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Diamond. Status. 3 beamlines with users, 1 starting commissioning. datasets > 20 images 2007 - 856 total 2008 – 521 (first 3 months despite problems!) Total data = 5.5Tb some compressed some not…. Directory structure. Data is stored in /dls/$BEAMLINE/data/$YEAR/”proposal-visit”:

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  • 3 beamlines with users, 1 starting commissioning.
  • datasets > 20 images
    • 2007 - 856 total
    • 2008 – 521 (first 3 months despite problems!)
  • Total data = 5.5Tb some compressed some not….
directory structure
Directory structure
  • Data is stored in /dls/$BEAMLINE/data/$YEAR/”proposal-visit”:
    • Where proposal is proposal number and visit is session on any beamline
    • Read-only* for backup and archive reasons
  • Subdirectories of “proposal-visit” created automatically:
    • spool : used by other beamlines
    • *processing: writeable area to be used for processing data by user (no quota)
    • jpegs: contains jpeg and thumbnails of all images
    • $HOME: quota enabled areas
    • Other subdirectories can be created by the user through GDA
  • Future directories
    • processed: will contain results from any processing software automatically run by diamond
    • jpegs of the crystal and loop from the inline viewing system will need to be stored
archiving progress
Archiving Progress
  • ISPyB
    • Testing of GDA automatically writing to ISPyB underway
    • DNA ISPyB integration still to do but should be based on work already done
  • CBF
    • Archive of CBF (ImgCIF) or Vendor data format yet to be decided
    • Reliable migration/conversion tools now available
  • Data backup and remote access
    • Testing is underway for automatic archive of data onto tape and download from data portal. (Project currently subject to delays due to STFC “changes”)
software on beamlines
Software on Beamlines
  • Software is being made available through the ‘module’ system
  • Data processing packages available include:
    • Mosflm
    • XDS
    • HKL2000
    • D*trek being investigated
automated data collection
Automated Data Collection
  • DNA
    • Version 1.1 of DNA has been successfully tested on I03 in ‘manual’ mode
    • This has not been made available to users or tested on I02 and I04
  • EDNA
    • Diamond is currently committed to EDNA as a successor to DNA
automated data processing
Automated data processing
  • On datasets with >20 images, testing is underway to use a cluster to:
    • Process the data using XIA2 in both 2D (Mosflm) and 3D (XDS). (thanks to G. Winter)
  • Other packages e.g. ELVES are being investigated. Suggestions welcome.
cluster environment for ccp4
Cluster environment for CCP4?

Classic Cluster

  • 24 dual dual core nodes
  • Sun Grid Engine
  • Future replacement


  • Massively multithreaded SIMD Architecture.
    • Thousands of threads required for efficiency
  • Per £3500 1U rack mount unit
    • ≈ 400 times the calculation performance of a single core Intel processor (optimized external to DLS, Financial Monte Carlo)
    • 40 times the performance for data heavy analysis (relatively unoptimized internal DLS code, tomographic reconstruction)
multi user shared environment and ccp4
Multi user shared environment and CCP4
  • Automatic updates
    • Software managers mailing list? Monolithic releases are nice but…. Users don’t have permissions….
  • Old CCP4i
    • No shared projects – future looks good though
  • Permissions problems?
    • Coot-backup
  • No coherent plan for exploiting high performance computing?
  • But as there are ‘resources’ at a large site it is possible within certain constraints.
ccp4 and diamond
CCP4 and Diamond
  • Diamond does not do much with CCP4 and CCP4 does not do much with Diamond
    • Some exceptions mostly in data processing.
  • Areas we could do more together
    • General software developments (parallelisation, tools, testing, releases….)
      • Some information exchange both ways.
    • Technique developments and automation.
    • Vehicle to the users through their data.
  • But can anyone be bothered?
the staff
Beamline Scientists

Thomas Sorensen, Liz Duke, Katherine McAuley, Dave Hall, Gwyndaf Evans, Ralf Flaig, Armin Wagner

Support Scientists

James Sandy, Mark Williams, (Alice Douangamath)

Post Docs

Mike Latchem, David Waterman


David Butler, Mic Harding, Trevor Orpin, Adam Prescott, Adam Taylor


Martin Burt, Jeff Preece, Jerry Nash


Andy Foster, James O’Hea


Jun Aishima, Alun Ashton, Josephine Chan, Paul Gibbons, Karl Levik, Richard Woolliscroft


Beamline Scientists

Support Scientists

Industrial Liaison Scientist

The Staff