Αποθηκευτικά συστήματα με δυνατότητα κλιμάκωσης σε eXascale περιβάλλοντα

Οι επιστημονικοί υπολογισμοί μεγάλης κλίμακας είναι εξαιρετικά απαιτητικοί με αποτέλεσμα να έχουν μεγάλες ανάγκες σε υπολογιστική ισχύ. Οι παράλληλοι υπολογισμοί και τα παράλληλα συστήματα αρχείων αναγνωρίζονται ως η μόνη εφικτή λύση σε αυτού του είδους τα προβλήματα, ενώ οι διεργασίες εισόδου/εξόδου αποτελούν το σημαντικότερο σημείο συμφόρησης στην απόδοση των εφαρμογών. Οι σημαντικότεροι παράγοντες που επηρεάζουν την I/O απόδοση είναι ο αριθμός των παράλληλων διεργασιών που συμμετέχουν στις μεταφορές των δεδομένων, το μέγεθος της κάθε μεταφοράς καθώς και τα διάφορα I/O μοτίβα πρόσβασης. Τα διαμοιραζόμενα συστήματα αρχείων έχουν σημαντικούς περιορισμούς όταν εφαρμόζονται σε μεγάλης κλίμακας συστήματα, επειδή το εύρος ζώνης δεν κλιμακώνει οικονομικά αλλά και γιατί η I/O κίνηση στην δικτυακή υποδομή και στους αποθηκευτικούς κόμβους μπορεί να επηρεαστεί από άλλες ξένες διεργασίες/εφαρμογές. Στοχεύοντας στην επίλυση των πιο πάνω περιορισμών αναπτύχθηκε το πλαίσιο ΙΚΑΡΟΣ ως ένας μηχανισμός που επιτρέπει το συντονισμό, με δυναμικό τρόπο, της Ι/Ο αρχιτεκτονικής, χρησιμοποιώντας συγκεκριμένες παραμέτρους εισόδου. Το ΙΚΑΡΟΣ παρέχει συντονισμένες παράλληλες μεταφορές δεδομένων στην συνολική ροή (τοπική- απομακρυσμένη πρόσβαση), με αποτέλεσμα τη μείωση του ανταγωνισμού, για πόρους, μεταξύ των αποθηκευτικών και δικτυακών μέσων. Δημιουργεί, δυναμικά, αποκλειστικές/ήμι-αποκλειστικές συστοιχίες αποθηκευτικών μέσων ανά διεργασία, με αποτέλεσμα τη βελτίωση της Ι/Ο απόδοσης κατά 33% χρησιμοποιώντας το 1/3 των διαθέσιμων σκληρών δίσκων.High performance computing (HPC) has crossed the Petaflop mark and is reaching the Exaflop range quickly. The exascale system is projected to have millions of nodes, with thousands of cores for each node. At such an extreme scale, the substantial amount of concurrency can cause a critical contention issue for I/O system. This study proposes a dynamically coordinated I/O architecture for addressing some of the limitations that current parallel file systems and storage architectures are facing with very large-scale systems. The fundamental idea is to coordinate I/O accesses according to the topology/profile of the infrastructure, the load metrics, and the I/O demands of each application. The measurements have shown that by using IKAROS approach we can fully utilize the provided I/O and network resources, minimize disk and network contention, and achieve better performance

Strategy, design, management and administration of large Digital Libraries and Archives

Institute of Information Studies and LibrarianshipÚstav informačních studií a knihovnictvíFaculty of ArtsFilozofická fakult

Union Catalogs at the Crossroad

The Andrew W. Mellon Foundation and the National Library of Estonia organized a Conference on Union Catalogs which took place in Tallinn, in the National Library of Estonia on October 17-19, 2002. The Conference presented and discussed analytical papers dealing with various aspects of designing and implementing union catalogs and shared cataloging systems as revealed through the experiences of Eastern European, Baltic and South African research libraries. Here you can find the texts of the conference papers and the list of contributors and participants

Library Automation Domain Ontology

Disertace je věnována problematice automatizace knihoven. Zkoumá vztahy mezi oblastí automatizace knihoven a knihovními systémy a zohledňuje přitom potřeby knihoven v souvislosti s problematikou výběru knihovního softwaru. Cílem disertace bylo vytvořit doménovou ontologii pro oblast automatizace knihoven a navrhnout nástroje pro podporu rozhodování při výběru knihovního softwaru. V rámci disertace byla vytvořena doménová ontologie popisující oblast automatizace knihoven ve vztahu ke knihovním systémům, které jsou zasazeny do širšího kontextu oblasti automatizace knihoven a je na ně nahlíženo z hlediska potřeb knihoven. Z účelem získání termínů pro názvy entit v ontologii byla provedena analýza odborných textů vztahujících se k problematice automatizace knihoven a knihovních systémů, pro kterou byl využit softwarový nástroj Voyant Tools. Vlastnosti a vztahy entit v ontologii jsou založeny na výsledcích kvalitativního průzkumu potřeb knihoven ve vztahu ke knihovním softwarům. Na základě doménové ontologie byly vytvořeny vývojové diagramy, které ilustrují rozhodovací proces knihovny při výběru knihovního systému. Vedlejším výstupem disertační práce je metodická příručka pro knihovny Připravujeme změnu knihovního softwaru.The dissertation focuses on library automation. It examines relationships between the field of library automation and library management systems and the needs of libraries in relation to the process of library software selection. The main goal of the dissertation has been to create a library automation domain ontology and to develop tools to support a decision-making process of library software selection. The domain ontology has been created; it describes the field of library automation in relation to library systems, which are set in the broader context of the field of library automation and are regarded in terms of needs of libraries in connection to library software change. To obtain terms for ontology entity names both quantitative and mixed research methods were used, namely the analysis of scholarly texts on library automation and library systems; text analyses were performed using Voyant Tools software. Object properties and relationships among entities in ontology are based on the results of a qualitative survey of the needs of libraries in relation to the library management software. Based on the domain ontology, flowcharts have been created that illustrate the library's decision-making process when selecting a library management system. During the work on the dissertation, a methodological...Institute of Information Studies and LibrarianshipÚstav informačních studií a knihovnictvíFaculty of ArtsFilozofická fakult

Radio spectroscopy and space science with VLBI radio telescopes for Solar System research

Only a tiny fraction of the universe has been studied even though the possibilities are unlimited given the current technologies, the resources and the time. To optimize the use of resources, the Metsähovi antenna and the existing VLBI processing hardware were exploited to study a broad variety of space phenomena. The research began with radio spectroscopy of the celestial bodies of our Solar System. Every object emits certain spectral signatures at several radio frequencies depending on its chemical molecules. Earth-based observations of the emitted radio spectral signal help to determine the composition of the structure and atmosphere of the planets. A unique method for processing the data captured by VLBI radio telescopes for radio spectroscopy purposes was developed during this work. Although the initial research focused on planetary bodies, it later shifted to the spacecraft motion. This new aim included studying ground support to planetary and deep-space mission spacecraft with VLBI radio telescopes, which opened up possibilities for collaboration between space agencies and radio astronomers. In addition, with VLBI phase-referencing, a high accuracy estimation of the spacecraft state vectors could be obtained. These new tools provide an opportunity for studying a broad variety of physical processes, including the dynamics of planetary atmospheres, geodynamical diagnostics of the interior of planets, fundamental physics effects of spacecraft motion and solar wind characterization. For instance, we organised a VLBI tracking session of Venus Express that involved 10 antennae and it estimated the spacecraft position with a precision of few hundred metres. The most interesting physical process for further investigation was the characterisation of the solar wind along the propagation path. The phase fluctuations on the signal allowed us to study essential parameters of the interplanetary scintillations, such as the phase scintillation index, bandwidth of scintillations or spectral broadening and their dependence on the solar elongation, distance to the target, celestial position of the spacecraft and radio telescopes. A scintillation and electron density model as a function of solar elongation was developed based on the data collected during two years. This model is powerful for improving the accurate determination of the spacecraft state vectors

The early development of the thought of Christos Yannaras

EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Development and application of methodologies and infrastructures for cancer genome analysis within Personalized Medicine

Programa de Doctorat en Biomedicina / Tesi realitzada al Barcelona Supercomputing Cener (BSC)[eng] Next-generation sequencing (NGS) has revolutionized biomedical sciences, especially in the area of cancer. It has nourished genomic research with extensive collections of sequenced genomes that are investigated to untangle the molecular bases of disease, as well as to identify potential targets for the design of new treatments. To exploit all this information, several initiatives have emerged worldwide, among which the Pan-Cancer project of the ICGC (International Cancer Genome Consortium) stands out. This project has jointly analyzed thousands of tumor genomes of different cancer types in order to elucidate the molecular bases of the origin and progression of cancer. To accomplish this task, new emerging technologies, including virtualization systems such as virtual machines or software containers, were used and had to be adapted to various computing centers. The portability of this system to the supercomputing infrastructure of the BSC (Barcelona Supercomputing Center) has been carried out during the first phase of the thesis. In parallel, other projects promote the application of genomics discoveries into the clinics. This is the case of MedPerCan, a national initiative to design a pilot project for the implementation of personalized medicine in oncology in Catalonia. In this context, we have centered our efforts on the methodological side, focusing on the detection and characterization of somatic variants in tumors. This step is a challenging action, due to the heterogeneity of the different methods, and an essential part, as it lays at the basis of all downstream analyses. On top of the methodological section of the thesis, we got into the biological interpretation of the results to study the evolution of chronic lymphocytic leukemia (CLL) in a close collaboration with the group of Dr. Elías Campo from the Hospital Clínic/IDIBAPS. In the first study, we have focused on the Richter transformation (RT), a transformation of CLL into a high-grade lymphoma that leads to a very poor prognosis and with unmet clinical needs. We found that RT has greater genomic, epigenomic and transcriptomic complexity than CLL. Its genome may reflect the imprint of therapies that the patients received prior to RT, indicating the presence of cells exposed to these mutagenic treatments which later expand giving rise to the clinical manifestation of the disease. Multiple NGS- based techniques, including whole-genome sequencing and single-cell DNA and RNA sequencing, among others, confirmed the pre-existence of cells with the RT characteristics years before their manifestation, up to the time of CLL diagnosis. The transcriptomic profile of RT is remarkably different from that of CLL. Of particular importance is the overexpression of the OXPHOS pathway, which could be used as a therapeutic vulnerability. Finally, in a second study, the analysis of a case of CLL in a young adult, based on whole genome and single-cell sequencing at different times of the disease, revealed that the founder clone of CLL did not present any somatic driver mutations and was characterized by germline variants in ATM, suggesting its role in the origin of the disease, and highlighting the possible contribution of germline variants or other non-genetic mechanisms in the initiation of CLL