The NOMAD1 (Novel Materials Discovery) …NoMaD – Project No. 676580 D3.1 Remote Visualization...

NoMaD–ProjectNo.676580

D3.1RemoteVisualizationGuide 1

TheNOMAD1(NovelMaterialsDiscovery)

Laboratory–aEuropeanCentreofExcellence

RemoteVisualizationGuide

Documentdate:02May2016Documentversion:1.0DeliverableNo:3.1

FullName ShortName

BeneficiaryNumber

Role

MAX-PLANCK-GESELLSCHAFT ZUR FOERDERUNG DERWISSENSCHAFTENE.V.

MPG2 1 Coordinator

KING'SCOLLEGELONDON KCL 2 BeneficiaryHUMBOLDT-UNIVERSITAETZUBERLIN HUB 3 BeneficiaryTHE CHANCELLOR, MASTERS AND SCHOLARS OF THEUNIVERSITYOF CAMBRIDGE

CAM 4 Beneficiary

UNIVERSITATDEBARCELONA UB 5 BeneficiaryAALTO-KORKEAKOULUSAATIO AALTO 6 BeneficiaryDANMARKSTEKNISKEUNIVERSITET DTU 7 BeneficiaryBAYERISCHEAKADEMIEDERWISSENSCHAFTEN LRZ 8 BeneficiaryCSC-TIETEENTIETOTEKNIIKANKESKUSOY CSC 9 BeneficiaryBARCELONA SUPERCOMPUTING CENTER - CENTRONACIONALDE SUPERCOMPUTACION

BSC 10 Beneficiary

PINTAILLIMITED PT 11 Beneficiary

1NotethattheabbreviationhasbeenchangedfromNoMaDtoNOMAD,andthiswillbeusedfromnowon.2BeneficiaryMPGincludesthreegroupsactiveintheNOMADLaboratoryCoE-FHI,MPCDFandMPSD.



Abstract

The main overall objective of work package 3 (WP3) is to develop a centralized visualizationservice(RVS) that enables scientific users of theNOMAD Laboratory CoE to interactively performcomprehensivedataexplorationandvisualization taskson theirowncomputerswithouthaving toinstallanyspecializedhardwareorsoftware.Tothisend,WP3willsetupanRVSwithasecureandconvenient, eventually browser-based connection and will provide a selection of analysis tools,preconfiguredworkflows,andcorrespondingdocumentationandguidance.Inthecourseofthefirstfewmonthsoftheproject,acompleteprototypeRVSwithan initialsuiteofvisualizationtoolshasbeenimplementedanddocumentedforNOMAD.TheNOMADConsortiumcannowalreadyataveryearly phase of the project test and assess these tools, which will give us ample time for theirrefinement.Usingtheprototyperemotevisualizationservice,asuccessfullivedemonstrationofthefirst use case was given, thus verifying the passing of the correspondingmilestone (MS7). In thisreport, we provide an overview of the remote visualization approach and its specific role in thecontext of the NOMAD Laboratory CoE. We describe our newly implemented prototype remotevisualizationservice,demonstrateitsreadinessfortheNOMADLaboratoryCoEwitharepresentativescientific application, and deliver a snapshot of a "remote visualization guide" which is the mainsourceofdocumentationforusers.

Copyright 2016 by theNOMADConsortium. The information in this document is proprietary totheNOMADConsortium.This document contains preliminary information and is not subject to any license agreement or any otheragreementwiththeNOMADConsortium.Thisdocumentcontainsonlyintendedstrategies,developments,andfunctionalitiesandisnotintendedtobebinding upon to any particular course of business, product strategy, and/or development oftheNOMADConsortium.TheNOMADConsortiumassume no responsibility for errors or omissions in this document. Furthermore,theNOMADConsortiumdoes not warrant the accuracy or completeness of the information, text, graphics,links,orotheritemscontainedwithinthismaterial.Thisdocumentisprovidedwithoutawarrantyofanykind,eitherexpressor implied, includingbutnot limitedtothe impliedwarrantiesofmerchantability, fitnessforaparticular purpose, or non-infringement. TheNOMADConsortiumshall have noliabilityfor damages of anykind includingwithout limitationdirect, special, indirect,orconsequentialdamages thatmayresult fromtheuse of these materials. This limitation shall not apply in cases of intent or gross negligence. Thestatutoryliabilityforpersonalinjuryanddefectiveproductsisnotaffected.Inaddition,thematerialspresentedandviewsexpressedherearetheresponsibilityoftheauthor(s)only.TheEUCommissiontakesnoresponsibilityforanyusemadeoftheinformationsetout.



RemoteVisualizationGuide

1 Introduction.................................................................................................................4

2 Background..................................................................................................................5

3 Approach......................................................................................................................6

4 Results.........................................................................................................................7

5 Impact........................................................................................................................14

6 Conclusion..................................................................................................................15

7 Appendix1.................................................................................................................16



1 IntroductionThemainoverallobjectiveofworkpackage3(WP3)istodevelopacentralizedvisualizationservicethatenablesscientificusersoftheNOMADLaboratoryCoE(i.e.,thematerialsdatabaseandthedataanalyticsplatform) to interactivelyperformcomprehensivedataexplorationandvisualization taskson their own computers (PC or laptop) without having to install any specialized hardware orsoftware.Toachievethis,wewillsetuparemotevisualizationservice(RVS)suchthatNOMADuserscanperformgraphicalanalysistaskswiththesameuser-experienceasifthesoftwarewereinstalledlocallyontheircomputers.

Figure 1: Schematic comparison of aremotevisualizationservice(RVS,left-handside) with the conventional localvisualization approach (right-hand side).When using a RVS, the rendering occursclose to the data repository andtransmission of massive raw data (e.g. inGaussian cube or HDF5 format, indicatedby thick arrows) over the network isavoided. Instead,onlyaremotedesktop istransferred over the network as a streamofcompressedjpegimagesinacompletelytransparent and application-agnostic way(thinarrow).

The remote visualization service is basedon awell-established server-side rendering technique, inwhichcallstothegraphics libraryareinterceptedontheserverside(i.e.,thesitewheretheRVSisoperated) insteadofbeing forwarded to theX-serveron the client'sdevice. Theadvantageof thistechnique is that powerful graphics hardware on the server-side can be used, and that only acompressedstreamofrenderedtwo-dimensionalimageshastobetransferredtotheclient’sdeviceand not the three-dimensional scenes themselves (cf. Figure 1). Server-side rendering techniquesutilizewide-areanetworks,usuallyviaaVNC-likeprotocol,whichalsohandles theuser interactionviamouseevents (cf.Figure2).UsingoptimizedsoftwaresuchasTurboVNC, server-side renderingcan be achieved in a very efficient, completely transparent, and application-agnosticway, i.e. theuserexperienceisthesameasifthe(arbitrarypieceof)graphicssoftwarewasinstalledlocallyontheuser's device.Most importantly, by virtue of running the graphical application “remotely” on theserversidethismethodobviatestheneedfortransferringanykindofrawdatatotheclient’sdevice,thusfacilitatingtheinteractiveanalysisofmassiveamountsofdataviawide-areanetworkswithonlyverymoderatebandwidthrequirements(cf.Figure1).

WP3 will set up an RVS with a secure and convenient, eventually browser-based connection.Together with a selection of capable graphical analysis tools, preconfigured work flows, andcorresponding documentation and guidance this RVSwill enable users to perform comprehensivevisualanalysisofmassivedatasetswhicharestoredinorgeneratedbytheNOMADLaboratoryCoE.

In the course of the first few months of the project, we have already implemented a completeprototype of our remote visualization service for NOMAD. The correspondingmilestoneMS7wasreachedwellaheadofschedule.ThisremotevisualizationserviceallowedustoprovidetheNOMAD



Consortiumwithaninitialsuiteofvisualizationtools.TheNOMADConsortium3cannowalreadyataveryearlyphaseof theproject testandassess these tools,whichwill giveusample time for theirrefinement.Usingtheprototyperemotevisualizationservice,wegavesuccessfullivedemonstrationof the firstusecase,which isbasedona representativedata setand includes challenginganalysisand visualization requirements. Due to the early availability of the visualization services,wewereable to produce a set of high-quality scientific images and movies, which can now be used foreducationalanddisseminationpurposes.

In this report,weprovideanoverviewof the remotevisualizationapproachand its specific role inthecontextoftheNOMADLaboratoryCoE.Wedescribeournewlyimplementedprototyperemotevisualization service, demonstrate its readiness for the NOMAD Laboratory CoE and deliver asnapshotofa“remotevisualizationguide”whichisthemainsourceofdocumentationforusers.Wefinallygiveanoutlookonfuturework.

2 BackgroundFiles intheNOMADArchiveandtheMaterialsEncyclopedia (cf.D2.1‘Code-independentdatabase’)aregenerallytoolargetobetransferredtotheuser’sdevice(laptop,PC)forperforminginteractive,visual analysis. For example, ab-initio (DFT)molecular simulations generate three-dimensional andtime-dependent scalar fields suchas theelectrondensityor time-dependentwave functions. Suchdata sets are typically in the range of several Gigabytes per individual simulation.Moreover, thehardware of the client's device might not be capable of rendering such data and the requiredsoftware tools are usually not installed. To overcome such shortcomings and to spare users thetechnical burden of having to install and maintain their own visualization software, remotevisualization services are nowadays provided by virtually every scientific (high-performance)

computingcenter.

Figure 2: Sketch of the main architecturalcomponents employed by the standardremote-rendering approach. Calls of thegraphical application (e.g. a visualization toollike VisIT, ParaView or VMD) to the graphicslibrary (GL) and interactions (X11 cmds, X11events) are transparently handled on theserver side (application server), thus allowingthe application to use the server's 3Dhardware. An X- proxy (TurboVNC, in mostsettings) channels the display and keyboard(KB)andmouseevents to/from thedevicesofthe users (Client 0,1,…,N). With this methodanyapplicationthatworksonalocal3Ddisplaycan also be operated remotely withoutmodification.(Source:www.virtualgl.org)

3NOMADConsortium-TheNOMADConsortium isthegroupofall13PIsoftheNOMADLaboratoryCoE.Specifically,theconsortium is represented by Matthias Scheffler (MPG-FHI), Stefan Heinzel (MPG-MPCDF), Angel Rubio (MPG-MPSD),Kristian Thygesen (DTU), Arndt Bode (LRZ), JoséMaria Cela (BSC), Alessandro De Vita (KCL), Claudia Draxl (HUB), DaanFrenkel(UCAM),FrancescIllas(UB),KimmoKoski(CSC)RistoNieminen(AALTO)andCiaranClissmann(PT).



WP3developssucharemotevisualizationservice(RVS)fortheNOMADLaboratoryCoEanddesignstheunderlyinginfrastructureincollaborationwithWP6.Thisdocumentreportsonthecompletionofthefirststepstowardsprovidingsuchaservice,namely:

• thetimelysetupofaprototypeRVS(pRVS)forproject-internalusewhichisbasedonawell-established, TurboVNC-based software solution and will be running on existing hardware(Task1),

• thedocumentationof theservice in the formofa "living"document in thepublicNOMADWiKi(Task1,2),

• a survey of software solutions for developing a production-type RVS with browser-basedaccess(Task1),and

• the selection, provisioning and assessment of software tools for interactive, visual dataanalysisfromab-initio(DFT)molecularsimulations(Task2).

3 ApproachAt the Max-Planck Computing and Data Facility (MPG-MPCDF; formerly: RZG), a prototype RVS(pRVS) has been set up for theNOMAD Laboratory CoE. It is based on the open source softwarepackagesVirtualGL/TurboVNCandbuildsontheMPG-MPCDF’sexperienceandexpertiseinrunningageneral-purpose RVS for scientific users of the Max-Planck Society. Specifically, for the NOMADLaboratoryCoE,usermanagementat theMPG-MPCDFwasextended incollaborationwithWP6toallowtheNOMADConsortiumaccesstothepRVS.Thistaskwascompletedattheendofmonth1.Inaddition,comprehensivedocumentationwasprovidedonhowtoconnect to thepRVSandhowtousetheavailablevisualizationtools.

TheprototypeRVSisservingasthetestandassessmentplatformfortoolsrequiredfortheNOMADLaboratory CoE (Task 2). Starting outwith common atomic structure (VMD, PyMOL), and general-purposevisualizationtools(VisITorParaView),acomprehensivesetofvisualizationtoolsrelevantforthe NOMAD Laboratory CoE is being established (MS8 ‘Basic toolkit’, due M12; MS10‘Comprehensive toolkit’,dueM18).Thespecificvisualizationtasksarebasedonthe followingdataclasses:

a) chemical structures: “Balls and sticks”-typeof visualizationof atom types, coordinates andbonds,

b) “spatial” data: scalar or vector fields in three-dimensional spacewith an additional fourthcoordinate(e.g.time),and

c) “abstract”datainamultidimensionalspaceofparameters.

Independent of the availability of data from the NOMAD database or the NOMAD data analyticsplatform,bothofwhichareunderdevelopment,dataofclassesa)andb)havealreadybeenusedinan “ad-hoc” way for assessing the pRVS in general and for selecting and evaluating specificvisualizationtools.Asafirstusecase,wehavevisualizeddatafromanab-initiomoleculardynamicssimulationperformedwiththeFHI-aimscode.Weinitiallyfocusedonanalyzing“spatial”data(classb).We considered VisIT and ParaView, because common visualization software in Chemistry (e.g.VMD or PyMOL) often cannot visualize periodic structures or periodic scalar fields as found incondensed matter simulations. VisIT and ParaView support comprehensive quantitative analysis



capabilities for “spatial” data and offer a large variety of standard manipulation and interactioncapabilitiessuchaszoom,clip(plane,sphere,iso-volume),slice(plane,iso-surface,…),state-of-the-artrendering(pseudo-colour,volume-rendering,…),andquantitativeanalysismethods(e.g.creatingderived mathematical expressions from primary data on the fly). Moreover, VisIT and ParaViewmightbecapableofhandlingalsodataofclassc).

The pRVS was set up and is operated by MPG-MPCDF. MPG-MPCDF and CSC have written thedocumentationforthepRVSandfortheusecase.ThepRVS-setupwasextensivelytestedbyMPG-FHI,CSCandMPG-MPCDF.LRZ,togetherwithMPG-MPCDFandCSChasstartedasurveyonbrowser-basedRVS solutions.MPG-FHIhas specified ause case andprovided thedata for theuse case. Inaddition, they specified requirements for the analysis and visualizationof thedata andperformedtheassessmentoftheVisITtooltogetherwiththeMPG-MPCDF.CSChasperformedtheevaluationofthe ParaView tool. CSC and BSC performed benchmarks for the use case on their respectiveproductionRVS.MPG-MPCDF,CSC,AALTOandLRZcontributedtothewritingofthedeliverable.

4 Results

4.1 ImplementationanddocumentationoftheprototypeRVSFortheprototypeRVSprovidedbyMPG-MPCDF,auser-guidetailoredforNOMADusagehasbeenwritten,whichdocumentsthefollowing:

• howtoaccessthepRVS,• howtoworkwithgeneral-purposegraphicalanalysistoolssuchasVisIT,ParaVieworVMD,

and• how to use the graphical analysis tool VisIT to work with a data set from an ab-initio

moleculardynamicssimulation(seebelowforadetaileddescriptionoftheusecase).

This remotevisualizationguide ismaintainedasasetofpages inmarkdownformatand ispubliclyaccessible under the NOMAD WiKi (https://gitlab.rzg.mpg.de/nomad-lab/public-wiki/wikis/remoteviz/home). It is continuously being extended and adapted. A snapshot of theremotevisualizationguide(asof15Apr2016) ispresentedinAppendix1.ThepRVSisopentotheNOMADConsortiumandexternalreviewers.Currently,aregularMPG-MPCDFuseraccounthastoberequestedviaanelectronicform.Theprocedureandclient-softwarerequirementsaredocumentedin the remote visualization guide (https://gitlab.rzg.mpg.de/nomad-lab/public-wiki/wikis/remoteviz/MPCDF-RVS).

4.2 AssessmentoftheprototypeRVS:firstusecaseOntheprototypeRVS,weinstalledseveralstandardvisualizationtoolssuchasVisIT,ParaView,VMD,andPyMOL.Additional software tools canbemadeavailableon request, typicallywitha responsetimeoflessthanaday.Asafirstusecase,wedecidedtovisualizedatafromanab-initiomoleculardynamicssimulationperformedwiththeFHI-aimscode.TheusecasesimulatestheadsorptionofaCO2molecule on a CaO(001) surface, a process that is relevant in catalysis. The data is stored inGaussiancubefileswithca.400files(1pertimestep)eachcontainingtheelectrondensitytabulatedonanequidistantCartesiangridwithca.100x100x100zonesandthepositionsandidentitiesofca.35atoms.Therequiredfunctionalityforaquantitativeanalysis(thisistheprimaryfocus),asworkedoutbyTask2,isasfollows:



1. predefineadefaultviewandenablecomprehensiveanalysisworkflowsfortheuser,2. basicuserinteraction:

a) start,pause,continuethetimeevolution,b) rotate,transfer,zoominorout,c) determinespeciestypeandatomnumberbyclickingthesphererepresentingthatatom,

andd) setandchangetheiso-valueforthedensity,andthecolourscaleforthevolumetricdata.

3. select a plane anddisplay a colourmapor a contour plot of the (interpolated) volumetricdata,

4. calculatethedensityintegralwithina3Dboxselection,5. displaydistances,angles,anddihedralanglesbyselectingatoms,and6. interactivelyreplicatetheunitcell.

Figure3:DefaultviewofthepreconfiguredVisITsessionoperatedonthepRVSatMPG-MPCDFfortheusecase described in the text. The leftmost panel provides the main interaction facilities for (from top tobottom):openingandclosingfiles,atime-sliderfornavigatingbetweentimesteps,buttonsforaddingplotsandoperators,aswellasanumberofpreconfiguredvisualizations(a“plot”withapipelineof“operators”).The plots are rendered in the main, central display, which also allows basic mouse interactions such asrotations, translations and zooming. In this example, the unit cell is replicated twice in each horizontaldirection(2x2x1)andavolume-renderingoftheelectrondensityisshownontopofaballs-and-sticksmodeloftheatoms.Therightmostpanelletstheuserchangethereplicationfactorsinanyofthethreedimensions.

Using theVisIT tool (in its latest version 2.10), a preconfigured “session” (VisIT allows to save thestate of an interactive session as an XML file which can easily be shared with other users) waspreparedwhich,afterconnectiontothepRVSandstartingupofthetool(preconfiguredasadesktoplauncher) presents the user with a number of predefined “views” of the data. Specifically, thefollowing“plots”and“operators”(thesearethefundamentalconceptsoftheVisITtool)havebeenpreparedbyus,a:



• pseudo-realisticvolume-renderingplotoftheelectrondensity,

• molecularplotshowingaballs-and-sticksmodeloftheatoms,

• pseudocolorplotwithselectedcontoursoftwoplanes(selectedbythesliceoperator),and

• pseudocolorplotofiso-surfacesoftheelectrondensity.

Figure4:Byselectingthecorrespondingplotsthatwerehiddeninthedefaultviewafterstartingthesession(cf. Figure3)and toggling the“Hide/Show”button in the interactionpanelahorizontal slice through theelectrondensityfieldwithcontoursisdisplayedinaddition.

Forallplots,a“replicate”operatorcontrolsthereplicationoftheunitcell (a2x2x1-foldreplicationwaschosenasadefault,asshowninthefigures).VisITcanautomaticallyextractthelatticevectorsfromthedatafilesin“Gaussiancube”format.ThescreenshotgivesabasicimpressionoftheoverallappearanceoftheTurboVNCsessionandbasiccontrolpanelsanddisplaysprovidedbyVisIT.

Theusecasedescribedabovewaspresentedasa livedemonstrationat theNOMADPImeeting inBerlin on 02March 2016. The demonstration is documented by a number of screenshots in thisreport,andcaneasilybereproduced, interactivelyexplored,andfurtherdevelopedbytheNOMADConsortium. For the live demonstration, a TurboVNC client installed on a standard laptop wasconnected to the pRVS at theMPG-MPCDF via a standard wireless network connection that wasavailableintheseminarroomoftheconferencecenter. Abasicassessmentofa)thefunctionality,andb)theperceiveduser-experienceandperformanceissummarizedinthefollowing:

a)Functionality:therequiredfunctionalities listedabovecouldbemet immediatelybyusingVisIT'sbuilt-in tools (cf. Figure 3 - Figure 6) with the exception of conveniently displaying distances andangles between selected atoms. The latterwarrants further investigation and possibly require theextensionoftheVisITtoolortheexplorationofalternativesoftware.Wehavestartedexploringthe



capabilitiesofParaViewatCSCandfoundthatParaViewindeedprovidesthedesiredmeasurements(cf.Figure7)butfallsshortinotheraspects.Forexample,ParaViewprovidesnoconvenientwayforreplicatingtheunitcellandthe file reader loads theGaussian-cubefiles individually,butnotasananimation.Theseproblemsmightbesolvablebysupplyingappropriatescripts.Furtherinvestigationsarenecessaryen route toMS8 (Basic toolkit’, dueM12), including the considerationof alternativetoolssuchasVMDorPyMOL.

Figure5:SameasFigure4,butshowingalatertimestepandusingadifferentcolourscaleandtransparencyforthehorizontalslice(selectableinthepanelonthebottomleft).

Figure 6: Same as Figure 3, but selecting a 4-fold replication of the unit cell in each horizontal direction(4x4x1),andapplyingahigh-qualityvolume-renderingalgorithm (raycasting)witha logarithmic scalingoftheelectrondensity.



b) Performance: for a given time step, which is stored in an individual cube file, basic userinteractions likerotate,zoom,shift,hide/showplotsetc.wereperceivedassmoothandfluent, i.e.“interactive”frameratesofatleast10-20framespersecond(fps)arereachedonthisdataset,evenafter4-foldto16-foldreplication.

Thelatencyofloadinganewtimestep,however,isontheorderofasecond,whichisnotsufficientfor experiencing a good visual impressionof thedynamicsof the systemwhen the timeevolutionplaysat1-2fps.ThisbehaviorwasconfirmedbytestsperformedbyNOMADpartnersBSCandCSCon theirproduction-level remote visualization systems. The reasonsare1) I/Operformanceof theRVShardware,2)datastructureandformatofGaussiancubefiles,and3)performanceofthevolumerenderingalgorithminVisIT.TomeetdeliverableD3.2(‘Firstassessmentofvisualizationtools’,dueM18)wewill1)improvetheI/Operformancebycopyingthecubefilestotheinternalsolid-statedisk(SSD)of the renderingnodeatMPG-MPCDF,which significantlyoutperforms the raw I/Ospeedofthestandardhard-diskbasedGPFSparallelfilesystem,2)considerformatsotherthanGaussiancubefiles (e.g. HDF5) for storing scalar fields such as the electron density, and 3) test a new, high-performancevolumerenderingalgorithmforGPUswhichwillsoonbereleasedbyNvidiaasaplugin(called“index”)forParaViewandVisIT.

Figure7:ScreenshotofaParaViewsessionforthesameusecaseasadoptedfortheanalysiswithVisIT.Thissession isretrievedbyopeningapreconfiguredParaViewstatefile.Theupperpanelonthe leftshowsthedataandthefiltersappliedtoit.Filterpropertiescanbechangedinthelowerpanel.Theanimationisplayedusingthevideobuttonsonthetop.



In summary, we have demonstrated that the pRVS enables users to perform comprehensivevisualization taskswith the sameuser-experience as if the softwarewere installed locally on theirdesktop.Notably, bydemonstrating “interactive” frame rates (the caseof an individual time step)during the live demonstration we could confirm that the remote visualization approach usingTurboVNCviaawirelessconnectionandawide-areanetworkispersenot limitingtheinteractivityandsmoothnessoftheanimations.

4.3Towardsbrowser-basedRVSaccess

Classical,terminal-basedremotevisualizationservicesareusuallyoperatedinenvironmentsinwhichsecurity is crucial, access is restricted and multiple ssh hops are required to access the remoterendering system. This also applies to theNOMAD prototype RVS as described above,which, likemoststandardsetupsincomputingcentres,requiresuserstoholdregularcomputingaccountsandto install a specific piece of client software on their device which establishes the connection andprovides the "viewport" to the remote display. Although client software (e.g. TurboVNC) is freelyavailable for all relevant operating systems and ssh hops can usually be straightforwardlyimplemented,e.g.withthehelpofscripts,weconsidersuchprerequisitestobeaseverelimitationforthewide-spreaduseoftheNOMADLaboratoryCoE.Thus,forthefinalRVSweenvisageaquickandcomfortablebrowser-basedaccessviawebinterfaces.Todecidewhichsoftwarewouldbemostappropriate,LRZsurveyedavailablesolutions. Inthefollowing,wepresentthetwomostpromisingapproaches,noVNCandxPra.

Figure8:noVNCLoginwindow(imagetakenfromnovnc.com)

noVNC

noVNC (http://novnc.com) is a browser based VNC client that uses the HTML5 <canvas> tag andWebSockets.Thewholedisplayoftheremotesystemistransferredintoabrowserwindow.noVNCgenerallysupportsallmodernwebbrowsersincludingmobileplatformssuchasiOSandAndroid.The



supportedVNCencodingsareraw,copyrect,rre,hextile,tight,aswellastightPNG.Communication,inputfromtheclientsideandtheresultingvideostream,ishandledviawebsockets.Figure8showstheweb interface for the initial VNC authentication. Figure 9 shows a Linux desktop environmentstreamed inaChromebrowser tab. The icons in the topbar canbeused for configurationand todisconnect.

ThearchitectureweproposefortheNOMADLaboratoryCoEreplicatestheproductionarchitecturesetupatLRZ.Itincludesthefollowingcomponents:

• ApacheWebserver,• noVNC,and• VirtualGL.

Figure9:AstreamednoVNCDesktopinsideabrowserinterface(imagetakenfromnovnc.com)

xPra(https://xpra.org/)

xPra (https://xpra.org) follows a similar philosophy as noVNC, facilitating easy access to remotesystemsorremoteapplications.UnlikenoVNC,xPraprovidesthechoicetograntusersaccesstoafulldesktopenvironmentortolimitthemtoindividualapplications.InxPra,videoistransmittedeitherasH.264,JPEG,PNGorRAWstream.AswithnoVNCwebsocketsareusedforcommunication.xPrahasbeensetupbyLRZstafffortheEuropeanProjectMrSymBioMath(IAPP324554).



Although web interfaces are generally more comfortable for the end user, they require moreinstallationandmaintenancetimeandeffort.Moreover,thevisualizationperformance isknowntobe reduced due to lower frame rates or due to additional lag.Within the next 6monthswewillperform a quantitative performance assessment and provide input for D6.1 ‘HPC platformrequirementsandarchitecture’(dueM12)

5 Impact

Figure 10: Snapshot from a sample movie for illustration and dissemination purposes. Due to the largerreplicationratio(8x8x1)andtheuseofahigh-qualityvolume-renderingalgorithmsuchanimationscannotbehandledinteractively,yettheycanbegeneratedseamlesslywithinthesamepreconfiguredVisITsessionthathasbeenoutlinedabove.

Our early set-up of a prototype remote visualization service (pRVS) has made several graphicalanalysistoolsavailabletotheNOMADConsortium.TheycannowbetestedandfurtherdevelopedbyNOMADpartnersandtheycanbeintegratedintothedataanalyticstoolsthataredevelopedaspartof theNOMADLaboratoryCoE. TheNOMADConsortium cannow investigate the functionalityandperformanceof various graphical analysis tools using a single software installation at a computingcenter, thus relieving projectmembers from the burden of individually installing,maintaining andoperating complex software packages. Moreover, we started the performance assessment of our



remote visualization approach already at a very early phase of the project. This will allow us toidentify and eliminate potential limitations. This, togetherwith a survey of solutions for browser-based access allows us to start thework on the specification of graphics hardware, software andoperational requirements to be implemented byWP6. In addition, the pRVSwith its initial set oftoolsanddocumentationcanalreadybeusedtoproducehigh-qualityrenderings(cf.Figure10),e.g.,fordisseminationpurposes.

With thecompletionof steps2a),2b)and the successfuldemovisualization (Section4),milestoneMS7 ‘Visualization Prototype’ has been achieved ahead of schedule according to the means ofverificationintheDescriptionofAction(‘Remotevisualizationinfrastructureprototypeready(demovisualization)’).

6 ConclusionAprototyperemotevisualizationservice(pRVS)hasbeenestablishedalreadyataveryearlystageoftheNOMAD Laboratory CoE. It provides centralized access to graphical analysis tools and enablestheirassessmentbyprojectmembersinanefficientway.AusermanualforthepRVSandits initialsetofvisualizationtoolshasbeenproduced.Afirstscientificusecasebasedonrepresentativedatafromanab-initiomoleculardynamicssimulationandchallengingrequirementsfortheiranalysisandvisualization has been designed for demonstrating the readiness of the pRVS and for starting theassessmentofvariousvisualizationsoftwaretools.Asuccessfullivedemonstrationwasgivenforthisusecaseon02March2016,thusverifyingtheearlyachievementofthefirstmilestone(MS7).Thesetof deployed tools will be extended over the course of the next six months to provide a basicvisualization toolkit (MS12, D3.2). In close collaboration with WP6, we will further develop thecurrent pRVS into a convenient and secure browser-based solution that uses dedicated NOMADhardwareanddatainfrastructure.



7 Appendix1

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