ParaFEM: Microstructurally Faithful Modelling of Materials. Louise M. Lever, University of Manchester
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1 ParaFEM: Microstructurally Faithful Modelling of Materials Louise M. Lever, University of Manchester HECToR dcse Seminar, NAG, Manchester, UK 9.30am Wednesday 5 October 2011
2 Overview Background Activities 1. The Speaker 2. ParaFEM 3. Manchester Imaging 1. dcse Project 2. ParaFEM OSS Strategy HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5th October
3 The Speaker
4 Biography Current employment, University of Manchester, present Senior Consultant, IT Services for Research Member of Eurographics UK Executive Committee Project manager and lead developer for AVS/Express development at Manchester International AVS Centre Multi-Pipe Edition Parallel Edition HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5th October
5 IT Services for UoM Supporting local researchers Collaborative, research driven support model Supporting national services CSAR (Manchester Computing) National Grid Service Access Grid Data Management (JISC Madam project) Academic support via Manchester Informatics (Mi) Key Themes Computational Shared Facility HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5th October
6 ParaFEM
7 ParaFEM ParaFEM is a freely available, portable library of subroutines for parallel finite element analysis. The subroutines are written in FORTRAN90/95 and use MPI for message passing. It is an extension of the software developed in Smith I.M. and Griffiths D.V. "Programming the Finite Element Method", Wiley, The ParaFEM project owner is Dr Lee Margetts, an HPC specialist at the University of Manchester, UK. The latest release, version , was published on 29 July HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5th October
8 Programming the Finite Element Method 2004 Programming the Finite Element Method I.M. Smith and D.V. Griffiths 4th Edition Easy to use example programs FORTRAN90/95 Parallel versions Over 500 Citations HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5th October
9 Static/Steady Analysis Capabilities of ParaFEM Static Linear Elastic Equilibrium (Small Strain) Static Elastoplastic Equilibrium Steady State Heat Flow & Seepage (Poisson equation) Steady Fluid Flow (Navier-Stokes equations) Large Strain Elasticity (St Venant-Kirchoff Material) Transient Analysis Explicit/Implicit Transient Flow Coupled Transient Deformation/Flow Dynamic Equilibrium of Elastic/Elastoplastic Solids Others Eigenvalues/vectors (elastic solids) HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5th October
10 Manchester Imaging
11 Manchester X-Ray Imaging Facility New facility at the University of Manchester Includes existing Henry Moseley X-Ray Imaging Facility (HMXIF) in Manchester And the University of Manchester has a beamline at the Diamond Light Source Facility New MXIF Experiment Management System [Future] HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5th October
12 HMXIF HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5 th October
13 Experiment Management System HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5 th October
14 HMXIF Examples Incremental crack growth in titanium/silicon carbide Pacemaker battery HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5 th October
15 Imaging Engineers historically used imaging techniques to simply look at materials Now using imaging to create the models And model how they behave HPC requirements at most stages of their workflow HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5th October
16 Webbed Tracks From Non-webbed feet Dr Phil Manning and Dr Peter Falkingham A mesh, not a photo! HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5th October
17 Image Based Meshing Dr Paul Mummery and Dr Philippe Young Tomography follows a Moore s Law for image resolution and number of detectors to voxels etc Requires Out-of-core and parallel grid based meshing Meshes with 2+ billion element models created Image source: HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5th October
18 Multiscale Modelling Dr Phil Manning and Dr Bill Sellers FE based micro-scale to macro-scale homogenization KUBC, SUBC and periodic boundary conditions Unit cell or RVE based characterization Based on separation of length scales Image source: HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5th October
19 Multiscale Modelling KUBC Kinematic Uniform Boundary Conditions - Apply the macro strain to the micro-scale, solve for micro stresses and compute macro stress. Macro stress-strain relationship gives "effective" Young's modulus. Image source: Peter Falkingham HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5 th October
20 Multiscale Modelling Dr Paul Mummery and Dr Philippe Young EDF homogenization benchmark problem 330+ million elements HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5th October
21 HECToR GPU Testbed Dr Paul Mummery and Dr Michael Bane Pilot evaluation of GPU acceleration for iterative solvers ParaFEM can be easily adapted to run on multiple compute nodes with GPU accelerators GPU implementation of the iterative solver needs to accelerate large loops of small matrix-vector multiplies Some special cases, voxelated meshes from CT images very suitable Single matrix, multiple vectors high level memory reuse HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5th October
22 dcse Project
23 Image Based Modelling Professor Philip Withers & Professor Paul Mummery Supporting Henry Moseley X-Ray Imaging Facility HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5th October
24 NAG dcse Dr Paul Mummery, Prof Stephane Bordas & Prof Karl Kadler ParaFEM interface to Abaqus UMATs (User Material Subroutines) Visualization of large datasets: ParaFEM-Viewer (MRBV), ParaView Example below 170M element model of aluminium foam HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5th October
25 Purpose of dcse The goal is to make it easier to use ParaFEM By allowing addition of new material models And enabling the visualization of large models Commercial sponsors have people wanting to use ParaFEM EDF; Microsoft; ESA; Rolls-Royce; and SMEs (using PaaS) Would like them to move away from systems like Abaqus Problem size limitations While simultaneously not wanting them to abandon Abaqus It s a closed environment and provides most things HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5th October
26 UMAT User MAterial Types are Fortran subroutines that implement a specific material behaviour Can add to Abaqus to extend modelling options Provide mechanism for users to quickly add the same UMATs to ParaFEM Not straightforward because the implementation depends on problem type and there are a huge number of types of problem HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5th October
27 Why use UMATs Different types of material behaviour require different types of solutions ParaFEM is limited in number of models supported For Large Strain Deformation a new type of model was required Materials like brain, skin and other tissue do not behave like traditional engineering materials Maths for aluminium block (small strain) is not the same as bio-material (large strain) HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5th October
28 UMAT Fortran API HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5th October
29 ParaFEM-Viewer Model viewer built on AVS/Express Custom reader for ParaFEM file format Custom application to enable users to visualize data rather than building visualization networks HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5th October
30
31 MRBV Massive Remote Batch Visualizer Extension of AVS/Express Parallel Edition Using Multi-Pipe and Distributed Data Renderer (DDR) And Parallel Support Toolkit (PST) for computation Parallel rendering without need for graphics hardware Ported to HECToR by George Leaver in dcse project HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5th October
32 MRBV Some problems with MPI on HECToR to overcome DDR already fully MPI based but no MPI on HECToR head node Focuses primarily on rendering of structured volumes Includes MPI and thread-based direct volume renderer HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5th October
33 Porting ParaFEM-Viewer to MRBV Wanted to port ParaFEM-Viewer Write parallel IO for ParaFEM file format Or convert to existing supported format such AVS UCD Replace serial modules in application with their parallel counterparts Add animation scripts to enable batch usage HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5th October
34 Experience with MRBV Developed conversion scripts to single and multi-file UCD Can read data in Serial: is then decomposed and distributed by parallel toolkit Parallel: each node reads a pre-decomposed file And see the model and results HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5th October
35 Problems with MRBV Problems encountered included Limitations of multi-file UCD: no time steps Limitations of parallel toolkit: no element data Effort to create a native parallel reader would have to include further development of AVS/MRBV Beyond scope of this dcse project Licensing Manchester is only academic site with license Very likely to change in 2012 Similar issue for desktop users And concern for ParaFEM open source plans HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5th October
36 Using ParaView Benefits Open Source, freely customizable, multi-platform Built on comprehensive and sophisticated VTK library Many visualization and parallelization strategies Drawbacks Takes users (initially) back to hands-on control of visualization pipeline Greater effort to provide a custom interface HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5th October
37 Moving to ParaView Data format handling No native ParaFEM reader for ParaView Beyond scope of dcse project Opted for conversion to supported EnSight Gold Format Issues ASCII only at the moment VTK reader code has errors and does not load partial data VTK code fixed but not submitted yet File access every time on loading of each time step Seems slow in comparison to AVS/Express HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5 th October
38 ParaFEM Results in ParaView HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5 th October
39 ParaFEM Results in ParaView HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5 th October
40 Remaining Work on dcse Tidying up of software Looking for more UMATs Load-balancing tests ParaFEM is perfectly balanced for simple material types Have non-linear parts in certain regions Will measure and profile how non-linearity affects load-balancing Have already integrated METIS tools into ParaFEM suite Re-partition with METIS See if we get better load-balancing with METIS partitions Have two strategies to compare HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5th October
41 6. ParaFEM OSS Strategy
42 Google Code Platform for Developers HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5th October
43 Google Code Platform HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5th October
44 HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5th October
45 Joomla Community Building Platform HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5th October
46 Joomla back end for parafem.org.uk HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5th October
47 How well are we doing? HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5th October
48 Visitors - code.google.com/p/parafem HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5th October
49 Visitors - code.google.com/p/parafem HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5th October
50 Acknowledgements NAG, Dr. Lee Margetts, Prof. Paul Mummery, Prof. Philip Withers, Dr. Phil Manning, Prof. Ian Smith, Dr. Peter Falkingham, Dr. Mohammed Sheikh, Mark Johnson, Dr. David Raymont, Dr. Phillipe Young, Dr. Bill Sellers, Dr. Michael Bane, Vendel Szeremi, Prof. Karl Kadler, George Leaver, Dr. Martin Turner, Dr. Robin Pinning, Dr. Tristan Lowe, Dr. Sam McDonald HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5th October
51 For further details, please contact HECToR dcse Seminar, NAG, Manchester, 9.30am Wednesday 5th October
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