospects for fur-
ther improvement of the basic elements of Grid systems, promoting the emer-
gence of new models of user interaction with them. In this work we present
Grid-DL - a prototype semantic Grid information service that relies on ontolo-
gies in order to build up a knowledge base of Grid resources and process user
queries to it. We share our experience designing an idea of “pluggable” ontolo-
gies and sufficient core system taxonomy, while facing severe performance
challenges implementing our system.
Keywords: Grid, information service, semantics, ontology, OWL
1 Introduction
Grid computing proved to be effective and powerful instrument for modern data-
intensive science and engineering. The idea was simple, yet very powerful – to inte-
grate geographically dispersed computing resources from multiple administrative
domains and provide shared access to them. A set of software libraries, called Grid
middleware, was developed to provide an extendable platform for creating virtual
organizations that would pool and share their resources in order to achieve some
common goals.
One of the distinct characteristics of grid system is resource heterogeneity. Every
Grid site is unique with respect to their hardware and software composition. Also
each resource, apart from being shared within a Grid environment, could be used and
managed by its immediate owner. Thus effective management and use of such com-
plex heterogeneous systems as Grids is entirely dependent on the availability, accura-
cy and relevance of information on all available resources, their characteristics, condi-
tion and usage policy. An access to this information should be as clear as possible for
a wide range of users and at the same time sufficiently flexible and adaptive for a
wide range of tasks.
Traditional Grid information services tend to force users to comply with its seman-
tics. Users describe requirements of software they want to run in terms of allowed
attributes. This quite often becomes a source of erroneous assignments of tasks to
Grid resources, reducing overall system throughput
In order to address this issue we hypothesize that semantic technologies, develop-
ing under the vision of the Semantic Web, can be effectively applied to Grid systems.
2 Grid resource ontology
Grid resource ontology is a keystone in our vision of semantic grid information
services. It gives us a foundation to build upon, as we introduce more complex and
specific ontologies on top of it.
The ontology we developed1 is based on a specially designed scheme for referenc-
ing Grid entities - Grid Laboratory Uniform Environment, GLUE [1]. This scheme
describes most of the Grid components and their characteristics, and is used in mod-
ern information services such as MDS [2] and BDII [3].
Terminological component of our ontology contains 65 classes, 33 object proper-
ties and 106 data properties. Ontology corresponds to the SHIF(D) expressiveness of
description logic, which relates it to OWL-Lite dialect.
There are 3 classes on the upper level of hierarchy: GridEntity, DomainConcept
and Enumeration. First class serves as the superclass of all core Grid entities, the se-
cond class defines the supporting domain concepts, and the latter is used for the enu-
merated concepts.
Ontology defines the following basic elements of the Grid system (Fig. 1):
i. CoreEntity: Service and Site
ii. ComputingResource: Cluster, SubCluster and ComputingElement
iii. StorageResource: StorageElement and StorageArea
Fig. 1. Hierarchy of base Grid concepts
1
http://grid-ontology.googlecode.com/files/GLUE.owl
Fig. 2 shows the class hierarchy of DomainConcept and Enumeration classes,
which are used to describe the basic elements the Grid system.
Fig. 2. Hierarchy of the supporting domain and enumeration concepts
Ontology was developed using the ontology editor and knowledge-building tool
Protégé [4]. Protégé editor does not perform any knowledge processing, i.e. does not
contain a reasoner. For these purposes, an external third-party OWL reasoners must
be connected through the OWLAPI interface [5].
However, to be of any use to us, ontology needs to be filled with a set of assertions
about individuals that represent physical Grid resources (ABox).
For the purpose of generating an ABox we have developed a program2 to import
data from the LHC Computing Grid (WLCG), the most ambitious Grid system to
date, which serves to carry out the experiments on the Large Hadron Collider.
Application is not only limited to the LHC Grid and can be used to import data
from any other Grid system that has BDII- or MDS-based information service.
3 Semantic information service architecture
To test out and refine our ideas we have built a prototype of Semantic Information
Service that we call Grid-DL. Grid-DL is an autonomous Web-application that con-
tains a set of Web-services and a simple Web-interface. Project is implemented using
Java 7 platform and requires Apache Ant tool to be compiled and packaged. The re-
sulting web-application in the form of war-file is ready for deployment in any J2EE-
compatible application server, such as Apache Tomcat. Figure 3 outlines overall Grid-
DL system architecture with all major components.
Fig. 3. Grid-DL system architecture
3.1 Backbone Grid information service
At this stage of approbation of our ideas we decided not to concern ourselves with
the developing of some new resource monitoring framework, but rather adapt to the
2
Source code available http://code.google.com/p/grid-ontology/source/checkout
traditional Grid information systems, widely uses in production. Thus a special mod-
ule in Grid-DL, called import manager retrieves all required information about online
Grid resources from the top-level information server. We consider BDII, GIIS and
EGIIS from gLite, Globus and ARC middleware respectively, as such top-level in-
formation providers.
For universality we developed a mechanism of adapters to connect Grid-DL to ar-
bitrary compatible Grid information service. Thanks to ontologies, all data obtained
from external information source will be given a generalized invariant representation.
3.2 Semantic Information Service
Based on the philosophy of the Grid systems, it is useful to distinguish between
two separate operational levels: a common Grid-wide space and an isolated virtual
organization where users do their tasks. We exploit this division by using two ontolo-
gies when working with information service: core system ontology and user ontology.
Core ontology described in the previous section (TBox) is relatively broad, over-
arching and static in its nature. Its purpose is to create a solid foundation for storing
all available data on resources acquired from a Grid information service and provide
material for user ontologies to be built upon.
Virtual organizations, on the other hand, are usually formed for solving some spe-
cific tasks within some domain, usually bringing together researchers from same or
relative fields of science. That is why we think that it is plausible to extend core sys-
tem ontology with additional domain-specific knowledge that will capture the speci-
ficity of these virtual organizations. We hope that multiple users that work in the same
field of study will collaborate and come up with an extension to core ontology that
will contain new constructs that would be helpful for them. Some possible extensions
could contain descriptions of various algorithms and methods, tools, terminologies
and any arbitrary assertions common to researches within this virtual organization.
Domain ontologies will be created and managed by the virtual organizations them-
selves thus such ontologies will be relatively specific and dynamic.
In Grid-DL (Fig.3.) information about all Grid resources is coming through an im-
port module (a) and based on the terminology presented in the core T-box (c) forms a
time stamped assertion box (b) that contains all the information on Grid resources. To
retrieve the core T-box a user must use provided web-service (d). TBox ontology is
read-only and identified by version number. ABox is stored with a time stamp in or-
der to manage relevance of the retrieved results.
For reasoning Grid-DL could use any OWL-reasoner (e) that supports OWLAPI
interface. Our test environment uses Pellet [6] for this purpose.
All interaction with semantic information service is carried out through a web-
service façade (f). We implemented this component using JAX-WS library from J2EE
platform in order to provide interoperability with any client that supports a standard-
ized web-service technology stack.
All requests coming to Grid-DL are validated (g) in order to find semantic errors
and logical inconsistencies in search queries. Additionally we cache (h) user requests
to increase performance.
3.3 Domain Ontology Repository
Domain ontology repository is available as a common platform for collaborative
ontology development and refinement that will be used with semantic information
service. This component could be viewed as a standalone server with installed revi-
sion control system (Mercurial in our case). This way, users can participate in the
joint development of domain ontologies, or use any available ontology that will suit
their needs. Semantic information service will be constantly referring to this reposito-
ry while processing user quires.
3.4 Users and clients of Grid-DL
Since all interaction with semantic information service is carried out via web-
services, any application that supports standard web-service technology stack (URI,
XML, SOAP, WSDL) could be a client of Grid-DL. The description of provided ser-
vices could be accessed through URL: "server:port/Grid-DL/ServiceFacade?wsdl".
To administrate Grid-DL and monitor the state of all incoming requests we devel-
oped a simply web-interface available through URL: "server:port/Grid-DL/qtasks".
4 Interaction with semantic information service
The query to Grid-DL must be an OWL-class expression that would represent the
instances of desired resources. Upon query submission, Grid-DL returns a unique
request Id that will be used to retrieve results.
In its simplest form, when we do not use or take into account the domain ontology
repository, users should be familiar with the content of core system TBox in order to
send a query request using OWL Manchester syntax [7].
When using domain ontology repository, a client must specify in its request what
ontologies should be used during classification. The path to ontologies is specified
relative to the root of the domain ontology repository. For example:
"/general/operatingSystems.owl". Upon incoming request, Grid-DL will synchronize
with domain ontology repository and acquire all the necessary files that will be used
by OWL-reasoner during a query execution.
An interaction with domain ontology repository is carried out according to usual
procedures of interaction with distributed control revision system.
Let us consider a small example. A user that has an access to Grid system and is a
member of some virtual organization wants to conduct a molecular dynamics compu-
tation. He starts by browsing what domain ontology is used within his organization
and sees following declarations:
MolDynSubCluster GROMACS_Cluster or LAMMPS_Cluster
MolDynCE ComputingElement and partOf some (Cluster and
contains some MolecularDynamicsSubCluster)
GROMACS_App ApplicationSoftware and hasRunTimeEnvironment
some string [pattern "GROMACS"]
GROMACS_Host Host and describedBy some GROMACS_App
GROMACS_Cluster MPI_SubCluster and X86_64_SubCluster and
(SubCluster and describedBy some GROMACS_Host)
This ontology, among other thing, defines molecular dynamics software packages
and Grid resources capable of running them. The definition of MPI_SubCluster
and X86_64_SubCluster is drawn from more general ontology, which is used in
all virtual organizations. In particular there will be a definition of a MPI-enabled clus-
ter and x86-64 platform:
OPENMPI ApplicationSoftware and hasRunTimeEnvironment
value "OPENMPI"
MPICH ApplicationSoftware and hasRunTimeEnvironment
value "MPICH"
MPI_Library MPICH or OPENMPI
MPI_Host Host and describedBy some MPI_Library
MPI_SubCluster SubCluster and describedBy some MPI_Host
MPI_Cluster Cluster and contains some MPI_SubCluster
X86_64_Arch Architecture and hasPlatformType value "x86_64"
X86_64_Host Host and describedBy some X86_64_Arch
X86_64_SubCluster SubCluster and describedBy some X86_64_Host
X86_64_Cluster Cluster and contains some X86_64_SubCluster
At this stage our user adds his personal assertions, such as an available computing
element and finally defines a computing element he is looking for (CEForMyWork):
Availible_CE ComputingElement and hasState some
(CEState and hasRunningJobs value 0 and hasWaitingJobs
value 0 and hasFreeJobSlots some integer[>0])
MyVoACL AccessControlBaseRule and hasPrefix value "VO"
and hasSCN value "myVO"
CEForMyWork MolDynCE and Availible_CE and
hasAccessControlBaseRule some MyVoACL
Finally user submits CEForMyWork query to Grid-DL, specifying ontologies he
just used and retrieves all available computing elements on the Grid that could carry
out his task. This way user stays almost isolated from the complexity of the Grid.
5 Future work
When working with the LCH Grid, we acquire a knowledge base with over
900,000 axioms for more than 21,000 named individuals, with data property asser-
tions being dominant.
All modern OWL reasoners have significant difficulties classifying ontology of
such size and structure. In fact it takes more than few hours to complete. That is the
reason we are currently moving away from the tableaux reasoners because of severe
performance penalties that come with it. We are also in the process of switching our
core ontology to the OWL EL profile for the same reasons, sacrificing some expres-
sivity for polynomial complexity.
Work is being done to switch to ELK [8] reasoner, which has proved to be one of
the most well optimized reasoners for EL profile. Currently we are working on a suf-
ficient datatype support3 for ELK beyond EL profile in order to carry out our task.
6 Conclusion
Application of semantic technology opens up many possibilities and prospects for
further improvement of the basic elements of Grid systems, promoting the emergence
of new models of user interaction with them. We set a goal for "intellectualization" of
key Grid systems to promote it to a larger audience of users that sometimes have dif-
ficulties adjusting to way Grid is operated.
A source code of presented prototype4 is freely available for application and im-
provement.
7 References
1. Andreozzi S., Burke S., Donno F. et. al.: GLUE Schema Specification (version 1.3) –
http://glueschema.forge.cnaf.infn.it/Spec/V13
2. Czajkowski K., Fitzgerald S., Foster I., Kesselman C.: Grid information services for
distributed resource sharing. Proc. of the 10-th IEEE International Symposium on High
Performance Distributed Computing. – IEEE Press. – 2001. – P. 181-195.
3. Berkeley Database Information Index V5 Documentation – https://twiki.cern.ch
/twiki/bin/view/EGEE/BDII/
4. The Protégé Ontology Editor and Knowledge Acquisition System –
http://protege.stanford.edu/
5. OWLAPI Project homepage, http://owlapi.sourceforge.net/
6. Sirin E., Parsia B., Grau B. et al.: Pellet: A practical OWL-DL reasoner. Web Semantics:
science, services and agents on the World Wide Web. – 2007. – Vol. 5, N 2. – P. 51-53.
7. Horridge M., Drummond N., Goodwin J.: The Manchester OWL syntax. Second Interna-
tional Workshop OWL: Experiences and Directions (OWLED 2006). – 2006. – Vol. 216.
8. Yevgeny Kazakov, Markus Krötzsch, František Simančík. Concurrent Classification of EL
Ontologies. In Aroyo et al. (eds.): Proceedings of the 10th International Semantic Web
Conference (ISWC-11). LNCS 7032, Springer 2011.
3
https://elk-reasoner.googlecode.com/svn/branches/elk-parent-datatypes/
4
https://github.com/pospishniy/Grid-DL