In order to cope with the challenges expected during the LHC Run 2 CMS put in a number of enhancements into the main software packages and the tools used for centrally managed processing. In the ...presentation we will highlight these improvements that allow CMS to deal with the increased trigger output rate, the increased pileup and the evolution in computing technology. The overall system aims at high flexibility, improved operational flexibility and largely automated procedures. The tight coupling of workflow classes to types of sites has been drastically relaxed. Reliable and high-performing networking between most of the computing sites and the successful deployment of a data-federation allow the execution of workflows using remote data access. That required the development of a largely automatized system to assign workflows and to handle necessary pre-staging of data. Another step towards flexibility has been the introduction of one large global HTCondor Pool for all types of processing workflows and analysis jobs. Besides classical Grid resources also some opportunistic resources as well as Cloud resources have been integrated into that Pool, which gives reach to more than 200k CPU cores.
Abstract
Particle accelerators are an important tool to study the fundamental properties of elementary particles. Currently the highest energy accelerator is the LHC at CERN, in Geneva, Switzerland. ...Each of its four major detectors, such as the CMS detector, produces dozens of Petabytes of data per year to be analyzed by a large international collaboration. The processing is carried out on the Worldwide LHC Computing Grid, that spans over more than 170 compute centers around the world and is used by a number of particle physics experiments. Recently the LHC experiments were encouraged to make increasing use of HPC resources. While Grid resources are homogeneous with respect to the used Grid middleware, HPC installations can be very different in their setup. In order to integrate HPC resources into the highly automatized processing setups of the CMS experiment a number of challenges need to be addressed. For processing, access to primary data and metadata as well as access to the software is required. At Grid sites all this is achieved via a number of services that are provided by each center. However at HPC sites many of these capabilities cannot be easily provided and have to be enabled in the user space or enabled by other means. At HPC centers there are often restrictions regarding network access to remote services, which is again a severe limitation. The paper discusses a number of solutions and recent experiences by the CMS experiment to include HPC resources in processing campaigns.
The aim of this study was to investigate the nature and severity of the arm complaints among breast cancer patients after axillary lymph node dissection (ALND) and to study the effects of this ...treatment-related morbidity on daily life and well-being. 400 women, who underwent ALND as part of breast cancer surgery, filled out a treatment-specific quality of life questionnaire. The mean time since ALND was 4.7 years (range 0.3–28 years). More than 20% of patients reported pain, numbness, or loss of strength and 9% reported severe oedema. None of the complaints appeared to diminish over time. Irradiation of the axilla and supraclavicular irradiation were associated with a 3.57-fold higher risk of oedema (ods ratio (OR) 3.57; 95% confidence interval (CI) 1.66–7.69) causing many patients to give up leisure activities or sport. Women who underwent irradiation of the breast or chest wall more often reported to have a sensitive scar than women who did not receive radiotherapy. Women <45 years of age had an approximately 6 times higher risk of numbness of the arm (OR 6.49; 95% CI 2.58–16.38) compared with those ⩾65 years of age; they also encountered more problems doing their household chores. The results of the present study support the introduction of less invasive techniques for the staging of the axilla, sentinel node biopsy being the most promising.
The prompt reconstruction of the data recorded from the Large Hadron Collider (LHC) detectors has always been addressed by dedicated resources at the CERN Tier-0. Such workloads come in spikes due to ...the nature of the operation of the accelerator and in special high load occasions experiments have commissioned methods to distribute (spill-over) a fraction of the load to sites outside CERN. The present work demonstrates a new way of supporting the Tier-0 environment by provisioning resources elastically for such spilled-over workflows onto the Piz Daint Supercomputer at CSCS. This is implemented using containers, tuning the existing batch scheduler and reinforcing the scratch file system, while still using standard Grid middleware. ATLAS, CMS and CSCS have jointly run selected prompt data reconstruction on up to several thousand cores on Piz Daint into a shared environment, thereby probing the viability of the CSCS high performance computer site as on demand extension of the CERN Tier-0, which could play a role in addressing the future LHC computing challenges for the high luminosity LHC.
How modern humans dispersed into Eurasia and Australasia, including the number of separate expansions and their timings, is highly debated 1, 2. Two categories of models are proposed for the ...dispersal of non-Africans: (1) single dispersal, i.e., a single major diffusion of modern humans across Eurasia and Australasia 3–5; and (2) multiple dispersal, i.e., additional earlier population expansions that may have contributed to the genetic diversity of some present-day humans outside of Africa 6–9. Many variants of these models focus largely on Asia and Australasia, neglecting human dispersal into Europe, thus explaining only a subset of the entire colonization process outside of Africa 3–5, 8, 9. The genetic diversity of the first modern humans who spread into Europe during the Late Pleistocene and the impact of subsequent climatic events on their demography are largely unknown. Here we analyze 55 complete human mitochondrial genomes (mtDNAs) of hunter-gatherers spanning ∼35,000 years of European prehistory. We unexpectedly find mtDNA lineage M in individuals prior to the Last Glacial Maximum (LGM). This lineage is absent in contemporary Europeans, although it is found at high frequency in modern Asians, Australasians, and Native Americans. Dating the most recent common ancestor of each of the modern non-African mtDNA clades reveals their single, late, and rapid dispersal less than 55,000 years ago. Demographic modeling not only indicates an LGM genetic bottleneck, but also provides surprising evidence of a major population turnover in Europe around 14,500 years ago during the Late Glacial, a period of climatic instability at the end of the Pleistocene.
•Newly generated pre-Neolithic European mtDNA genomes triple the number available•Clade M found for the first time in Europe, prior to the Last Glacial Maximum bottleneck•Rapid single dispersal of all non-Africans less than 55,000 years ago•Previously unknown major population shift in Europe at the end of the Pleistocene
Posth et al. recover 35 new mitochondrial genomes from Late Pleistocene and early Holocene European hunter-gatherers. Major human mtDNA haplogroup M, absent in contemporary Europeans, is discovered in several pre-Last Glacial Maximum individuals. Demographic modeling reveals a major population turnover during the Late Glacial ∼14,500 years ago.
CMS will require access to more than 125k processor cores for the beginning of Run 2 in 2015 to carry out its ambitious physics program with more and higher complexity events. During Run1 these ...resources were predominantly provided by a mix of grid sites and local batch resources. During the long shut down cloud infrastructures, diverse opportunistic resources and HPC supercomputing centers were made available to CMS, which further complicated the operations of the submission infrastructure. In this presentation we will discuss the CMS effort to adopt and deploy the glideinWMS system as a common resource provisioning layer to grid, cloud, local batch, and opportunistic resources and sites. We will address the challenges associated with integrating the various types of resources, the efficiency gains and simplifications associated with using a common resource provisioning layer, and discuss the solutions found. We will finish with an outlook of future plans for how CMS is moving forward on resource provisioning for more heterogenous architectures and services.
Almost 150 years after the first identification of Neandertal skeletal material, the cognitive and symbolic abilities of these populations remain a subject of intense debate. We present 99 new ...Neandertal remains from the Troisième caverne of Goyet (Belgium) dated to 40,500-45,500 calBP. The remains were identified through a multidisciplinary study that combines morphometrics, taphonomy, stable isotopes, radiocarbon dating and genetic analyses. The Goyet Neandertal bones show distinctive anthropogenic modifications, which provides clear evidence for butchery activities as well as four bones having been used for retouching stone tools. In addition to being the first site to have yielded multiple Neandertal bones used as retouchers, Goyet not only provides the first unambiguous evidence of Neandertal cannibalism in Northern Europe, but also highlights considerable diversity in mortuary behaviour among the region's late Neandertal population in the period immediately preceding their disappearance.
The CMS experiment at the LHC relies on 7 Tier-1 centres of the WLCG to perform the majority of its bulk processing activity, and to archive its data. During the first run of the LHC, these two ...functions were tightly coupled as each Tier-1 was constrained to process only the data archived on its hierarchical storage. This lack of flexibility in the assignment of processing workflows occasionally resulted in uneven resource utilisation and in an increased latency in the delivery of the results to the physics community. The long shutdown of the LHC in 2013-2014 was an opportunity to revisit this mode of operations, disentangling the processing and archive functionalities of the Tier-1 centres. The storage services at the Tier-1s were redeployed breaking the traditional hierarchical model: each site now provides a large disk storage to host input and output data for processing, and an independent tape storage used exclusively for archiving. Movement of data between the tape and disk endpoints is not automated, but triggered externally through the WLCG transfer management systems. With this new setup, CMS operations actively controls at any time which data is available on disk for processing and which data should be sent to archive. Thanks to the high-bandwidth connectivity guaranteed by the LHCOPN, input data can be freely transferred between disk endpoints as needed to take advantage of free CPU, turning the Tier-1s into a large pool of shared resources. The output data can be validated before archiving them permanently, and temporary data formats can be produced without wasting valuable tape resources. Finally, the data hosted on disk at Tier-1s can now be made available also for user analysis since there is no risk any longer of triggering chaotic staging from tape. In this contribution, we describe the technical solutions adopted for the new disk and tape endpoints at the sites, and we report on the commissioning and scale testing of the service. We detail the procedures implemented by CMS computing operations to actively manage data on disk at Tier-1 sites, and we give examples of the benefits brought to CMS workflows by the additional flexibility of the new system.
CMS computing operations during run 1 Adelman, J; Alderweireldt, S; Artieda, J ...
Journal of physics. Conference series,
01/2014, Letnik:
513, Številka:
3
Journal Article
Recenzirano
Odprti dostop
During the first run, CMS collected and processed more than 10B data events and simulated more than 15B events. Up to 100k processor cores were used simultaneously and 100PB of storage was managed. ...Each month petabytes of data were moved and hundreds of users accessed data samples. In this document we discuss the operational experience from this first run. We present the workflows and data flows that were executed, and we discuss the tools and services developed, and the operations and shift models used to sustain the system. Many techniques were followed from the original computing planning, but some were reactions to difficulties and opportunities. We also address the lessons learned from an operational perspective, and how this is shaping our thoughts for 2015.
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