From science gateways to commercial solutions

The European CloudSME project that incorporated 24 European SMEs, besides five academic partners, has finished its funded phase in March 2016. This presentation will provide a summary of the results of the project, and will analyze the challenges and differences when developing “SME Gateways”, when compared to “Science Gateways”. CloudSME started in 2013 with the aim to develop a cloud-based simulation platform for manufacturing and engineering SMEs. The project was based around industry use-cases, five of which were incorporated in the project from the start, and seven additional ones that were added as an outcome of an open call in January 2015. CloudSME utilized science gateway related technologies, such as the commercial CloudBroker Platform and the WS-PGRADE/gUSE Gateway Framework that were developed in the preceding SCI-BUS project. As most important outcome, the project successfully implemented 12 industry quality demonstrators that showcase how SMEs in the manufacturing and engineering sector can utilize cloud-based simulation services. Some of these solutions are already market-ready and currently being rolled out by the software vendor companies. Some others require further fine-tuning and the implementation of commercial interfaces before being put into the market. The CloudSME use-cases came from a very wide application spectrum. The project implemented, for example, an open marketplace for micro-breweries to optimize their production and distribution processes, an insole design validation service to be used by podiatrists and shoe manufacturers, a generic stock management solution for manufacturing SMEs, and also several “classical” high-performance computing case-studies, such as fluid dynamics simulations for model helicopter design, and dual-fuel internal combustion engine simulation. As the project generated significant impact and interest in the manufacturing sector, 10 CloudSME stakeholders established a follow-up company called CloudSME UG for the future commercialization of the results. Besides the success stories, this talk would also like to highlight the difficulties when transferring the outcomes of an academic research project to real commercial applications. The different mindset and approach of academic and industry partners presented a real challenge for the CloudSME project, with some interesting and valuable lessons learnt. The academic way of supporting SMEs did not always work well with the rather different working practices and culture of many participants. Also, the quality of support regarding operational solutions required by the SMEs is well beyond the typical support services academic institutions are prepared for. Finally, a clear lack of trust in academic solutions when compared to commercial solutions was also imminent. The talk will highlight some of these challenges underpinned by the implementation of the CloudSME use-cases

Towards Cloud Application Description Templates Supporting Quality of Service

Typical scientific, industrial and public sector applications require resource scalability and efficient resource utilization in order to serve a variable number of customers. Cloud computing provides an ideal solution to support such applications. However, the dynamic and intelligent utilization of cloud infrastructure resources from the perspective of cloud applications is not trivial. Although there have been several efforts to support the intelligent and coordinated deployment, and to a smaller extent also the run-time orchestration of cloud applications, no comprehensive solution has emerged until now that successfully leverages large scale near operational levels and ease of use. COLA is a European research project to provide a reference implementation of a generic and pluggable framework that supports the optimal and secure deployment and run-time orchestration of cloud applications. Such applications can then be embedded into workflows or science gateway frameworks to support complex application scenarios from user-friendly interfaces. A specific aspect of the cloud orchestration framework developed by COLA is the ability to describe complex application architectures incorporating several services. Besides the description of service components, the framework will also support the definition of various Quality of Service (QoS) parameters related to performance, economic viability and security. This paper concentrates on this latter aspect analysing how such application description templates can be developed based on existing standards and technologies

Virtual appliance size optimization with active fault injection

Virtual appliances store the required information to instantiate a functional Virtual Machine (VM) on Infrastructure as a Service (IaaS) cloud systems. Large appliance size obstructs IaaS systems to deliver dynamic and scalable infrastructures according to their promise. To overcome this issue, this paper offers a novel technique for virtual appliance developers to publish appliances for the dynamic environments of IaaS systems. Our solution achieves faster virtual machine instantiation by reducing the appliance size while maintaining its key functionality. The new virtual appliance optimization algorithm identifies the removable parts of the appliance. Then, it applies active fault injection to remove the identified parts. Afterward, our solution assesses the functionality of the reduced virtual appliance by applying the-appliance developer provided-validation algorithms. We also introduce a technique to parallelize the fault injection and validation phases of the algorithm. Finally, the prototype implementation of the algorithm is discussed to demonstrate the efficiency of the proposed algorithm through the optimization of two well-known virtual appliances. Results show that the algorithm significantly decreased virtual machine instantiation time and increased dynamism in IaaS systems. © 2012 IEEE

Molecular docking with Raccoon2 on clouds: extending desktop applications with cloud computing

Molecular docking is a computer simulation that predicts the binding affinity between two molecules, a ligand and a receptor. Large-scale docking simulations, using one receptor and many ligands, are known as structure-based virtual screening. Often used in drug discovery, virtual screening can be very computationally demanding. This is why user-friendly domain-specific web or desktop applications that enable running simulations on powerful computing infrastructures have been created. Cloud computing provides on-demand availability, pay-per-use pricing, and great scalability which can improve the performance and efficiency of scientific applications. This paper investigates how domain-specific desktop applications can be extended to run scientific simulations on various clouds. A generic approach based on scientific workflows is proposed, and a proof of concept is implemented using the Raccoon2 desktop application for virtual screening, WS-PGRADE workflows, and gUSE services with the CloudBroker platform. The presented analysis illustrates that this approach of extending a domain-specific desktop application can run workflows on different types of clouds, and indeed makes use of the on-demand scalability provided by cloud computing. It also facilitates the execution of virtual screening simulations by life scientists without requiring them to abandon their favourite desktop environment and providing them resources without major capital investment

High-level Description of Cloud Applications using TOSCA

Public sector organizations and SMEs are increasingly considering using cloud services in their everyday activities. At the one hand on-demand access to cloud services in a flexible and elastic way could result in significant cost savings due to more efficient and convenient utilization. Further it can also replace large investment costs with long-term operational costs. On the other hand, the take up of cloud computing by the public sector and Small- and Medium-size Enterprises (SME) is still relatively low due to limited application-level flexibility and shortages in cloud specific skills. To meet these requirements a generic framework is needed to support public sector organizations and SMEs to run large variety of applications in the cloud in a cost effective, flexible and seamless way. To address these challenges the European funded COLA (Cloud Orchestration at the Level of Application) [1] project is designing and developing a modular architecture called MiCADO (Microservices-based Cloud Application-level Dynamic Orchestrator) [2]. It provides optimized deployment and run-time orchestration for cloud applications. MiCADO can manage applications considering their specific deployment, execution, scalability and security requirements. To further address this challenge COLA uses TOSCA (Topology and Orchestration Specification for Cloud Applications [3] to describe applications to be executed in the cloud. Application developers can create so called Application Description Templates (ADT) to specify and submit their applications to the cloud through MiCADO. ADTs define two key properties of applications: topologies and policies. There are two approaches to define ADTs: using either command-line interfaces or graphical user interfaces. Command-line interface requires deep knowledge of the TOSCA specification and good YAML knowledge. Since application developers in the public sector organizations and at SMEs may not have this knowledge COLA’s priority is providing a GUI–based environment to enable application developers to describe their applications. The project investigated several GUI-based TOSCA development environments such as, OpenTOSCA Winery [4] and Alien 4 Cloud [5]. Winery generates XML-based specification of application topologies. The current Winery version automatically translates the XML-based TOSCA specifications into YAML to make them compatible with the latest TOSCA specification. Since each translation has its own limitations, some TOSCA features that are required in COLA, are lost in translation. The other limitation of Winery is that it does not support the definition of TOSCA policy specifications. Fig. 1 presents a simple topology template developed in Winery. Although Alien 4 Cloud supports the definition of cloud applications through a GUI environment, the generated description is not fully TOSCA compliant and cannot be parsed with most widely used TOSCA parsers. Considering the above listed limitations, COLA is developing a GUI-based environment to support application specification in TOSCA YAML v1.0. The extra feature of this environment will be a wide range support for policy specification, for example enabling development of deployment, execution, scalability and security policies

A Generic Framework and Methodology for Implementing Science Gateways for Analysing Molecular Docking Results

Molecular docking and virtual screening experiments require large computational and data resources and high-level user interfaces in the form of science gateways. While science gateways supporting such experiments are relatively common, there is a clearly identified need to design and implement more complex environments for further analysis of docking results. This paper describes a generic framework and a related methodology that supports the efficient development of such environments. The framework is modular enabling the reuse of already existing components. The methodology is agile and encourages the input and participation of end-users. A prototype implementation, based on the framework and methodology, of a science-gateway-based molecular docking environment for recommending a ligand-protein pair for next docking experiment is also presented and evaluated

Sharing Science Gateway Artefacts Through Repositories

Researchers want to run scientific experiments focusing on their disciplines. They do not want to know how and where the experiments are executed. Science gateways hide details by coordinating the execution of experiments using different infrastructures and workflow systems. ER-flow/SHIWA and SCI-BUS project developed repositories to share artefacts such as applications, portlets, workflows, etc. inside and among research communities. Sharing artefacts in re-positories enable gateway developers to reuse them when building a new gateway and/or creating a new application

Workflow level interoperation of grid data resources

The lack of widely accepted standards and the use of different middleware solutions divide today’s Grid resources into non-interoperable production Grid islands. On the other hand, more and more experiments require such a large number of resources that the interoperation of existing production Grids becomes inevitable. This paper, based on the current results of grid interoperation studies, defines generic requirements towards the workflow level interoperation of grid solutions. It concentrates on intra-workflow interoperation of grid data resources, as one of the key areas of generic interoperation, and describes through an example how existing tools can be extended to achieve the required level of interoperation

Extending Molecular Docking Desktop Applications with Cloud Computing Support and Analysis of Results

Structure-based virtual screening simulations, which are often used in drug discovery, can be very computationally demanding. This is why user-friendly domain-specific web or desktop applications that enable running simulations on powerful computing infrastructures have been created. This article investigates how domain-specific desktop applications can be extended to use cloud computing and how they can be part of scenarios that require sharing and analysing previous molecular docking results. A generic approach based on interviews with scientists and analysis of existing systems is proposed. A proof of concept is implemented using the Raccoon2 desktop application for virtual screening, WS-PGRADE workflows, gUSE services with the CloudBroker Platform, the structural alignment tool DeepAlign, and the ligand similarity tool LIGSIFT. The presented analysis illustrates that this approach of extending a domainspecific desktop application can use different types of clouds, thus facilitating the execution of virtual screening simulations by life scientists without requiring them to abandon their favourite desktop environment and providing them resources without major capital investment. It also shows that storing and sharing molecular docking results can produce additional conclusions such as viewing similar docking input files for verification or learning

Simulating Business Processes of Manufacturing SMEs on the Cloud

Simulating the efficiency of business processes could reveal crucial bottlenecks for manufacturing companies and could lead to significant optimizations resulting in decreased time to market, more efficient resource utilization, and larger profit. While such business optimization software is widely utilized by larger companies, SMEs typically do not have the required expertise and resources to efficiently exploit these advantages. The aim of this work is to explore how simulation software vendors and consultancies can extend their portfolio to SMEs by providing business process optimization based on a cloud computing platform. By executing simulation runs on the cloud, software vendors and associated business consultancies can get access to large computing power and data storage capacity on demand, run large simulation scenarios on behalf of their clients, analyze simulation results, and advise their clients regarding process optimization. The solution is mutually beneficial for both vendor/consultant and the end-user SME. End-user companies will only pay for the service without requiring large upfront costs for software licenses and expensive hardware. Software vendors can extend their business towards the SME market with potentially huge benefits