44 research outputs found
Proceedings of the 5th bwHPC Symposium
In modern science, the demand for more powerful and integrated research
infrastructures is growing constantly to address computational challenges
in data analysis, modeling and simulation. The bwHPC initiative, founded
by the Ministry of Science, Research and the Arts and the universities in
Baden-Württemberg, is a state-wide federated approach aimed at assisting
scientists with mastering these challenges. At the 5th bwHPC Symposium
in September 2018, scientific users, technical operators and government
representatives came together for two days at the University of Freiburg. The
symposium provided an opportunity to present scientific results that were
obtained with the help of bwHPC resources. Additionally, the symposium served
as a platform for discussing and exchanging ideas concerning the use of these
large scientific infrastructures as well as its further development
Virtualized Research Environments on the bwForCluster NEMO
The bwForCluster NEMO offers high performance
computing resources to three quite different scientific communities
(Elementary Particle Physics, Neuroscience and Microsystems
Engineering) encompassing more than 200 individual
researchers. To provide a broad range of software packages and
deal with the individual requirements, the NEMO operators seek
novel approaches to cluster operation [1]. Virtualized Research
Environments (VREs) can help to both separate different software
environments as well as the responsibilities for maintaining
the software stack. Research groups become more independent
from the base software environment defined by the cluster
operators. Operating VREs brings advantages like scientific
reproducibility, but may introduce caveats like lost cycles or the
need for layered job scheduling. VREs might open advanced
possibilities as e.g. job migration or checkpointing
A Sorting Hat For Clusters. Dynamic Provisioning of Compute Nodes for Colocated Large Scale Computational Research Infrastructures
Current large scale computational research infrastructures are composed of multitudes
of compute nodes fitted with similar or identical hardware. For practical
purposes, the deployment of the software operating environment to each compute
node is done in an automated fashion. If a data centre hosts more than one of
these systems – for example cloud and HPC clusters – it is beneficial to use the
same provisioning method for all of them. The uniform provisioning approach
unifies administration of the various systems and allows flexible dedication and
reconfiguration of computational resources. In particular, we will highlight the
requirements on the underlying network infrastructure for unified remote boot
but segregated service operations. Building upon this, we will present the Boot
Selection Service, allowing for the addition, removal or rededication of a node to
a given research infrastructure with a simple reconfiguration
bwForCluster NEMO. Forschungscluster für die Wissenschaft
In den ersten zweieinhalb Jahren seiner Betriebszeit entwickelte sich der bwFor-
Cluster NEMO zu einem signifikanten Baustein in den landesweiten Forschungsinfrastrukturen
für das »High Performance Computing«. Der in der Zwischenzeit
erhebliche Ausbau und die Erweiterung des Systems durch Shareholder ist ein Beleg
für die Tragfähigkeit seines Betriebsmodells und das Vertrauen in das landesweite
HPC-Konzept. Hierzu tragen nicht nur die lokale und landesweite Governance
bei, sondern ebenfalls der enge Austausch innerhalb der NEMO-Community.
Mit dem System wird eine stabile Umgebung für die diversen Bedürfnisse der
Wissenschafts-Communities bereitgestellt. Parallel dazu werden neue Betriebsund
Monitoring-Konzepte entwickelt und getestet. Aktuelle und neuartige Herausforderungen
liegen in der Unterstützung von »Virtualisierten Forschungsumgebungen
« und zukünftigen digitalen Workflows ebenso wie in der Containerisierung
und der Implementierung effektiver Betriebsmodelle gemeinsam mit den am
Standort Freiburg betriebenen Cloud-Infrastrukturen
Vorwort
Vorwort zu den "Proceedings of the 5th bwHPC Symposium
Elevated dietary zinc oxide levels do not have a substantial effect on porcine reproductive and respiratory syndrome virus (PPRSV) vaccination and infection
Background Porcine reproductive and respiratory syndrome virus (PRRSV) is one
of the most important infectious agents for the swine industry worldwide. Zinc
(Zn) salts, which are widely used as a dietary supplement in swine nutrition,
have shown antiviral effects in vitro as well as in vivo. The purpose of this
study was to determine the influence of dietary zinc oxide supplementation on
vaccination and challenge infection with PRRSV. Findings The clinical course
of PRRS and the success of vaccination with an experimental inactivated
vaccine were compared between animals receiving a conventional diet (50 ppm
Zn, control group) and diets supplemented with Zn oxide (ZnO) at final Zn
concentrations of 150 or 2,500 ppm. Pigs receiving higher dietary Zn levels
showed a tendency towards higher neutralizing antibody levels after infection,
while dietary Zn levels did not substantially influence the number of
antiviral IFN-gamma secreting cells (IFN-gamma-SC) or percentages of blood
immune cell subsets after infection. Finally, feeding higher dietary Zn levels
reduced neither clinical symptoms nor viral loads. Conclusions Our results
suggest that higher levels of dietary ZnO do not have the potential to
stimulate or modulate systemic immune responses after vaccination and
heterologous PRRSV infection to an extent that could improve the clinical and
virological outcome
Dynamic provisioning of a HEP computing infrastructure on a shared hybrid HPC system
Experiments in high-energy physics (HEP) rely on elaborate hardware, software and computing systems to sustain the high data rates necessary to study rare physics processes. The Institut fr Experimentelle Kernphysik (EKP) at KIT is a member of the CMS and Belle II experiments, located at the LHC and the Super-KEKB accelerators, respectively. These detectors share the requirement, that enormous amounts of measurement data must be processed and analyzed and a comparable amount of simulated events is required to compare experimental results with theoretical predictions. Classical HEP computing centers are dedicated sites which support multiple experiments and have the required software pre-installed. Nowadays, funding agencies encourage research groups to participate in shared HPC cluster models, where scientist from different domains use the same hardware to increase synergies. This shared usage proves to be challenging for HEP groups, due to their specialized software setup which includes a custom OS (often Scientific Linux), libraries and applications.
To overcome this hurdle, the EKP and data center team of the University of Freiburg have developed a system to enable the HEP use case on a shared HPC cluster. To achieve this, an OpenStack-based virtualization layer is installed on top of a bare-metal cluster. While other user groups can run their batch jobs via the Moab workload manager directly on bare-metal, HEP users can request virtual machines with a specialized machine image which contains a dedicated operating system and software stack. In contrast to similar installations, in this hybrid setup, no static partitioning of the cluster into a physical and virtualized segment is required. As a unique feature, the placement of the virtual machine on the cluster nodes is scheduled by Moab and the job lifetime is coupled to the lifetime of the virtual machine. This allows for a seamless integration with the jobs sent by other user groups and honors the fairshare policies of the cluster. The developed thin integration layer between OpenStack and Moab can be adapted to other batch servers and virtualization systems, making the concept also applicable for other cluster operators.
This contribution will report on the concept and implementation of an OpenStack-virtualized cluster used for HEP work ows. While the full cluster will be installed in spring 2016, a test-bed setup with 800 cores has been used to study the overall system performance and dedicated HEP jobs were run in a virtualized environment over many weeks. Furthermore, the dynamic integration of the virtualized worker nodes, depending on the workload at the institute\u27s computing system, will be described
Dynamic Virtualized Deployment of Particle Physics Environments on a High Performance Computing Cluster
The NEMO High Performance Computing Cluster at the University of Freiburg has
been made available to researchers of the ATLAS and CMS experiments. Users
access the cluster from external machines connected to the World-wide LHC
Computing Grid (WLCG). This paper describes how the full software environment
of the WLCG is provided in a virtual machine image. The interplay between the
schedulers for NEMO and for the external clusters is coordinated through the
ROCED service. A cloud computing infrastructure is deployed at NEMO to
orchestrate the simultaneous usage by bare metal and virtualized jobs. Through
the setup, resources are provided to users in a transparent, automatized, and
on-demand way. The performance of the virtualized environment has been
evaluated for particle physics applications
High-dose dietary zinc oxide mitigates infection with transmissible gastroenteritis virus in piglets
Zinc (Zn) supplementation has been shown to reduce the incidence of diarrhea
and to protect animals from intestinal diseases, but the mechanisms of this
protective effect against virus infection in vivo have not yet been
elucidated. Transmissible gastroenteritis virus (TGEV) causes diarrhea in
piglets with an age-dependent decrease of severity. RESULTS: We used 60 weaned
piglets that were divided into three groups to evaluate the effect of
different Zn levels added to a conventional diet (50 mg Zn/kg diet, Znlow,
control group). The other groups received the diet supplemented with ZnO at
final concentrations of 150 mg Zn/kg diet (Znmed), or 2,500 mg/kg diet
(Znhigh). Oral challenge infection with TGEV was performed when the pigs had
been fed for 1 week with the respective diet. Half of the piglets of each
group were sacrificed at day 1 and 18 after challenge infection. Fecal
consistency was improved and body weights increased in the Znhigh group when
compared to the other groups, but no direct effect of Zn concentrations in the
diet on fecal TGEV shedding and mucosal immune responses was detectable.
However, in the Znhigh group, we found a prevention of villus atrophy and
decreased caspase-3-mediated apoptosis of jejunal epithelium. Furthermore,
pigs receiving high Zn diet showed a down-regulation of interferon (IFN)-α,
oligoadenylate synthetase (OAS), Zn transporter SLC39A4 (ZIP4), but up-
regulation of metallothionein-1 (MT1), as well as the Zn transporters SLC30A1
(ZnT1) and SLC30A5 (ZnT5). In addition, forskolin-induced chloride secretion
and epithelial resistance were controlled at a physiological level in the
Znhigh but not the other groups. Finally, in the Znhigh group, we documented
an earlier and higher systemic TGEV-specific serum antibody response.
CONCLUSIONS: These results suggest that high dietary Zn could provide enhanced
protection in the intestinal tract and stimulate the systemic humoral immune
response against TGEV infection