ClusterRAID: Architecture and Prototype of a Distributed Fault-Tolerant Mass Storage System for Clusters

During the past few years clusters built from commodity off-the-shelf (COTS) components have emerged as the predominant supercomputer architecture. Typically comprising a collection of standard PCs or workstations and an interconnection network, they have replaced the traditionally used integrated systems due to their better price/performance ratio. As paradigms shift from mere computing intensive to I/O intensive applications, mass storage solutions for cluster installations become a more and more crucial aspect of these systems. The inherent unreliability of the underlying components is one of the reasons why no system has been established as a standard storage solution for clusters yet. This thesis sets out the architecture and prototype implementation of a novel distributed mass storage system for commodity off-the-shelf clusters and addresses the issue of the unreliable constituent components. The key concept of the presented system is the conversion of the local hard disk drive of a cluster node into a reliable device while preserving the block device interface. By the deployment of sophisticated erasure-correcting codes, the system allows the adjustment of the number of tolerable failures and thus the overall reliability. In addition, the applied data layout considers the access behaviour of a broad range of applications and minimizes the number of required network transactions. Extensive measurements and functionality tests of the prototype, both stand-alone and in conjunction with local or distributed file systems, show the validity of the concept

Supramolecular electrode assemblies for bioelectrochemistry

For more than three decades, the field of bioelectrochemistry has provided novel insights into the catalytic mechanisms of enzymes, the principles that govern biological electron transfer, and has elucidated the basic principles for bioelectrocatalytic systems. Progress in biochemistry, bionanotechnology, and our ever increasing ability to control the chemistry and structure of electrode surfaces has enabled the study of ever more complex systems with bioelectrochemistry. This feature article highlights developments over the last decade, where supramolecular approaches have been employed to develop electrode assemblies that increase enzyme loading on the electrode or create more biocompatible environments for membrane enzymes. Two approaches are particularly highlighted: the use of layer-by-layer assembly, and the modification of electrodes with planar lipid membranes

Benchmarks and implementation of the ALICE high level trigger

The ALICE high level trigger combines and processes the full information from all major detectors in a large computer cluster. Data rate reduction is achieved by reducing the event rate by selecting interesting events (software trigger) and by reducing the event size by selecting sub-events and by advanced data compression. Reconstruction chains for the barrel detectors and the forward muon spectrometer have been benchmarked. The HLT receives a replica of the raw data via the standard ALICE DDL link into a custom PCI receiver card (HLT-RORC). These boards also provide a FPGA co-processor for data-intensive tasks of pattern recognition. Some of the pattern recognition algorithms (cluster finder, Hough transformation) have been re-designed in VHDL to be executed in the Virtex-4 FPGA on the HLT-RORC. HLT prototypes were operated during the beam tests of the TPC and TRD detectors. The input and output interfaces to DAQ and the data flow inside of HLT were successfully tested. A full-scale prototype of the dimuon-HLT achieved the expected data flow performance. This system was finally embedded in a GRID-like system of several distributed clusters demonstrating the scalability and fault-tolerance of the HL

AFS Monitoring: The CERN AFS Console

CERN's AFS installation serves between 1 and 2 billion accesses per day to its around 20'000 users. Keeping track of the system's overall status and trying to find problems before the users do is not a trivial task, esp. as the installation is growing in almost all aspects. This talk will present CERN's AFS Console, a Lemon- and web-based monitoring tool used by the AFS administrators at CERN to quickly identify problematic entities (servers, partitions, volumes etc.) and to assist them in solving the issues found

Synthese, Vergleich und Anwendung von Oxazolin Liganden für die Homogene Katalyse

For the first time, a collection of different oxazoline ligands with the core structures 2,2´-bioxazoline (box), 2-(pyridine-2-yl)-oxazoline (pyrox), 2-(2-methylpyridine-2-yl)-oxazoline (mepyrox) and 2-(quinolin-2-yl)-oxazoline (quinox) was prepared and studied regarding their sterical and electronical properties as well as the catalytic activity of their Ir(I) complexes. For the investigation of electronical and sterical properties with IR spectroscopy, Ir(I) carbonyl complexes of the oxazoline ligands were prepared. The application of the same Ir(I) metal center guaranteed a high comparability of the carbonyl complexes and the pre catalysts for C H activation and hydrogentation. Furthermore, the oxazolines were applied as ligands in heteroleptic Ru(II) complexes for surface immobilisation. For the synthesis of box structures, a three step procedure and for pyrox, mepyrox and quinox a two step procedure was developed. Both procedures were optimized to obtain high conversions and to allow easy workup of the single steps. In the first step, commercially available chiral aminols were coupled with carboxylic acids. Since a large variety of substituted starting materials is commercially available, a comprehensive variation of the target structures is possible. Good to excellent total yields were achieved for 20 structurally related compounds which were prepared in half gram scale. For the evaluation of the electronic properties of the oxazoline ligands, square planar Ir(I) dicarbonyl complexes were prepared and their corresponding νCO absorption frequencies were measured by IR spectroscopy. To prepare the complexes, [Ir(cis,cis-1,5-cyclooctadiene)Cl]2 was initially treated with different silver salts (AgPF6, AgBF4, Ag[tetrakis(3,5-bis(trifluoromethyl)phenyl)borate)], to exchange the chloride for a non coordinating counterion. Subsequently, the ligand was added to give complexes of the general composition [Ir(ligand)(cod)]X. These complexes were converted into dicarbonyl complexes by addition of stoichiometric amounts of CO gas at atmospheric pressure. The CO complexes were studied by ATR IR measurements of the solid compound or as solution in tetrahydrofurane. The interpretation of the IR measurements was supported by DFT calculations. The carbonyl stretching frequencies of the square planar dicarbonyl complexes[Ir(ligand)(CO)2]PF6 turned out to be mainly influenced by the steric properties of the oxazoline ligands, while trigonal bipyramidal monocarbonyl complexes [Ir(ligand)(cis,cis-1,5-cyclooctadiene)(CO)]PF6 reflected more the electronical properties of the ligands. The formation of heteroleptic Ru(II) complexes of the general composition [Ru(oxazoline)(bipyridine)X2] was investigated. The complexes were designed to contain an oxazoline ligand carrying the chiral information and a substituted bipyridine ligand, suitable for further functionalisation and immobilisation on an electrode surface. The complex synthesis started with [Ru(p-cymene)Cl2]2 or [Ru(S(CH3)2O)4(Cl)2] and the oxazoline ligand was introduced as first or second ligand. If the oxazoline was introduced as first ligand, the addition of a bipyridine led to bisheteroleptic bipyridine complexes. If the oxazoline was introduced as second ligand, an inseperable mixture, probably isomers, was obtained. The prepared oxazolines were tested as ligands in direct aromatic and aliphatic borylation. As catalytic system [Ir(cis,cis-1,5-cyclooctadiene)(OCH3)]2 was used in combination with the respective ligand and bis(picanolato)diboron served as boron source. Aromatic borylations were carried out in the neat monosubstituted arenes such as toluene, tert-butylbenzene, anisole, cyclohexylbenzene, trifluorotoluene and ethyl benzoate. The meta:para ratios of the products were investigated by 1H NMR spectroscopy, showing a purely substrate induced effect on the regioselectivity. Aliphatic borylations of n-octane and n-hexane were unsuccessful under the applied conditions. Hydridosilylether directed γ C H activation was carried out with a catalytic system of [Ir(cis,cis-1,5-cyclooctadiene)(OCH3)]2 and an oxazoline ligand instead of the usually applied 3,4,7,8 tetramethylphenanthroline ligand. Initially ketones or alcohols were transformed into their (hydrido)silyl ether derivatives, followed by a γ C H activation which led to the formation of an oxasilolane. Norbornene was added stochiometrically as hydrogen acceptor. The (hydrido)silyl ether formation was optimized and the stereochemical influence of the chiral ligands in the C H activation step was investigated. A racemic mixture of ((3,7 dimethyloctan 3 yl)oxy)diethylsilane served for this purpose as substrate regarding its kinetic resolution. The products were obtained in enantiomeric excess up to 44% ee. Precatalysts for homogeneous hydrogenation had the general composition [Ir(ligand)(cod)] [tetrakis(3,5-bis(trifluoromethyl)phenyl)borate)] and were prepared by initial mixing of [Ir(cis,cis-1,5-cyclooctadiene)(Cl)]2 with Ag[tetrakis(3,5-bis(trifluoromethyl)phenyl)borate)] and subsequent addition of the oxazoline ligand. The hydrogenations were carried out in neat substrate or in dichloromethane at 40 bar hydrogen pressure. The products were analyzed by 1H NMR spectroscopy and/or GC FID measurements. The oxazoline containing complexes led to yields up to 99% and showed a high chemoselectivity for C C double bonds when they were applied for the hydrogenation of α,β unsaturated ketones, but no stereoselectivity was observed.Erstmalig wurde eine Sammlung verschiedener Oxazolinliganden mit den Strukturtypen 2,2´-Bioxazolin (box), 2-(Pyridine-2-yl)-oxazolin (pyrox), 2-(2-Methylpyridine-2-yl)-oxazolin (mepyrox) und 2-(‚Chinolin-2-yl)-oxazolin (quinox), angelegt und deren sterische sowie elektronische Eigenschaften, sowie die katalytische Aktivität ihrer Ir(I) Komplexe, untersucht. Zur Analyse der elektronischen und sterischen Eigenschaften mit Hilfe der IR Spektroskopie wurden Ir(I) Carbonylkomplexe der Oxazoline synthetisiert. Die konsistente Verwendung des Ir(I) Metallzentrums gewährleistet eine gute Vergleichbarkeit zwischen den Carbonylkomplexen und den Präkatalysatoren für C H Aktivierung und Hydrierung. Des Weiteren wurden die dargestellten Oxazolinstrukturen als Liganden in heteroleptischen Ru(II) Komplexen zur zukünftigen Oberflächenimmobilisierung verwendet. Für die Darstellung der box Strukturen wurde eine zwei stufige und für die pyrox, mepyrox und quinox Strukturen eine drei stufige Syntheseroute entwickelt. In beiden Syntheserouten wurde der Schwerpunkt auf möglichst vollständige Umsätze gelegt, um zeitintensive Aufreinigungsschritte zu vermeiden. Als Reaktionspartner für die chiralen Aminole wurden kommerziell erhältliche Carbonsäuren gewählt. Durch die Vielfalt der kommerziell erhältlichen Ausgangsstoffe besteht die Möglichtkeit zur umfangreichen Variation der Zielstrukturen. Mit den entwickelten Syntheserouten wurden gute bis hervorragende Gesamtausbeuten erreicht und insgesamt 20 strukturell verwandte Verbindungen im halb Gramm Maßstab dargestellt. Für die Evaluierung der elektronischen Eigenschaften der Oxazolinliganden wurden quadratisch planare Ir(I) Dicarbonylkomplexe dargestellt und deren νCO Schwingungsfrequenzen mit Hilfe der Infrarotspektroskopie (IR) gemessen. Die Komplexe wurden ausgehend von [Ir(cis,cis-1,5-cyclooctadiene)Cl]2 durch eine neuentwickelte Syntheseroute dargestellt. Das [Ir(cis,cis-1,5-cyclooctadiene)Cl]2 wurde zunächst mit einem Silbersalz (AgPF6, AgBF4, Ag[tetrakis(3,5-bis(trifluoromethyl)phenyl)borat] zur Reaktion gebracht, um das Chlorid gegen ein nicht koordinierendes Gegenion auszutauschen. Daraufolgend wurde der Ligand zugegeben, um so Komplexe der allgemeinen Zusammensetzung [Ir(Ligand)(cis,cis-1,5-cyclooctadiene)]X zu erhalten. Diese Komplexe wurden durch die stöchiometrische Zugabe von CO Gas bei Atmosphärendruck in ihre Dicarbonylkomplexe überführt. Die Analyse der Carbonylkomplexe erfolgte per ATR IR Spektroskopie der festen Substanzen sowie durch Messungen ihrer Lösungen in Tetrahydrofuran. Die Interpretation der IR Daten wurde durch DFT Rechnungern unterstützt. Die Carbonyl schwingungsabsorptionen der Dicarbonylkomplexe [Ir(ligand)(CO)2]PF6 wurden überwiegend von den sterischen Eigenschaften der Oxazolinliganden beeinflusst, während die der Monocarbonylkomplexe [Ir(ligand)(cis,cis-1,5-cyclooctadiene)(CO)]PF6 hauptsächlich die elektronischen Eigenschaften der Liganden widerspigelten. Die Synthese von heteroleptischen Ru(II) Komplexen der allgemeinen Zusammensetzung [Ru(Oxazolin)(Bipyridin)X2] wurde ebenfalls untersucht. Die Komplexe sollten einen chiralen Oxazolinliganden sowie einen substituierten Bipyridin Liganden tragen. Der Bipyridinligand sollte zur Immobilisierung auf einer Elektrodenoberfläche geeignet sein, da in zukünftigen Projekten die Redoxeigenschaften der Komplexe auf einer solchen Elektrodenoberfläche studiert werden sollen. Die Komplexsynthese wurde entweder ausgehend von [Ru(p-cymene)Cl2]2 oder [Ru(S(CH3)2O)4(Cl)2] durchgeführt, wobei der Oxazolinligand als erster oder zweiter Ligand eingeführt wurde. Allerding konnte ein Bipyridin Ligand den zuerst eingeführten Oxazolinliganden vollständig aus dem Komplex verdrängen, sodass fast ausschließlich bisheteroleptische Bipyridinkomplexe gebildet wurden. Wurde der Oxazolin Ligand als zweiter eingeführt, bildeten sich die Produktkomplexe als untrennbare Mischungen, vermutlich aus verschiedenen Isomeren. Die gewünschten heteroleptischen Rutheniumkomplexes konnten nicht als isolierte Strukturen dargestellt werden. Die dargestellten Oxazoline wurden als Liganden in direkter aromatischer und aliphatischer Borylierung verwendet. Als katalytisches System wurde eine Kombination aus [Ir(cis,cis-1,5-cyclooctadiene)(OCH3)]2 und dem entsprechenden Liganden verwendet, wobei Bis(picanolato)diboran als Borquelle fungierte und die Reaktionen in reinem Substrat durchgeführt wurden. In der aromatischen Borylierung fanden monosubstituierte Aromaten wie Toluol, tert-Butylbenzol, Anisol, Cyclohexylbenzol, Trifluortoluol und Ethylbenzoat als Substrate Verwendung. Gegenstand der Analyse war die Bestimmung des meta:para Verhältnisses der Produkte durch 1H NMR Spektroskopie, wobei ein reiner substratinduzierter Effekt auf die Regioselektivität festgestellt werden konnte. Die aliphatische Borylierung von n-Oktan und n-Hexan gelang unter den angewendeten Bedingungen nicht. Die hydridosilylether dirigierte γ C H Aktivierung wurden mit einem katalytischen System aus [Ir(cis,cis-1,5-cyclooctadiene)(OCH3)]2 und einem Oxazolinliganden, der den üblicherweise verwendeten 3,4,7,8 tetramethylphenanthrolin Liganden ersetzte, durchgeführt. Zunächst wurden Ketone oder Alkohole in ihre (Hydrido)silylether umgesetzt, woraufhin eine γ C H Aktivierung unter Ausbildung eines Oxasilolans stattfand. Norbornen wurde als stöchiometrisch eingesetzter Wasserstoffakzeptor den Reaktionsmischungen zugefügt. Die Bildung der Hydridosilylether wurde optimiert und der stereochemische Einfluss der chiralen Liganden in der C H Aktivierung untersucht. Als Substrat diente für diesen Zweck ((3,7 Dimethyloctan 3 yl)oxy)diethylsilan, dessen kinetische Racemattrennung analysiert wurde. Die Produkte wurden mit enantiomeren Überschüssen bis zu 44% ee erhalten. Präkatalysatoren für die homogene Hydrierung waren von der generellen Zusammensetzung [Ir(ligand)(cis,cis-1,5-cyclooctadiene)][tetrakis(3,5-bis(trifluoromethyl)phenyl)borat] und wurden durch vorangehendes Mischen von [Ir(cis,cis-1,5-cyclooctadiene)Cl]2 mit Ag[tetrakis(3,5-bis(trifluoromethyl)phenyl)borat] und anschließender Zugabe des entsprechenden Oxazolin Liganden dargestellt. Die Hydrierungen wurden in reinem Substrat oder in Dichlormethan bei einem Wasserstoffdruck von 40 bar durchgeführt und die Produkte anhand von 1H-NMR Spektroskopie und/oder GC FID analysiert. Die oxazolinhaltigen Komplexe erzielten Ausbeuten bis zu 99% und zeigten eine hohe Chemoselektivität für C C Doppelbindungen bei der Verwendung von α,β ungesättigten Ketonen als Substrate. Eine Stereoselektivität konnte nicht beobachtet werden

OpenStack Summit

In response to the user demand for a light-weight provisioning of distributed file system shares, the OpenStack and Ceph teams at CERN have recently added Manila/CephFS to their service catalogues. While leveraging the operational experience with a 190'000 core OpenStack deployment and a 12 PB Ceph cluster for such a self-service kiosque suggested itself, the service design and setup phases were followed by a number of functionality and stress tests to ensure the individual components are ready for production use. The final service design and the results obtained during the pre-production phase, for instance when scaling to a large number of Manila and CephFS clients or the integration with Magnum/Kubernetes, will be presented alongside the initial use cases and our first experiences running these new services in production

Building an organic block storage service at CERN with Ceph

Emerging storage requirements, such as the need for block storage for both OpenStack VMs and file services like AFS and NFS, have motivated the development of a generic backend storage service for CERN IT. The goals for such a service include (a) vendor neutrality, (b) horizontal scalability with commodity hardware, (c) fault tolerance at the disk, host, and network levels, and (d) support for geo-replication. Ceph is an attractive option due to its native block device layer RBD which is built upon its scalable, reliable, and performant object storage system, RADOS. It can be considered an 'organic' storage solution because of its ability to balance and heal itself while living on an ever-changing set of heterogeneous disk servers. This work will present the outcome of a petabyte-scale test deployment of Ceph by CERN IT. We will first present the architecture and configuration of our cluster, including a summary of best practices learned from the community and discovered internally. Next the results of various functionality and performance tests will be shown: the cluster has been used as a backend block storage system for AFS and NFS servers as well as a large OpenStack cluster at CERN. Finally, we will discuss the next steps and future possibilities for Ceph at CERN