The Diamond Light Source Sample Clauses

The Diamond Light Source. Pilot As described in detail in CompBioMed deliverable D6.3 (Report on Workflow system provision), large scale data transfer between the Diamond Light Source and the EPCC Xxxxxx HPC facility is needed to perform the BoneDVC workflow. This uses the GridFTP data transfer infrastructure and the Globus framework for authentication. Data transfer is requested by the user from a client machine and all authentication to the Diamond and EPCC systems is performed through the Globus API. Here we briefly review the details reported in deliverable D6.3 in the context of the wider development of data infrastructures within CompBioMed described within this deliverable. The BoneDVC workflow involves the processing of very large X-ray micro- and nano-tomography datasets collected at the Diamond Light Source, the UK's national synchrotron science facility. These datasets are typically hundreds of Gigabytes, presenting a challenge for robust and efficient data transfer to an HPC centre for further processing. Workflow data stored at the Diamond facility may be located either • on short term online storage, or • in long term tape archive storage If archival storage is used, data must first be ‘staged’ to online storage; i.e., reading the data from tape, recovering it to an internet connected server to allow onward transfer. ‘Staging’ of data from the Diamond facility is possible using the ‘TopCat’ [8] web interface, through the following steps; • User logs in and is presented with a list of their available data • Individual files/directories may be selected and added to the ‘download cart’ • Once all data is in the download cart, staging is requested by opening the cart and selecting the download option Once staging is requested the data is copied from tape to the data transfer node at the Diamond Facility. This process can take several hours to complete, and the user can opt to receive an email when the data is ready for transfer. Two options are available for download; • Exposure using the http protocol with a standard web browser • Transfer using GridFTP (that uses parallel ftp) with the Globus [9] system for authentication For transfer to the UK Research Data Facility [10] (UK-RDF) attached to the Xxxxxx HPC, GridFTP was chosen due to its improved speed and command line access without requiring web browser access on the HPC platform. GridFTP handles all aspects of file transfer, managing authentication at both source and destination endpoints and ensures the transfer com...
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