Wendy Mason, AuScope Research Assistant (Underworld E
Contents
1. optional any extra linux command flags pute advanced Browse InputFile Underworld NM File s optional E model file Ste Local OE path Usesjwmasor Additional File s share UV AE optional P Koala any other files included ye listed in the model file grisu ssh P required Submit MONASH University RS e Research Centre MCA 14 Auscope Parcs F Z2A RAYLEIGHTAYLORBENCHMARK WORKSHOP XML e Rayleigh Taylor convection benchmark as detailed in P E van Keken et al A comparison of methods for the modelling of thermochemical convection Journal of Geophysical Research 102 B10 22 477 22 495 1997 e See Underworld User Manual for details of benchmark comparison how to create one s own models using this example p ON MONASH University avec r 15 7 e Hesearch Centre DE Auscope Parcs 9 O00 Grisu client Job submission Monitoring File management File transfers D l Basic job properties Job parameters LE Workshop Jobname CPUs Workshop RTE Parallel V Applications underworld Walltime Days Hours Minutes No of cpus 0 0 v 30 2 ms Submission details Display all available Queues Site VPAC E Queue dque tango m E Version Select version Auto select 1 2 0 Notify me when job V starts V finishes Email wendy mason sci monash edu au AAA Grisu clien2. window 00350 png 76 KB window 00360 png 74 KB window 00370 png 76 KB window 00380 png 79 KB window 00390 png 81 KB window 00400 png 84 KB gt Lr UL y a underworld Particle Density Job directory Job details Strain Rate Invariant Size 84 KB Last modified Sun Jun 07 15 27 03 EST 2009 copy window 00360 png 74 KB _ window 00370 png 76 KB window 00380 png 79 KB 1 window 00390 png 81 KB window 00400 png 84 KB window mpeg 1M y By zl i T Window UU35U png 76 KB underworld N O EEN 0 00012 0 013 Preview e Job directory Job details Site Local Share copy HH Path Users wmason Desktop Movies A l Files 4 JOB DETAILS amp UNDERWORLD OUTPUT Particle Density Strain Rate Invariant _ 1 UI 3 9e 05 0 0088 C AuSc ope arcs N MONASH University 4 e hau Hesearch Centre 22 JOB DETAILS amp UNDERWORLD OUTPUT e Full time stamped version of the XML file used flattened e FrequentOutput dat file e Underworld comes with the visualisation package gLucifer png image outputs are created by default lt param name maxTimeSteps gt 400 lt param gt lt param name dumpEvery gt 10 lt param gt movie generation mpeg is NOT on by d
3. AuScope art CS MONASH University g amp IVEC UNDERWORLD MODULE INSTALLATIONS e List of Underworld module installations ARCS amp NCI NF sites http nf nci org au facilities software software php software Underworld amp all sites yes JUS National AHAS ooms mel s II National Computational Infrastructure older modules in this list are no longer grid enabled only 1 2 0 MONASH University e Research Centre e Monash Sun Grid MSG currently Monash access only command line Monash is looking into connecting the MSG to the ARCS Grid http www monash edu au eresearch services mceg mse html Zs MONASH University OA AVEC Hesearch Centre C AuScope ars 40 ADVANCED COMPUTING UNDERWORLD MODULE INSTALLATIONS e Underworld module installations are planned for additional sites e f there is no Underworld module installed on a cluster on the Grid that you want to use already have access to please let AuScope know underworld users vpac org we ll get one installed amp grid enabled for you e List of ARCS sites High Performance Computing HPC facilities http www arcs org au products services systems services compute services hpc facilities MONASH University Carne T e Hesearch Centre VEAC 41 od Auscope Parcs S ARCS IDP amp SERVICES e You have been using the ARCS IdP e Institutional IdPs will be available in coming months
4. user defined name gt lt param name Type component class type lt param gt param name input parameter gt value lt param gt lt struct gt lt struct MONASH University 4 LE AiVEC 7 o Research Centre gm 33 C AuScope arcs UNDERWORLD INPUT FILE STRUCTURE Simulation control parameters e g output checkpointing e Geometry amp mesh setup e g param name dim 2 lt param gt dimensions lt param name elementResI 64 lt param gt lt param name elementResJ gt 64 param resolution lt param name elementResK gt 1 lt param gt lt param name minX 0 0 lt param gt lt param name minY 0 lt param gt lt param name minZ 0 lt param gt box size lt param name maxX 9142 lt param gt lt param name maxY 0 lt param gt lt param name maxZ 0 lt param gt e Initial amp boundary conditions VV VV M H HOOO ANN C AuScope ars MONASH University 4 T Hesearch Centre VAC 34 UNDERWORLD INPUT FILE STRUCTURE e Visualisation files parameters viewports in Underworld Viewports e g lt include gt Underworld Viewports ParticleDensityVP xml lt include gt lt include gt Underworld Viewports StrainRateInvariantVP xml lt include gt window s containing viewports defined in above files e g lt include gt glucifer window xml lt include gt struct name components mergeType merge gt struct name window
5. including Monash University will mean you can login to Grisu amp other ARCS Services using your insitutional username and password e g authcate for Monash users ARCS and your new IdP can arrange for secure transfer of your auEduPersonSharedToken from the ARCS IdP to your new IdP participating members listed at https www federation org au FedManasger listMembers do MONASH University AVEC e Research Centre od Auscope Parcs 2 ADVANCED COMPUTING VIRTUAL ORGANISATIONS VOS e Workshop VO will last until 19 June 2009 download or copy today s output to your StartUp VO before this date e StartUp VO only allows for 15 minute test jobs e Each research group can have a Virtual Organisation VO contact ARCS to create your group s VO ask the relevant site to support your group s VO cluster usage charges may apply e g the MonashGeo VO has been set up for the AuScope Underworld user community at Monash University to use VPAC cluster resources e Users within a VO cannot see each other s data in Grisu although still have access if the paths are known e Users can see and access each other s data using other GridFTP tools e g Hermes Zs MONASH University aa T o Research Centre Memes VANG de oe 43 ADVANCED COMPUTING p j Auscope Marcs 9 YC J Mw ce O OTHER FUTURE DEVELOPMENTS e Next Underworld stable release amp expanded u
6. mergeType merge param name Viewport gt ParticleDensityVP StrainRateInvariantVP lt param gt lt struct gt lt struct gt movie generation not included by default lt include gt glucifer 9 BuildMovies xml include Key luc Window lucViewport gt lucDrawingObject C AuScope n arcs N MONASH University e Hesearch Centre 35 Za SLABSUBDUCTION WORKSHOP XML e Slab model as described in D R Stegman et al Influence of trench width on subduction hinge retreat rates in 3 D models of slab rollback Geochemistry Geophysics Geosystems 7 Q03012 2006 e 3D chemical convection model simulating a falling lithospheric slab dense lithospheric slab with a perturbed tip to initiate subduction Viscosity stratification between upper mantle amp lower mantle Ze MONASH University P SS baud Hesearch Centre C OE V Nas 36 ADVANCED COMPUTING Auscope Parcs 9 Za SLABSUBDUCTION WORKSHOP XML e Modified output path lt param name outputPath gt lt param gt Note this is to illustrate that the Underworld post processing panel will not activate if FrequentOutput dat is not located ina subdirectory defined by this parameter Modified visualisation file SlabViewports_Particles_Workshop xml e Revisualising from supplied checkpoint files checkpoint files w
7. v Notify me when job V starts V finishes Email wendy mason sci monash edu au O00 Grisu client File transfers Job submission Monitoring File management mn Basic job properties Job parameters StartUp Additional Command s optional Enter any additional commands in this field otherwise leave blank Applications underworld E InputFile file Users wmason Desktop RayleighTaylorBenchmark Workshop restart xml S Additional File s optional Select files one by one or by whole subdirectory Site VPAC Path grisu jobs Workshop RTB C eckpoins Share ng2 vpac org Workshop amp F checkpoints J output RayleighTaylorBenchmark_Workshop xml 3 KB stderr txt 1 KB stdout txt 697 KB ss C required A 3 M ULTITHERMALDIFFUSIVITY WORKSHOP XML e Contains 3 strips of constant isoviscous material aligned in the y axis Each material has a different diffusivity e The fluid is driven by a thermal packet which spreads over each material SA INN arcs MONASH University A At AA V INC ustrali E i Hesearch Ce ntre EINE 29 C AuScope 3 M ULTITHERMALDIFFUSIVITY WORKSHOP XML TemperatureField and Velocity Arrows Particle Types 0 0058 A auscope ars N vs MONASH University te T Hesearch Centre VICTORIAN PARTNERSHIP FOR 30 ADVANCED COMPUTING UNDERWORLD INPUT FILE STRUCTURE e Underworld is set up
8. 700 800 17 125 269 0 00084036 31 7037 Time 18 128 381 0 000885755 33 8577 19 131 277 0 000929951 36 0246 20 133 989 0 000974441 37 8649 M 19 JOB DETAILS amp UNDERWORLD OUTPUT Job directory panel underworld Job directory Job details e All files staged in E g checkpoints output error stderr txt Cd x ee moerse MG oe 3 KB output stdout txt stdout txt 697 KB Preview A files e output subdirectory lt param name outputPath gt output lt param gt e checkpoints subdirectory if applicable lt param name checkpointPath gt checkpoints lt param gt lt param name checkpointEvery gt 400 lt param gt snapshot of fields amp swarm can be used to restart simulations from previous runs vs MONASH University an Research Centre memes MEET ee 20 ADVANCED COMPUTING Auscope Parcs 9 E y yv SS we ERE LL dd ee window 00170 png 62 KB window 00180 png 63 KB window 00190 png 63 KB window 00200 png 64 KB _ window 00210 png 65 KB window 00220 png 65 KB window 00230 png 66 KB window 00240 png 65 KB window 00250 png 66 KB window 00260 png 66 KB window 00270 png 65 KB window 00280 png 65 KB window 00290 png 66 KB window 00300 png 67 KB window 00310 png 69 KB _ window 00320 png 70 KB window 00330 png 73 KB window 00340 png 76 KB
9. a long term geodynamics simulation platform UNDERWORLD GRID WORKSHOP 20009 Monash University Caulfield Campus Wednesday 10 June 2009 Presenter Wendy Mason Support Markus Binsteiner amp John Mansour AuScope ars N vs MONASH University ERS bd Hesearch Centre WORKSHOP SPONSORS Acknowledgments amp thanks Steve Quenette Julian Giordani AuScope John Mansour Patrick Sunter amp Kathleen Humble X Jim McGovern Darran Carey PAN af cs Markus Binsteiner Sam Morrison iste Research Collaboration Service d An dy botti n 9 Ys MONASH University e Research Centre ANN VOAD AVEC VICTORIAN PARTNERSHIP FOR ADVANCED COMPUTING providing onsite support today ABOUT THIS WORKSHOP e For potential new and current users of Underworld e Sample workflow for running Underworld models on computer clusters across the ARCS Grid Grid submission client Grisu graphical user interface pre installed copies of Underworld 1 2 0 release no need to install your own copy of Underworld submit sample models view amp retrieve results e Brief overview of structure of Underworld model files e Workshop slides will be posted on Underworld Project website details at end of workshop p vs MONASH University C T Research Centre ems Auscope Parcs 9 GETTING HELP e Underworld user forum AuScope support underworld users vpac org AuScope can provide individualis
10. e 4 Submission Host VO Workshop RTB Active Sun Jun 07 15 14 15 EST 2009 ng2 vpac org ARCS Workshop Kill amp clean Rebuild Joblist takes longer Refresh all JOB DETAILS amp UNDERWORLD OUTPUT Underworld post processing panel Previews contents of FrequentOutput dat data generated by output plugins amp plots a graph from selected data columns C AuScope Mars 9 Australian Research Collaboration Service http www jfrec org jfreechart MONASH University 4 e Research Centre a AVEC VICTORIAN PARTNERSHIP FOR ADVANCED COMPUTING AAA l underworld Job directory Job details FrequentOutput dat for job Workshop RTB X Axis Time 0 00325 z y Axis Vrms 00 8 0 00300 4 P 0 00275 Timestep 400 400 0 00250 0 00225 4 Timestep Time Vrms CPU_Time D 1 O 0 000184787 3 05688 P 0 00200 2 17 0476 0 000221 4 90546 3 31 3203 0 000256014 6 51523 2 0 00175 4 43 6534 0 000291793 8 69838 z 5 54 4517 0 00032739 10 6396 0 00150 6 64 0569 0 000365399 12 5549 0 00125 7 72 661 0 000404527 14 1765 8 80 403 0 000443129 15 9899 0 00100 9 87 4509 0 000485157 17 8927 10 93 8807 0 000527447 19 4863 0 00075 11 99 7863 0 000572369 22 5567 v 12 105 142 0 000616226 24 4717 13 109 969 0 000661687 25 8755 0 00025 14 114 32 0 00070653 27 1675 15 118 281 0 00075125 28 4599 16 121 912 0 000795707 30 0614 0 100 200 300 400 500 600
11. ed assistance amp support with setting up your own models after the workshop to subscribe to and receive emails from this group go to http lists vpac org cgi bin mailman listinfo underworld users Underworld website http www underworldproject ors documentation html guide to getting started on the ARCS Grid Underworld User Manual Component Codex online amp download Underworld installation guide basic linux skills required e ARCS website amp helpdesk http www arcs org au support Grisu ARCS Compute Grid amp other ARCS Services vs MONASH University OA AVEC 7 o Research Centre EE 4 Auscope Parcs ARCS IDP AND SERVICES e You have already been added as a member of the ARCS Identity Provider registered for ARCS Services e http www arcs org au Quick Launch XX EVO Video Conferencing Parcs Australian Research Collaboration Service gt Register Register for ARCS Services d gt BPT 10 B ot 614m ARCS Data Fabric gt PIT Lr INA TA ARCS OPeNDAP Digital Library ele Tie ad e tE Use the ARCS Grid gt ARCS ID Create an ARCS Identity g MONASH University e Research Centre Auscope Marcs 9 D GRISU GRID SUBMISSION LLIENT e P Compute Jobs download grisu jnlp to your desktop e Double click on Standard login MyProxy login grisu jnlp M Your IDP ARCS IdP v Refresh m Shibboleth Login Us
12. efault lt include gt glucifer BuildMovies xml lt include gt interactive mode off by default only available on local machine not on clusters or the ARCS Grid e See Component Codex for other output amp checkpoint parameters amp output components vs MONASH University Lr baud Hesearch Centre Do EV NX 23 ADVANCED COMPUTING Auscope Parcs 9 JOB DETAILS amp UNDERWORLD OUTPUT CY HV OY Job details panel _underworld Job directory Job details Details for job Workshop_RTB Status Done Application underworld Faan ARCS Workshop Submission host ng2 vpac org Submission queue dque tango m Submission date Sun Jun 07 15 14 15 EST 2009 No cpu s n a Other properties factoryType PBS maxTimesteps 400 underworldOutputDirectory output executionHostFileS ystem gsiftp ng2 vpac org home grid workshop DC au DC org DC arcs di l gt IN C AuScope Arcs CS MONASH U a Ive SIty DAE N C pS IV w e Hesearch Centre Vti rU FILE MANAGEMENT TRANSFERS e Copy to local drive or account on another cluster OOD Grisu client TJ SSS Mm Job submission Monitoring File management File transfers Site VPAC v Path grisu jobs Worksl Site Local v Path Users wmasc nO umar nex fiiacebchar LA TA Share ng2 vpac org Workshop a Share 1 FI 2 checkpoints output RayleighTaylorBenchmark Workshop xml 4 KB _ stde
13. ere created on 4 processors revisualising in visual only mode on 2 processors Note checkpoint files senerated on one cluster may not work on another architecture Not generating a movie in this model run MONASH University OA AVEC T Hesearch Centre C AuScope arcs 37 ADVANCED COMPUTING Grisu client Job submission File transfers Monitoring File management Current VO StartUp Additional Command s optional Enter any additional commands in this field otherwise leave blank Basic job properties Job parameters Applications underworld visualOnly 1 InputFile file Users wmason Desktop SlabSubduction Workshop revis xml ind Browse Additional File s optional Select files one by one or by whole subdirectory Site boud a path Users wmasor SlabViewports Particles Workshop xmlI checkpoints Share H amp 4 Files checkpoints DS Store 42 KB GMT bb info 36 B gmtcommands4 106 B p v y hu et lt 4 A Za SLABSUBDUCTION WORKSHOP XML Template visualisation Example revisualisation BENE aum EE AEN 1 6e 05 0 011 1 6e 05 0 011 SlabViewports xml SlabViewports Particles Workshop xml slab isosurface draped in logscale slab particles plotted in logscale of of strain rate invariant strain rate invariant isosurface of lower mantle in red
14. ername Password ARCS IdP enter username amp new password Servicelnterface to connect to https grisu vpac org grisu ws services grisu M Login e Note At least Java 1 5 5 0 required Advanced connection properties c MONASH University FN ZiVEC 7 eResearch Centre YEA k 6 Auscope Marcs 9 VIRTUAL ORGANISATIONS VOS e Click on the Change button and select the Workshop VO StartUp all new users of ARCS Services limited access Workshop a temporary VO for this workshop until 19 June A AA Grisu client l Job submission Monitoring File management File transfers Current VO StartUp Applications MONASH University xe AIVEC T Hesearch Centre MERE Auscope Parcs 7 UNDERWORLD TEMPLATE e Click on button e Select the underworld template click on Add button Grisu client Jobsubmission Monitoring File management File transfers Current VO startup Add application Change beast Applications blast generic gulp g lamarc mrbayes namd Daup WELCOME TO THE UNDERWORLD OF THE ARCS GRID C AuScope arcs amp 3 MONASH University 7 e e Hesearch Centre O00 Grisu client Job submission Monitoring File management File transfers EK WE Basic job properties Job parameters StartUp Jobname CPUs underworld job 000000 Parallel Applica
15. rr txt 660 B stdout txt 860 KB 4 lt Copy Files vj AAA Grisu client Job submission Monitoring File management File transfers Sources Target Status X MONASH University lt NAICS CS v MONA Centre FANS IV i s 25 VICTORIAN PARTNERSHIP FOR ADVANCED COMPUTING 2 B RAYLEIGHTAYLORBENCHMARK WO RKSHOP RESTART XML e Now let s restart the previous model from checkpointed files e Revised output parameters lt param name maxTimeSteps gt lt param gt lt param name dumpEvery gt 10 lt param gt lt param name outputPath gt output lt param gt e Revised checkpoint parameters lt param name checkpointPath gt checkpoints lt param gt lt param name restartTimestep gt 400 lt param gt Note checkpoint files generated on one cluster may not work on another architecture AuScope arcs X MONASH University 4 tralian Research Cl Te Hesearch Centre SANGER GE 26 Grisu client Job submission Monitoring File management File transfers Current VO Basic job properties Job parameters Workshop Jobname CPUs C change Workshop_RTB_restart Parallel V Applications underworld Walltime Days Hours Minutes No of cpus le wl 20 v 0 0 20 iz m Submission details Display all available Queues Site VPAC d Queue dque tango m E Version Select version Auto select 1 2 0 r
16. ser documentation http www underworldproject org See http www underworldproject org documentation UnderworldGridWorkshop2009 html for today s workshop slides Metascheduling submit a compute job to the Grid rather than a specific site to run on the first available applicable resource e ARCS Data Fabric beta http www arcs org au products services data services Hear more about ARCS Systems tomorrow Jim McGovern Systems Services Manager ARCS ARCS Systems from Grid to Cloud Computing 10 to 11 am Room 135 Building 26 Clayton Campus XX AAN Oe C AuScope AarCS MONASH University AVEC u e Hesearch Centre wee
17. t Job submission Monitoring File management File transfers Se N Basic job properties Job parameters b DM S LOU LL Workshop Additional Command s optional Enter any additional commands in this field otherwise leave blank Applications underworld w InputFile file Users wmason Desktop RayleighTaylorBenchmark Workshop xml Browse Additional File s optional Select files one by one or by whole subdirectory a Site Local Path Users wmasor Share HH J Koala O Trash glite globus 5 grisu ssh mee G a fl 4 C v r CO C E A O00 Grisu client Job submission Monitoring File management File transfers Current VO Workshop Submission started Applications TemplateNodes filled underworld TemplateNodes processed Job created on server Modules processed Uploading local file Users wmason Desktop RayleighTaylorBenchmark Workshop x ml to gsiftp ng2 vpac org home grid workshop DC au DC org DC arcs DC slcs O ARCS IdP CN Wendy Mason iAXmEACqQIWVNPUFxvQbndijlixA grisu jobs Works hop RTB RayleighTaylorBenchmark Workshop xml PostProcessors executed successfully Job description stored on server Job submitted to endpoint Additional job properties stored on server Job submission successful O OO Grisu client Job submission Monitoring File management File transfers Filter Jobname Status Submission Tim
18. tions underworld Walltime Days Hours Minutes No of cpus 0 7 0 v 10 v 1 os Submission details Display all available Queues Site NCI NF Queue express acpbs Ha Version Select version Auto select 1 1 0 a i Notify me when job V starts M finishes Email wendy mason sci monash edu au SN WORKSHOP EXERCISES e Download files for today s exercise from http www underworldproject org documentation UnderworldGridWorkshop2009 html e These exercises are modified versions of following four of the several template models that come with Underworld Extension xml MultiThermalDiffusivity xml RayleiehTaylorBenchmark xml SlabSubduction xml e Note that the resolution in today s examples is set very low for the purposes of demonstration e Afull set of template model files for each recent release of Underworld can be downloaded from http www underworldproject oreg downloads MONASH University ERS T Hesearch Centre em 10 Auscope P Marcs S EQUATIONS IN UNDERWORLD E val DET exe X giu f Viscoelastic stress prediction 2 Tijj Pi Plastic correction to yield surface Momentum and Mass conservation DI Scheme for plastic correction Energy conservation Advection of materials MONASH University e Research Centre Auscope Parcs 11 7 1 EXTENSION WORKSHOP XML e High viscosit
19. to use a hierarchy of XMLs so your model setup can be split into separate XML files to be included in your Input File e g different parameter sets e All included files not part of the Underworld code must be Staged in as additional files MONASH University RS Au5cope I ars T Hesearch Centre 31 UNDERWORLD INPUT FILE STRUCTURE All Underworld XML files start amp finish with StGermainData xmlns http www vpac org StGermain XML IO Handler Jun2003 gt lt StGermainData gt e You can add comments to your XML files lt comment gt e Base application Underworld BaseApps e g lt include gt Underworld BaseApps RayleighTaylor xml lt include gt e Plugins mostly output plugins e g list name plugins mergeType merge gt lt Output Plugins gt lt param gt StgFEM FrequentOutput lt param gt lt param gt Underworld Vrms lt param gt lt param gt StgFEM CPUTime lt param gt lt list gt cz MONASH University 4 n e VANG UY c esearrc a O ntre VICTORIAN PARTNERSHIP FOR 3 2 ADVANCED COMPUTING Auscope PMarcs S UNDERWORLD INPUT FILE STRUCTURE e Component list Component Codex http www auscope monash edu au codex v1 2 0 work in progress has been further developed since parent child relationships between components all component lists must use the following format struct name components mergeType merge gt struct name
20. y incompressible bar shaped region which yields according to the VonMises model in a low viscosity compressible material e Aweak zone is located approximately half way along the bottom of the region to facilitate localisation of deformation e The domain is stretched horizontally as determined by extensional boundary conditions MONASH University lt 4 e Research Centre OU SVN 12 ADVANCED COMPUTING C AuScope arcs N BASIC JOB PROPERTIES e Jobname name of output directory e Walltime maximum length of time job will run e CPUs number of processors at least 2 for mpi jobs e Site organisation s to which your VO has access hosting grid enabled cluster s which have grid enabled Underworld modules installed e Queue grid enabled cluster s at the site amp their queue s e Version grid enabled Underworld modules installed on the cluster 1 2 0 recommended e Notification receive an email when your job starts amp or finishes note that Jobname will be shortened in email auscope ars A MONASH University ae T Hesearch Centre QRAN PARTNERSHIP FOR 13 ADVANCED COMPUTING JOB PARAMETERS Grisu client Job submission Monitoring File management File transfers Se vo Basic job properties Job parameters StartUp NEN Change Additional Command s optional 2 Applications Enter any additional commands in this field otherwise leave blank Ad d t O n a Co m m a n d s sa
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