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SCD/STFCScientific Computing Division
Some details of the CCP Support and
“How to make 1.16 FTE pa appear a lot”
Who we are
Diamond Light Source
ISIS Neutron Source
Central Laser Facility
Large Facilities
Visualisation
& Computing
central laser facility
RAL Space
Capabilities– Non Destructive Evaluation
Central Laser
Facility
ISIS Neutron
Source
Diamond Light
Source
• High intensity laser systems
• Ultra-fast sources
• Neutron diffraction
• Neutron spectroscopy
• Small angle scattering
• X-Ray imaging and tomography
• Infra-Red microscopy
• X-Ray fluorescence mapping
Hartree Multipurpose data platformsBlueGene/Q & iDataplex cluster
o 98,304 + 8192 cores
o Over 5 PB disc and 15 PB tape stores
o A total of 1.2 Pflops
BlueGene /Advanced Storage
o 2 x 16384 + 2048 cores
o 256 TB Flash
o Data Intensive systems
Dedicated Big Data Cluster
o Big Insights (912 cores, 2.6TB RAM)
o Streams (128 cores, 1TB RAM)
o InfoSphere Data Explorer (96 Cores, 192GB RAM)
o SPSS (16 cores, 128GB RAM)
o Infosphere Content Analytics (8 cores, 32GB RAM)
o Cognos (24 cores, 192 GB RAM)
Few Links and Contact [email protected]
• CCPForge
• CCP PET/MR Core Developers
• CCP Top slice (7%), administration
• EPSRC SLA requirements
• Total number of CCPs etc.
• CCPi activities – example
• Research Council assistance
CCPForgehttp://www.softeng-support.ac.uk/
CCPForge provides the following for registered projects:
• Revision control for files with CVS, Subversion git, bazaar and Mercurial
• Software release downloads for source or pre-compiled versions
• Flexible licensing of software
• User forums for help from other users and developer discussions
• Tracking of support and feature requests
• Traditional mailing lists
• Task managements
• Documentation repository
• Flexible access control to information based on "roles"
Statistics CCPForge(October 2014)
• Started: 2006
• Current number of users: 2971
• Current number of projects: 107
– Milestone of 100 hit on 15 July 2014
• DL_POLY Classic most downloaded project: 52,597
CCP PET/MR - Core
Staffing for developer Core level support:
• 1.16 FTE for Five Years
Core support is reduced (from 1.25FTE)
• 7% top sliced
Management organised by EPSRC for future bids
• Daniel Emmerson: [email protected]
Job Plans: PET/MR
Establish website, mailing lists, source code archivesOngoing
Organise working group meeting/ user-conference involvement, and monthly joint show-
and-tell sessions
Ongoing
Support current training courses and organise developer workshop (C++, SWIG to interface
to matlab and python, git)
Q3 2015
Establish database for both simulated and acquired data (i.e. set-up of framework, will
slowly be filled over the project)
Q4 2015
Visit sites in the network to gain experience with a few selected packages for image
reconstruction
one key site per Quarter
Support benchmarking and testing of a few selected packagesQ4 2015
Creation and maintenance of test-cases of PET/MR data and reconstructions - Q4 2015 and
release Q1 2016
Q1 2016
Profiling and (if necessary initial speed-up) of 1 PET and 1 MR image reconstruction
package - Q3 2015 and Q1 2016
Q1 2016
MilestonesPreliminary Plan
1. GROUP NAME and CONTACT DETAILS
2. Progress Against Job Plans
3. Training / Outreach
4. Scientific Highlights
5. Deviation of OTL Bookings
6. Major Code Developments
7. Highlight Papers
8. Suggestions for Other Areas of Impact Metrics
The current metrics that we base our reporting on are publications, presentations,
citations and training days. If you have suggestions for other areas of impact that could
demonstrate the value of the SLA programme (eg: number of software downloads, size
of community etc) please make suggestions:
A list of publications that relate to the SLA – title, author, category
A list of presentations that relate to the SLA – title, presenter, category
A list of training courses that relate to the SLA – event title, number of days, number of
participants, category
Citations: Please provide the number of citations for your project:
SLA Reporting Requirements
Every six months CCP Steering Panel Meeting
Next is Wednesday 24 June 2015
Chairs Report
1. Background
2. Highlights for the Current Reporting Period
3. Outreach and networking
4. Workshops and New Opportunities
5. Issues and Problems
Prior should be a CCP PET/MR Working Group meeting to plan Work Plans and next set
of events as well as review past events.
There is also a EPSRC SLA Steering Panel meeting that you may be invited to.
CCP Chair Reporting
CCP PET/MR – Top Slice
Oversight of the SLA programme is the responsibility of
Paul Sherwood (head of Applications Division), assisted
by Dr Barbara Montanari (deputy head of Applications
Division, and leader of the Theoretical and
Computational Physics Group).
Paul Sherwood: <[email protected]>
Barbara Montanari: <[email protected]>
CCP PET/MR – Top Slice
Some areas where we believe that improvements are possible are
• Helping the science teams to share their results with the communities
beyond their projects or collaborators, identifying highlights and assisting with
bulletins, press releases, web content, social media, etc. A calendar
including all SLA connected events will be maintained on the SCD web site.
• Develop materials for an SLA programme presence at conferences,
meetings and trade shows.
• Helping to integrate the different parts of the programme together, organising
SLA team meetings with opportunities for experience and best practice to be
shared between the different groups
• Financial monitoring, including recurrent spend and effort levels deployed.
• Supporting Sherwood and Montanari in the coordination of plans and reports,
with additional progress checks and plan updates in between the reporting
deadlines for meetings
CCP PET/MR – Top Slice
There will be:
• Project Support and Communications officer
• Specialised IT support for the SLA projects
Administration:
Damian Jones ([email protected]) role as SLA project officer.
• will be convening a meeting of all CCP support probably in June.
• “Normal practice over recent years has been that we will help with meetings
(including the processing of costs from those meetings, which Tracey will bill
to UCL for PET/MR)”.
• Damian’s role will extend to outreach (making sure outputs from the SLA are
shared better than has been true in the past), including synergies between
projects as well as publicity outside.
1. CCP4 Prof David Brown Macromolecular Crystallography
2. CCP5 Prof Stephen Parker The Computer Simulation of Condensed Phases
3. CCP9 Prof Mike Payne Computational Electronic Structure of Condensed Matter
4. CCP12 Prof Stewart Cant High Performance Computing in Engineering
5. CCP-ASEArch Prof Mike Giles Algorithms and Software for Emerging Architecture
6. CCP-BioSim Prof Adrian Mulholland Biomolecular Simulation at the Life Sciences Interface
7. CCP-EM Dr Martyn Winn Electron Cryo-Microscopy
8. CCPi Prof Philip Withers Tomographic Imaging
9. CCPN Prof Geerten Vuister NMR
10. CCP-NC Dr Jonathan Yates NMR Crystallography
11. CCPP Dr Tony Arber Computational Plasma Physics
12. CCPQ * Prof Tania Monteiro Quantum Dynamics in Atomic, Molecular and Optical Physic
13. CCP-SAS Prof Steve Perkins Analysis of Structural Data in Chemical Biology and Soft Condensed Matter
14. CCPForge Prof Chris Greenough Collaborative Software Development Environment Tool
Previous CCPs
CCPihttp://www.ccpi.ac.uk/
Collaborative Computational Project in Tomographic Imaging has been funded for
the next phase 2015-2020 and will use a range of computational HPC facilities.
Tomography Data
CCPi Tomography• Was 1.5 FTE now 1.25FTE (and then -7% !)
“The CCPi prioritises the two areas of reconstruction
and quantitative analysis. It aims to provide the UK
tomography community with a toolbox of algorithms that
increases the quality and level of information that can
be extracted by computer tomography. Key components
continue to be to increase usage, training and software
deposits, as well as integration of new iterative methods
within the toolkits.”
CCPi Tomography
Highlights (December)“Reconstruction Core algorithms: The optimisation of the iterative code for Diamond data sets is complete and has been tested on a sequence of reduced projection data from I13. Results look promising and the full sequence will be processed in 2015 Q1.The Windows GUI for lab based instruments has now been released to the wider community via a ccpforge download. This includes improved projection algorithms based on recent work by Will Thompson at Manchester. As a result a mode of the XTekinstrument that is not currently supported has been identified. Support for this mode and other instruments is likely to be discussed at the next developers day.
CCPi Tomography
Highlights (December)Quantitative visualisation: Work on supporting the CCPi archive has continued and the current algorithms are available on multiple operating systems (Linux, Windows and Mac) and software products (Avizo, ParaView and ImageJ). Several new algorithms have been identified from the community that would be useful to include in the software repository and discussions held with the developers. A new implementation of a beam hardening correction algorithm (from Graham Davis) is currently being developed, in collaboration with users at RaCH and Leeds University. Another algorithm identified is measurement of tortuosity in 3D tube-like structure from Robert Bradley at MXIF and access to the source code is expected shortly. In collaboration with Diamond, a ParaView reader for NeXus data files has been developed and released.
CCPi Tomography
Highlights (December)Flagship project software outcomes: The non-local regularization package (patch-based method) for 2D/3D tomographic reconstruction is available on GPU and CPU. The modified version of the package has been used for improving spatial-temporal resolution of the simulated and real (neutron) data. Two novel methods available for multi-modal reconstruction, which can be useful for image fusion and also hybrid tomographic reconstruction, such as SPECT/CT, PET/MR etc. are being tested. The work continues on embedding the set of regularization tools (CPU and GPU versions) into the CCPi iterative reconstruction code.
CCPi Tomography
Highlights (December)A test tomography reconstruction and remote viewing system for the ISIS neutron spallation source has been complete and a set of evaluation code to create a service is currently being created.
The service product is due for operation in April 2015.”
CCPi Tomography
Networking and Outreach (December)• Celebration of The University of Manchester's Queen's Anniversary Prize
• Stand at the EuroVis (June 2014)
• The annual Tomography for Scientific Advancement (ToScA) Symposium 1-3 September 2014, hosted at the Natural History Museum
• Workshops / Training; We continue to support training courses from the network
• Social meetings at RAL (coffee-and-tomography) has hosted its 18th monthly meeting (total attendance now at 266).
• Developers’ workshop occur each quarter considering a specific focus
• Set of papers including a Royal Society Phil Trans A special edition
• Widening participation: Set of visiting fellows
• EU involvement: There has been exchanges with the EU e-COST programme (EXTREME)
• CCP Cross-collaborations: 1. CCP-ASEArch collaboration: 2. The SLA EPSRC funded vis needs survey
• Industrial Projects: 30 June 2014 there was a TSB (UK Innovate) Kick-off meeting (project code 37972-241197) for an approved project within the Towards Zero Prototyping programme.
CCPi Tomography
Issues and Problems (December)
There is a still need to foster inter- and intra-networking
between the two groups; the developers group and the user
community. This requires improved communication across
sites and involvement of remote participants. Increased
levels of outreach as well as submitting proposal for
increased resources; all are needed to gain a higher level of
trust across the partners.
CCPi Tomography
http://tinyurl.com/STFCVis
CCPi Tomography
http://tinyurl.com/STFCVis
CCPi Tomography
http://tinyurl.com/STFCVis
CCPi Tomography
http://tinyurl.com/STFCVis
CCPi Tomography
http://tinyurl.com/STFCVis
CCPi Tomography
http://tinyurl.com/STFCVis
All fun but is this sustainable…
Need to leverage support from other sources.
CCPi Tomography• CCP Widening Participation Fellowships: ~2-4
months each
• CCP Flagship: Daniil Kazantsev ~ 2.5 yrs
• Visiting Fellows/Scientists – travel/ ~one-two weeks
• Links with other CCPs: CCP-ASEArch
• ISIS Neutron Tomography Project
Extra EPSRC Grant
Extra EPSRC Grant
Extra Cross Link
Extra Project
CCPi Tomography
• Visualisation User Needs Survey
• TSB Proposal on zero-prototyping: Industrial Tomography
Extra SLA Allowance
Extra UK Innovate (TSB)
CCPi Tomography
• Series of new projects
Themes for proposals given five year planning:- Aim for proposals to be submitted within 9 months.
- Fast changing processes (big data) tomography
- Joint tomography
- Rich tomography
- Robust (integrated analysis/reconstruction) for quant/segmentation
- Item involving open data and open sourcing code: Software for the Future
