Georg Birkenheuer

Non-intrusive virtualization management using libvirt

The success of server virtualization has let to the deployment of a huge number of virtual machines in todays data centers, making a manual virtualization management very labor-intensive. The development of appropriate management solutions is hindered by the various management interfaces of different hypervisors. Therefore, a uniform management can be simplified by a layer abstracting from these dedicated hypervisor interfaces. The libvirt management library provides such an interface to different hypervisors. Unfortunately, remote hypervisor management using libvirt has not been possible without altering the managed servers. To overcome this limitation, we have integrated remote hypervisor management facilities into the libvirt driver infrastructure for VMware ESX and Microsoft Hyper-V. This paper presents the resulting architecture as well as experiences gained during the implementation process.

A Single Sign-On Infrastructure for Science Gateways on a Use Case for Structural Bioinformatics

Structural bioinformatics applies computational methods to analyze and model three-dimensional molecular structures. There is a huge number of applications available to work with structural data on large scale. Using these tools on distributed computing infrastructures (DCIs), however, is often complicated due to a lack of suitable interfaces. The MoSGrid (Molecular Simulation Grid) science gateway provides an intuitive user interface to several widely-used applications for structural bioinformatics, molecular modeling, and quantum chemistry. It ensures the confidentiality, integrity, and availability of data via a granular security concept, which covers all layers of the infrastructure. The security concept applies SAML (Security Assertion Markup Language) and allows trust delegation from the user interface layer across the high-level middleware layer and the Grid middleware layer down to the HPC facilities. SAML assertions had to be integrated into the MoSGrid infrastructure in several places: the workflow-enabled Grid portal WS-PGRADE (Web Services Parallel Grid Runtime and Developer Environment), the gUSE (Grid User Support Environment) DCI services, and the cloud file system XtreemFS. The presented security infrastructure allows a single sign-on process to all involved DCI components and, therefore, lowers the hurdle for users to utilize large HPC infrastructures for structural bioinformatics.

The Gain of Overbooking

This paper analyzes the effect of overbooking for scheduling systems in a commercial environment. In this scenario each job is associated with a release time and a finishing deadline as well as a fee for a successful execution and a penalty for violating the deadline. The core idea is to exploit overestimations of required job execution times, providing an opportunity to aggressively schedule additional jobs. The proposed probabilistic scheduler is based on histories of job execution times, device failure rates, and penalties for SLA service violations. This paper includes a theoretical background and a mathematical model of the overbooking approach and a simulative evaluation with a synthetic workload on a single-processor system.

Reformulating XPath queries and XSLT queries on XSLT views

Applications using XML for data representation very often use different XML formats and thus require the transformation of XML data. The common approach transforms entire XML documents from one format into another, e.g. by using an XSLT stylesheet. Different from this approach, we use an XSLT stylesheet in order to transform a given XPath query or a given XSLT query so that we retrieve and transform only that part of the XML document, which is sufficient to answer the given query. Among other things, our approach avoids problems of replication, saves processing time, and in distributed scenarios, transportation costs.

Quantum chemical meta-workflows in MoSGrid

Quantum chemical workflows can be built up within the science gateway Molecular Simulation Grid. Complex workflows required by the end users are dissected into smaller workflows that can be combined freely to larger meta‐workflows. General quantum chemical workflows are described here as well as the real use case of a spectroscopic analysis resulting in an end‐user desired meta‐workflow. All workflow features are implemented via Web Services Parallel Grid Runtime and Developer Environment and submitted to UNICORE. The workflows are stored in the Molecular Simulation Grid repository and ported to the SHIWA repository. Copyright

Virtualized HPC: a contradiction in terms?

System virtualization has become the enabling technology to manage the increasing number of different applications inside data centers. The abstraction from the underlying hardware and the provision of multiple virtual machines (VM) on a single physical server have led to a consolidation and more efficient usage of physical servers. The abstraction from the hardware also eases the provision of applications on different data centers, as applied in several cloud computing environments. In this case, the application need not adapt to the environment of the cloud computing provider, but can travel around with its own VM image, including its own operating system and libraries. System virtualization and cloud computing could also be very attractive in the context of high‐performance computing (HPC). Today, HPC centers have to cope with both, the management of the infrastructure and also the applications. Virtualization technology would enable these centers to focus on the infrastructure, while the users, collaborating inside their virtual organizations (VOs), would be able to provide the software. Nevertheless, there seems to be a contradiction between HPC and cloud computing, as there are very few successful approaches to virtualize HPC centers. This work discusses the underlying reasons, including the management and performance, and presents solutions to overcome the contradiction, including a set of new libraries. The viability of the presented approach is shown based on evaluating a selected parallel, scientific application in a virtualized HPC environment. Copyright

Reservation-Based Overbooking for HPC Clusters

HPC environments are not only used in research and academia anymore, but are also becoming commercially available and successful. HPC resource providers, which offer HPC services over the Internet, have to ensure a very high utilization rate to be competitive and profitable. One solution to improve utilization is the use of overbooking. This paper shows an improved overbooking approach for HPC providers that serves this purpose. Resources are not assigned to a job until it actually starts. This enhances the schedulers degree of freedom and therefore improves the overbooking performance. We evaluated the potential of this approach using real-world job traces. Given a sufficient expected demand, overbooking is applicable and provides additional profit.

Workflow-enhanced conformational analysis of guanidine zinc complexes via a science gateway

The new science gateway MoSGrid (Molecular Simulation Grid) enables users to submit and process molecular simulation studies on a large scale. A conformational analysis of guanidine zinc complexes, which are active catalysts in the ring-opening polymerization of lactide, is presented as an example. Such a large-scale quantum chemical study is enabled by workflow technologies. Two times 40 conformers have been generated, for two guanidine zinc complexes. Their structures were optimized using Gaussian03 and the energies processed within the quantum chemistry portlet of the MoSGrid portal. All meta- and post-processing steps have been performed in this portlet. All workflow features are implemented via WS-PGRADE and submitted to UNICORE.

A Science Gateway Getting Ready for Serving the International Molecular Simulation Community

The project MoSGrid (Molecular Simulation Grid) has been developing a web-based science gateway supporting the community with various services for quantum chemistry, molecular modeling, and docking. Users gain access to distributed computing infrastructures (DCIs) via intuitive user interfaces for sophisticated tools, specialized workflows, and distributed repositories. Currently, the MoSGrid community consists of about 120 users from a number of fields related to chemistry and bioinformatics located in Germany. However, the underlying security infrastructure is generally applicable and can be deployed in arbitrary projects. MoSGrid intends to address the international community by participating in the EU-projects SCI-BUS (Scientific gateway Based User Support) and ER-flow (Building an European Research Community through Interoperable Workflows and Data), and collaborating with the EU-project EDGI (European Desktop Grid Initiative).

Molecular simulation grid

MoSGrid is the acronym for Molecular Simulation Grid, a BMBF funded joint research project with the aim to offer grid services for the broad field of molecular simulations in the D-Grid infrastructure. Besides tendering various codes ranging from quantum molecular calculations (e.g. Gaussian, Turbomole) via molecular dynamics (e.g. Gromacs) to docking approaches (e.g. FlexX) for high performance computing, one of the main goals is the integration of metadata annotation for data mining and knowledge generation. Molecular simulation codes and computational resources are accessed via the MoSGrid portal (http://www.mosgrid.de), which will offer intuitive access to various tools and will support the users with workflows, for an easy import of molecular data, a simple setup and submission of calculations as well as extraction of relevant results. The portal will hide the complexity of the underlying technology by providing a unified user interface making computational chemistry in general more readily available. MoSGrid’s server-based portal is available as open-access and open-source software. Users are relieved from software installations and do not need to have knowledge about the underlying infrastructure. The portal includes portlets specifically set up for the various simulation programs. Commonly used workflows, simple or complex, can be stored in recipe repositories and are available for every user. Moreover, users can develop, improve, publish, and use workflows for their everyday tasks.