Replay of digitally-recorded holograms using Grid computing

2018-12-14T10:55:12Z (GMT) by Henry Nebrensky
<p>Holography has found application in the analysis of particulates in many fields, from snowflakes to plankton. Digital recording of holograms (with a CCD or CMOS sensor) has many advantages over traditional methods such as glass plates coated with a silver-halide emulsion, especially for the portability and robustness of field equipment, and the resulting digital holograms can be reconstructed by a computer code such as HoloReco [1] and either viewed on screen or passed onward to for automated analysis.</p><p>The hologram is a recording of a volume, and so typically one reconstructs a series of slices in depth and then extracts further information (such as the presence of any particles) from those images. The numerical reconstruction is computationally expensive, and we have previously suggested using a Grid computing framework to replay the images and store them for further analysis [2].</p><p>This spreadsheet contains data about Grid submission of hologram-replay tasks, to assess the utility of Grid computing for this application. The sample hologram and replay software were uploaded to a Grid Storage Element (SE) at Brunel University. Jobs were then submitted to run on the Grid, with each pulling down the executable and sample hologram, reconstructing some number of slices, and uploading the results back to the SE at Brunel University.</p><p>For the initial tests in 2005 (tabs Test01 and Test02), varying numbers of Grid jobs were submitted with each returning only a single slice. From 2007 on, each Grid job returned a pre-determined number of slices such that the number of Grid jobs needed to complete the full task (usually 2200 slices) was reduced as each did more work.</p><p>The rate at which completed slices were made available (by being uploaded to the Grid storage) was compared with serial replay on single machines (references "F", "D" and "y"; tabs Test02 and 07test02).</p><p>For more details see [3] and [4]. This data has also been incorporated into [5] and other works. Tabs Test01 and Test02 include the data used for [3].</p><p>The scripts for Grid submission, and sample holograms, are included with HoloReco [1] and described in more detail in [4].</p><p>GridResults-2005.xls is an early version of the results spreadsheet, before some of the charts got corrupted, and Grid-HoloReplay.zip contains some of the initial raw data still in text format. </p><p><u>Acknowledgements:</u></p><p>Henry Nebrensky submitted the jobs to the Grid, monitored their progress and tabulated the results. </p><p>Initial Grid deployments were tested on the Worldwide-LCG Grid courtesy of the CMS VO.</p><p>Tests from 2007 onwards were made within the London Tier 2 of the UK GridPP Grid, under the LondonGrid VO.</p><p><u>References</u></p><p>1. "<em>HoloReco</em>" digital hologram reconstruction code, DOI: <a href="https://doi.org/10.17633/rd.brunel.4570327">10.17633/rd.brunel.4570327</a> (2008)</p><p>2. J.J. Nebrensky, P.R. Hobson and P.C. Fryer: "Grid computing for the numerical reconstruction of digital holograms" <em>Proceedings of SPIE</em> <strong>5775</strong> pp. 285-296, DOI: <a href="https://doi.org/10.1117/12.610677">10.1117/12.610677</a> (2005)</p><p>3. J.J. Nebrensky and P.R. Hobson: "The reconstruction of digital holograms on a computational grid" <em>Proceedings of SPIE</em> <strong>6252</strong> p. 62521I, DOI: <a href="https://doi.org/10.1117/12.677160">10.1117/12.677160</a> (2006)</p><p>4. J.J. Nebrensky and P.R. Hobson: "<em>Replay of digitally-recorded holograms using a computational Grid</em>" Brunel University <a href="https://bura.brunel.ac.uk/handle/2438/3443">https://bura.brunel.ac.uk/handle/2438/3443</a> (2009)</p><p>5. I.D. Reid, J.J. Nebrensky and P.R. Hobson: "Challenges in using GPUs for the reconstruction of digital hologram images" <em>Journal of Physics: Conference Series</em>, <strong>368</strong> 012025, DOI: <a href="https://doi.org/10.1088/1742-6596/368/1/012025">10.1088/1742-6596/368/1/012025</a> (2012)<br></p>