OpenTEA Super-User Guide
Contents
1. 25 4 2 Batch execution of scripts The reusable scripts are written this way from XDR import def process_xor ds xor ds getValue xorchoice ie E SSA e a A RE E AR value ds getValue temperature print temperature value ie Soir e a a value ds getValue pressure print pressure value Hoama SS aA init process_xor getDsout finish In this pattern the function process_xor is callable ether by the GUI or by a separate python script which could be read as follow from XDR import import process_xor import process_multiple import process_defaults dsin dsout init dummy xml process _xor process _xor dsout process_multiple process_multiple dsout process_defaults process_defaults dsout 26 Python scripts hands on Errors while getting setting values The 1ib_lite application is voluntarily ill formed with tree parame ters named reali one in the multiple tab two nested in the defaults tab This redundancy will illustrate how XDR find the correct values in the memory of the application even if other share the same names In the lib_lite application sources open the python script process_default py The file should be similar to from XDR import def process_defaults ds print Processing defaults value float ds getValue reali dataset lib_lite defaults simple add print Real 1 is value ds setV2. param param21 iparam3 lparam4 1 hese 1 bees 1 ae 1 lees param 12 param22 lparam32 lparam42 lparam 12 param22 lparam32 lparam42 lparam 13 lparam33 lparam43 lparam 13 lparam33 lparam43 param44 lparam44 Figure 2 CFD solver information Figure 1 CFD solver information shown as a directed graph 17 ver tices for 16 edges stored in as a directed graph in cluding the cross dependencies 17 vertices for 35 edges The graph theory yields two conclusions 1 The hierarchical part of the setup or the way the user comprehend the setup can be implicitly modeled by the structure of a directed tree 2 The cross dependencies can link any parameters and cannot be implic itly modeled by the structure of a directed tree If the tree structure is used these dependencies must be explicitly declared Note that the implicit modeling of hierarchy makes native the error tracking according to the graph of Fig 1 setting the integer parameter Dimensions to 1 3 makes the vertex false The path Dimensions Domain CFD solver is recursively set to false The user can quickly track down the parame ter blocking the whole setup using this highlighted path This process is illustrated in Fig 3 Coupled parameters are common in scientific solvers because they gather the different aspects of the same approach For example the wall modeling and the sub grid scale modeling is a reccurent couple i
3. proc readPipe win address global widgetInfo DStree metaTree if gets widgetInfo address actionChan line gt 0 The python script is executed in the context of this channel Any stan dard output like print hello world will be redirected to the log of the GUI The key bind Esc send the signal to close the current channel On some architecture this is enough to stop the process but brute force os better As the process is a child of openTea an external stop of the child process such as kill 9 pid in unix will result in a simple error execution on OpenTEA giving back the control on the GUI Do not be afraid to kill zombies 28 5 Code execution Plugins scripts OpenTEA handles code execution through a peculiar layer of scripts the pluginsScripts After a brief look on the XDR execute which should re place any use of python execute inside OpenTEA scripts this section fo cuses on the global approach of pluginsScripts 29 5 1 The bare XDR execute command This command replaces the classical Python execute with a proper analysis of the command given in argument and an adjustable level of verbosity Note the use of subprocess Popen and not execute which gives a realtime output channel def execute command always _print err False silent True won This procedure searches for the specified executable in the script directory if Not it tries to execute the command itself The co
4. Neither the status nor the visibility of a node are related to the content of a project On the contrary these two element must be recomputed at each startup This is the only way to ensure that status are updated even when the application specifications have changed The statuses at the startup of an existing project depends on the way it was saved e Save All The default saving of OpenTEA is a direct dump of the memory tmpTree All informations are stored even default values spurious data and incorrect values option e Save Only Green The cleanup Saving of OpenTEA only the data related to green tabs are stored red and orange tabs are ignored It is a good habit to use regularly the Save Only Green op tion during the lifetime of a project to get rid of unnecessary data 12 XML projects hands on amp Project edition Open th exemple application opentea code exemple Process the tab and check the result 30 12 42 Then quit using Save all option Edit the XML project on the operator by replac ing addition by multiply Re open the XML project within opentea opentea code exemple file test_exemple xml The radio button must have changed Simplest application edition Edit the XML file of the application exemple named calc xml add the fourth operator division Edit the script file associated to the tab process_calc py in order to handle the division operator Re open the XML project
5. P Faber and P Heymans Introducing tvl a text based feature modelling language In Proceedings of the Fourth International Workshop on Variability Modelling of Software intensive Systems VaMoS 10 Linz Austria January pages 27 29 T Bray J Paoli and CM Sperberg McQueen Extensible markup lan guage xml 1 0 1999 P J Cameron Combinatorics topics techniques algorithms Cam bridge Univ Pr 1994 K Czarnecki S Helsen and U Eisenecker Staged configuration using feature models Software Product Lines pages 162 164 2004 K C Kang S G Cohen J A Hess W E Novak and A S Peterson Feature oriented domain analysis feasibility study Software Engineering Institute Pittsburgh CMU SEI 90 TR 21 1990 37
6. 3 Further reading The graph theory behind OpenTEA From the user point of view the input parameters of a solver are intuitively clustered in groups and subgroups However the interdependencies between all parameters do not necessarily respect a hierarchical segregation Both hierarchical vision and verification of dependencies are compulsory for an industrialized software the user will use the first one to navigate through parameters and the second one to know the implications of his actions The best approach to describe hierarchical vision and verification of dependencies is to use graph theories First a parameter is a variable to specify to the solver A parameter can have many different natures integer real boolean choice filename coor dinates The ensemble of parameters or parametrization defines a unique instance of the solver By definition 5 graphs describe the connectedness of systems and can help to create a formal model of parameter setups A general graph is a set V of vertices with a set E of 2 subsets of V called edges If the edges have an orientation so that they go from one vertex to another they are directed edges and the graph is a directed graph In the present context the vertices are linked to the parameters and the directed edges to their dependencies More precisely each vertex includes a boolean information about the validity of the parameter If the validity of parameter B needs to be tested when para
7. It is possible to customize OPenTEA by redefining the logo the name and even add additional engine capabilities In the case of C3Sm OpenTEA must be considered as a mere component powering the GUIs of the C3Sm software suite the combustion community and Safran users do not know about openTEA Moreover some extensions of the engine are private developed only for Safran group and are not under the terms of Cecill B licence In this case the GUIs are called with a simple variation of the initial script export PYTHONPATH 0PENTEA_HOME library PYTHONPATH export PYTHONPATH 0PENTEA_HOME XDRpy PYTHONPATH wish OPENTEA_HOME c3sm c3sm tcl config OPENTEAHOME myconfig xml o The Tcl Tk pre script c3sm tcl is sourcing the core opentea tcl after the surcharge of several variables and the declaration of one additional wid get coolac Ce programme depend des accords 1 ACCORD DE COOPERATION AVBP Gilg UIP Sil WOE Voir la fin du programme pour plus de details global additionalWidgets set pathEngine file normalize file dirname info script Customization of C3Sm image create photo icon_gui_small file file join pathEngine IMAGES_PRIV logo_c3sm_small gif image create photo icon_gui_tiny file file join pathEngine IMAGES_PRIV logo_c3sm_tiny gif icones d application image create photo icon_hmg file file join pathEngine IMAGES_ PRIV
8. OpenTEA application require other packages such as Scipy the developer must mention explicitly this dependency and include an explicit error handling about this topic in his scripts 24 4 1 The link between the GUI and the Python scripts Scripts are associated to the application on tabs lt tab name xor order 1 title Test XOR script process_xor py gt The script must be present at the startup else the following error is raised Error in startup script File not found Volumes library lib_lite scripts process_multiple py The script can be written in a standalone version from XDR import init xor getValue xorchoice if oxor si pha nie value getValue temperature print temperature value foror Uparan value getValue pressure print pressure value finish The following structure is compulsory from XDR import init actual actions finish e from XDR import to import the OpenTEA memory module e init to download the memory of the GUI tmpTree in the python context e finish to upload the altered memory of python context into the GUI The actual actions in the script are handled by classical python actions Note the memory access using the XDR function getValue node optional disambiguation The memory alteration is done using the reverse XDR function setValue value node optional disambiguation
9. Smago nb LES ane spec TPFL ___ Species e pen e Te giy eqs Se Q TPE Ea evap euler Laminar ici se fficiency avbp s o combustion T FM Zan 5 E Thickened _ omega0 Ce A exclude ET gasout domain o mesh Z a ignition T energydeposition gt requires Noslip wall 2 Slip requires Mandatory aw IN Go o Optional i boundaries ES toe i No ee init outlet Pressure velo laminar l Or temperature y7 turbulent z profil lt f fat Alternative XOr tpfvelo z Tequired O tpfcompo excluded Figure 8 Feature Diagram of the CFD LES code AVBP 6 26 using the notation of Kang 7 The diagram is simplified more than sixty boundary conditions are available and only the major model parameters are shown 3 3 3 Practical implementation On the way to simplify the communication between solvers teams and in dustrialization teams Boucher et al 3 suggests a text based approach to 19 describe the softwares and shows an application of the concept to a family of printer drivers This reduces the knowledge overlap to an exchange of text files As the language needed to model research software will be used only reluctantly by solver teams there is a strong constraint this language must be research oriented i e as explicit as possible handled by the classi cal academic tools editing with a vi emacs zredit console grafting pruning with a console cp mv rm or
10. e off GUI edition of projects Creating a proper project without GUI This section ends with a detailed review of the principles that let to the actual OpenTEA data structure 3 1 Getting started with OpenTEA Projects OpenTEA project are an XML file foo xml and a homonym folder foo sharing the same location The XML project is usually divided in two blocks within the dataset block one block for the solver e g example and one block meta for the context of execution of the project For a full save of a project the XML file reads as lt xml version 1 0 encoding UTF 8 gt lt dataset gt lt exemple value gt lt calculatrice value gt lt basic value gt lt number_a value 30 gt lt operator value addition gt lt number_b value 12 gt lt result value 42 0 gt lt basic gt lt calculatrice gt lt exemple gt lt meta gt lt solver gt lt name value exemple gt lt solver gt lt project gt lt name value test_calc gt lt address value Volumes Data Users dauptain Documents TEST_C3SM test_calc xml gt lt username value G Hannebique gt lt company value cerfacs gt lt project gt lt action gt lt callingAddress value root exemple calculatrice gt lt action gt lt temporary gt lt scriptSuccess value 1 J gt lt engine gt lt name value OpenTEA gt lt launchCommand value System Library Frameworks Tk framework Versions 8 5 Re
11. grafting operation The advantage of storing the description of each model into a specific file is twofold 1 Like any source code subroutine in academia these small files can be edited with lightweight editors e g vi managed by release managers e g SVN CVS and installed uninstalled from a console or a file browser Adding simply one file to the arborescence gives more au tonomy in a trial and error attempt In all aspects researchers can interact with these files like they do with source code 2 Contractually each of these files becomes the deliverable entities as sociated to the industrialization of the associated model Each file has its own traceability and its own confidentiality properties The deliverable is paid to the solver team redirecting the industrialization funding towards the scientific team 3 3 6 Toward multi physics applications A multi physics application can be addressed either by a multi physics solver monolithic approach or by several dedicated solvers that exchange bound ary conditions coupled approach Industrialization of a monolithic ap proach is straightforward with the present methodology but a coupled ap proach rises new issues Conjugate Heat Transfer CHT problems treated by coupled legacy codes are a good illustration of these issues This solu tion has the advantage of using existing state of the art codes to solve fluid 21 and solid equations and of being able to exchange one
12. within opentea opentea code exemple file test_exemple xm1 and test the extension to the division Finally mod ify the XML named calc xml to prevent a division by zero Status modifications Open the library lib_lite Process the first tab then exit using Save Only Green making a file dummy xm1 Check the content of the project Only the data related to the first tab xor is stored Reopen the project and check statuses The first tab is green others are still orange Exit again using the Save All and check the content of the project There is also data for the last tab defaults Reopen the project since data is filled and valid for the last tab the status is green Exit again Edit the type attribute of the parameter dafaults simple reali from type double_gt0O to type double_1t0 Reopen the project and chaco that the status went to red at startup Have a break stay calm and drink coffee Corrupted project salvage Open the library lib_lite set the first XOR to the beta option 13 process save and quit Edit the library lib_lite xor xor by renaming the model beta into newbeta Reopen the former project The engine will raise a popup error of the type POPUP ERROR The option beta is no longer available in the XOR root lib_lite Please remove this item from the XML Edit the project and remove the references to texttt beta LOr Or then reopen the p 14 oject 3
13. 3Sm engine and interpreted for the graphical display The XML content being the one and only data source it IS the source code of the application It can be seen as a high level declarative programming language section Execution A python script is associated to this tab with three steps item It reads the data stored in the GUI item It make some operations item Il send back new data to the interface The first and last step are already part of the C3Sm engine An application developper only focuses on the middle step lt docu gt lt model gt One can see that all the specifications needed to build the GUI are present in this file In particular parameters number_a operator number_b are all set by this file 11 3 2 About statuses During the GUI execution the project is loaded in the memory in a Tcl array named tmpTree readting to all the user actions Therefore the tmpTree is the exact real time image of the GUI content When the user is is processing a TAB in the GUI the valid tmpTree branches are dumped into an other array DSTree working as a saving point filled only with consistent informations Tip Both tmpTree and DS tree arrays can be browsed using the Debug gt tmpTree resp Debug gt DSTree main menu While looking into the tmpTree one can see both visibility and status are also provided for each node These information are never stored for the following reason
14. A is a Graphical User Interface factory developed at Cerfacs 1 1 Description The OpenTEA protocol is focused on scentific software with complex d o f degrees of freedom This protocol is threefold 1 Add to the software a set of metadata These metadata are meant to ease the understanding rise the possibilities and secure the setup of the software These constraints often make the metadata largely different from the initial input data This part is discussed in section 3 2 Add to the software a set of successive setup processes These processes are usually meant to translate the metadata into input file Note that the same metadata can lead to several input files for different versions of the same software This part is discussed in section 4 3 Add to the software execution a flexible encapsulation to ease the porting and increase robustness This part is discussed in section 5 1 2 Licensing The software is under the terms of Cecill B licence therefore Open Source with any applications possibles including commercial applications The Cecill B license is fully compatible with BSD like licenses BSD X11 MIT which have a strong attribution requirement which goes much further than a simple copyright notice a requirement normally not allowed by the GPL itself which describes it as an advertising requirement This license is also defined to make BSD like and FSF s LGPL licenses enforceable internation ally under WIPO
15. A pluginScript is a pythonScript dedicated to the use of a specific resource by OpenTEA The same plugin is used by all users for all applications on this resource A typical plugin scripts shows the following structure 1 The initialisation part e getting values in the GUI for the selected plugin e checking the connexion e checking the distant folder 2 The declaration of supported application using the decorator line XDR supported_applications 3 The distantCommand script e global initializations 9 e 3 lines of Te TE TE TE TP TP TP TP TP ATP TP TP TP e application specific commands a 99 Te de de pe pp EHH H Jf Jf jf Jp o 3 lines of AHHHHHHHHHHH e sending the directory gathering the necessary files e execution of the command via ssh 4 The retrieveDirectory script 5 The removeDirectory script This structure is the most general When the plugin with a local ex ecution on the same resource as OpenTEA many simplifications can be done 1 The initialisation par e getting values in the GUI for the selected plugin 31 2 The declaration of supported application using the decorator line XDR supported_applications 3 The distantCommand script e global initializations 9 ALHA e 3 lines of te Tt TT TP TP TP TP TP e application specific commands e 3 lines of H H H H LE fp fy Le ye Hh 4 The retrieveDirectory script void 5 The rem
16. OpenTEA Super User Guide A Dauptain December 16 2014 Contents 1 OpenTEA 1 1 Description m ie g o eee ee ee Dae ee 1 2 Licensing 4 4 2 472 ey As ee we Ra Eee ae oe Installation Getting started 2 1 Requirements TclITK 8 5 Python 2 6 6 2 2 Installation 3s o 4 0 4 A ee el ete ee trea a 2 2 1 Default Installation 20 2 2 2 2 Custom Installations 2 2 3 Hiding OpenTEA Adding private extensions Data structure of OpenTEA projects 3 1 Getting started with OpenTEA Projects 3 2 About statuses se yk ae ela eae eR eee Spee h 3 3 Further reading The graph theory behind OpenTEA 3 3 1 Operations on the tree model 3 3 2 The Feature Modeling 3 3 3 Practical implementation 3 3 4 XML files with explicit Feature Model notations 3 3 5 Scattering files 2 208 3 3 6 Toward multi physics applications Processes for the setup Python scripts 4 1 The link between the GUI and the Python scripts 4 2 Batch execution of scripts 20 4 4 3 Further reading Behind the scene the execution process Code execution Plugins scripts 5 1 The bare XDR execute command 4 5 2 pluginScripts contents 0 a eee eee 5 2 1 More about XDR sshsend 5 3 pluginScripts use 1 ee 24 25 26 28 1 OpenTEA OpenTE
17. _send command command execute command always_print_err True The basic requirement of this strategy is to have an access via ssh with out typing keyword i e with a RSA or DSA authentication key Keywords could be handled in OpenTEA using Expect but this would open an ex tremely dangerous security weakness on all the resources If the user distant profile profile or the likes is set in a way that some text is sent to the Standard Output as soon as the ssh is called this text will be treated as an error code and will eventually crash for any ssh attempt from OpenTEA 34 5 3 pluginScripts use The pluginsScript are used in OpenTEA in the following pattern feel te plugin plugin plugin plugin plugin eal p path_name temp_path ensureDirectory temp_path_name clean True tmp_track loadToolPlugin sendDirectory temp _path_name executeDistantCommand c3sm_auto_track temp path_name retrieveDirectory temp path_name removeDirectory temp_path_name tool_avbp 21 In other words a temporary folder is created gathering all the necessary data The plugin is loaded accordingly to the user setup see myconfig xm1 The file is sent executed retrieved and cleaned Note the arguments of two keywords c3sm_auto_track and tool_avbp621 in the executeDistantCommand These keywords must meet their counterparts in the plugins amp in the case of a local exe
18. a browser management with a CVS SVN like file manager The perception of this language by researchers is the cardinal point which will condition the ease of solver teams to reach the GUI compliant state A Domain Specific Language is therefore the best option with a tree shaped data structure and the six notations of FM to enrich the nodes The present section explains why an eXtensive Markup Language XML is a good candidate to this purpose what vocabulary is necessary for markups and why a scattered cloud of XML files is more suited to the present context Afterwards a quick overview on the GUI engine completes the picture of the methodology 3 3 4 XML files with explicit Feature Model notations XML is a set of rules 4 to write data structures Each file is composed of structured elements An element begins with a start tag and end with an end tag Attributes can be attached to start tags to describe the element and content is what is between the start tag and the end tag If no content is written the element can just be an only tag named empty element tag XML is not primarily made to handle cycled graph and as mentioned before only the hierarchical part of the graph is stored in the XML file The introduction of FM notations in the XML structure is a matter of vocabulary A possible example is shown in Fig 9 The six notations mandatory op tional or Xor require exclude are explicitly shown In this example both CFD and bo
19. alue value 3 1416 reali dataset lib_lite defaults simple add ds setValue value 3 1416 reali pass he SG ewe oe PY Na aa init process_defaults getDsout finish Remove the optional arguments on the ds getValue until the process crashes Try the same exercise on the ds setValue The same exercise can be done while changing the target address in the XML specification For example rename the real1parameter of the tab defaults into real1_dummy The process should yield to explicit error messages amp Using OpenTEA python scripts in batch mode Create a python script with a python loop able to relaunch the 3 scripts of lib_lite 100 times changing the prameter temperature each time This can be used either to setup and launch parametric runs or to automatically regenerate the input files from an existing project without the GUI 27 4 3 Further reading Behind the scene the execution pro cess The execution of scripts is done in the context of a Tcl pipe file open pipe With address being the tree address of the node usually the corresponding tab in the GUI and execCommand a command usually of the form python my_script py the pipe is started with the following lines set widgetInfo address actionChan open execCommand r fileevent widgetInfo address actionChan readable readPipe win address The action Channel is then read in real time by
20. ations Indeed a cycling simulation need some inputs specific to the cycling procedure in the left branch of Fig 5 plus several in stances of the same solver shown in the right branch of Fig 5 The coupling configuration is identical excepted that the global setup need the instances of different solvers right branch of Fig 11 17 2 The tree pruning operation is the removal of a vertex with all its chil dren from the tree A particular use of pruning is found when com paring two trees by tree substraction The tree substraction A B is the pruning of vertices of A which are in B and do not have differing children Figure 7 illustrates the concept and enhance the noncommu tativity of the operation The tree substraction is useful to compare exhaustively two arbitrary setups of the same computation and to solve frontward backward compatibility issues pruned eiti path Figure 7 Pruning op Figure 5 Grafting op eration for a cycling setup phases corre sponding to several se tups of the same CFD solver b 8 35 6 O Figure 6 Grafting op eration for a coupling setup a CFD solver coupled with a thermal solver eration for tree com parisons The operator substraction is non commutative Some vertices must be kept to find the path to the dif ferences 3 3 2 The Feature Modeling The requirements or research softwares being known by the graph theory are they compatible with the FM approac
21. cution the script is exactly the same but the commands plugin sendDirectory and plugin retrievedDirectory are void A slightly more complex pattern is i temp plugin duml XDR dir_path dum2 shutil shutil plugin plugin plugin plugin iret path_name temp_path ensureDirectory temp_path_name copy os path join getScriptDir script_track py temp _path tmp eater ec kee clean True load ToolPlugin imp find_module XDR copy XDR dir_path temp_path sendDirectory temp _path_name executeDistantCommand c3sm_auto_track temp_ path_name retrieveDirectory temp_path_name removeDirectory temp_path_name tool_avbp421 In this last pattern an OpenTEA script script_track py is sent to gether with the XDR python library to take care of the execution This is useful when the distant action is a sequential execution of several FORTRAN executables is far easier data is send once for all a the beginning and the debugging to debug a distant script rename the file out_dateset xml1 into dataset xml then re interpret the script using python script_track py This way you can execute interactvely the distant script on the final resource several times in a row 35 pluginScripts hands on amp The first FORTRAN execution Execute the following fortran program from the application exemple script process_calc py assuming the file squar
22. dePlugins In this case the startup script is similar to export PYTHONPATH 0PENTEA_HOME library PYTHONPATH export PYTHONPATH 0PENTEA_HOME XDRpy PYTHONPATH wish OPENTEA HOME opentea opentea tcl config OPENTEAHOME myconfig xml o The PYTHONPATH environment variable must be explicitly set for both the library and the XDRpy folder The wish command is finished by to enable additional keywords The wish command must be the last of the script The config keyword is compulsory in order to setup explicitly the actual config file of the user Missing this argument rises the following console dialog plus a popup window POPUP ERROR Error keyword config is compulsory to set explicitely your config file On the other hand a wrong path rises the following dialog on the console Error in startup script can t read configPath no such variable while executing file copy force configPath env HOME invoked from within Waite bintomexdistis k y tontigIk i set configPathtmp file normalize file join pwd key_config if file exists configPathtmp GIGS Cw ao oe file Volumes Data Users opentea opentea tcl line 166 This tedious argument is motivated by numerous errors caused by im plicit config files The config file usually named myconfig xml is similar to the following lt xml version 1 0 encoding utf 8 gt lt dataset g
23. ed choices is already in the working directory program squared open 10 file squared choices read 10 value close 10 result valuex 2 open 20 file squared out write 20 result close 20 end program The use of the command XDR execute is compulsory 4 FORTRAN giving data to the GUI In the same script read the data from squared out and fill the result GUI field with this data 4 FORTRAN getting data from the GUI In the same script write the file squared choices with the con tent of number_a The GUI is now operational for a FORTRAN square computation amp Creating your own Plugin Use the templates PluginsScripts stored in folderDATA to create your own pluginScript adapted to your resource The usage can be local or distant Do not forget to create the associated XML and to set your config file on this Plugin Adapt your square computation in order to use the script The use of the command XDR executeDistantCommand is compulsory 36 References 1 A Th venin A Piacentini T Morel and F Duchaine O palm An open source dynamic parallel coupler In IV International Conference on Computational Methods for Coupled Problems in Science and Engi neering Coupled Problems 2011 Kos Island Greece June 2011 A V Aho J E Hopcroft and J Ullman Data structures and algorithms Addison Wesley Longman Publishing Co Inc Boston MA USA 1983 Q Boucher A Classen
24. h Can a research software be regarded as Software Product Line SPL i e a family of related programs The basic Feature Model notation includes relationships between a parent feature and its child features e Mandatory child feature is required Can be extended to multiple e Optional child feature is optional e Or one or more sub features must be selected e Alternative xor only one of the sub features must be selected 18 In addition to the parental relationships between features cross tree con straints are allowed The most common are e A requires B The selection of A in a product implies the selection of B e A excludes B A and B cannot be part of the same product This basic model can be extended 6 by describing multiplicities of some mandatory resp optional features mandatory multiple means A must have 1 or more B children resp optional multiple means A can have 0 1 or more B children These six notations on a directed tree are sufficient to describe the parametrization of a research software The parametrization of the Computational Fluid Dynamics Large Eddy Simulation code AVBP is showed thought a Feature Modeling diagram in Fig 8 For the sake of clarity only five out of the sixty boundary conditions available in AVBP 6 28 and only major parameters are shown _ smu2 m AV lt 4 iW e smu K TTGC oie np CH4 lt e queue C02 te lt z algo Emoe time o rum local _____ mp TPFE we z diam
25. ing the following dialog in the log window Saving Project As file home cfd1 dauptain toto xml Script home rolex c3smgit library lib_lite scripts process _tast py is completed Error in script home rolex c3smgit library lib_lite scripts process_tast py Traceback most recent call last File home rolex c3smgit library lib_lite scripts process_tast py ine A alin F import avbp File home rolex c3smgit library avbp __init__ py ine Do im rom scripts import File home rolex c3smgit library avbp scripts __init__ py ines Do iom rom plugin avbp import File home rolex c3smgit library avbp scripts plugin_avbp py ine 3 im import XDR File home rolex c3smgit XDRpy XDR py ine 29 in raise Exception Exception Must be run with python version at least 2 6 6 and not python 3 Your version is 2 4 3 Tip Tcl Tk errors reads top to bottom first the actual problem then the nesting of this error On the other hand Python errors reads bottom to top the nesting of this error down to the actual problem 2 2 Installation 2 2 1 Default Installation The usual installation of OpenTEA is a bundle of the graphical engine opentea the XDR python library XDR and the repository of applications library This last repository also carry the reserved DATA repository with the Plugins repositories see Sec 5 OPENTEA HOME XDR opentea library DATA pluginscripts toolPlugins co
26. logo _hmg gif for the config and the footer of the app snecma image create photo icon_snecma file file join pathEngine IMAGES PRIV logo snecma gif THAT TH PTAA PAT Additionnal widget must be of the form create_mywidget tcl stored in folder SOURCES_PRIV The node mywidget will be automatically recognized widget for the coolant GUI lappend additionalWidgets coolac iho oenauatesee he LP Ce eee e I sess S s86e5 YU Coes 2 Cessa Vessel asss aesa I asana DM araroa annaas K oarece A Nellellels source file join pathEngine opentea tcl Using this pre script users know only about C3Sm instead of OpenTEA The same setup can be done for any group of applications Installation hands on Basic install Use the material of Sec 2 to install a distribution of OpenTEA on your computer Advanced install Create a custom library folder mylibrary and several copies of the engine opentea and XDR folders to mimic several versions of the en gine Adapt the startup scrip in order to switch the engine versions while using the same library 3 Data structure of OpenTEA projects After a practical description of OpenTEA projects a serie of hands on is proposed to get the following competencies e load and save From the trivial aspect of load and saving to the subtle handling of status e investigate and debug Handling ill formed or corrupted OpenTEA projects
27. meter A changes the associated graph is A gt B To ease the discussion in the relation A gt B A is the child of B and B is the father of A Furthermore validity is recessive i e if Ay gt B and Ag gt B then B can be true only if both A and Ag are true In other words a parameter can be valid only if all its children parameters are valid The parametrization of an arbitrary CFD solver is shown as a directed graph in Fig 1 taking into account the hierarchical dependencies only In the hierarchical graph of Fig 1 one can show that the n vertices are con nected by exactly n 1 edges by construction since all parameters are grafted either to the root vertex CFD solver or to a pre existing vertex By theorem 5 this graph is a tree i e a connected graph without circuits This particular graph allows a very efficient data storage 2 used by all filesystem browsers A second graph sketched in Fig 2 includes the cross dependencies be tween parameters of different kinds By construction the n vertices are connected by more than n 1 edges excluding this graph from the tree family 5 The descriptions of coupled parameters like the choice between a tetrahedron based numerical scheme and a hexahedron based one are rep 15 resented with a circuit cf example mesh file scheme of Fig 2 These circuits rise the complexity of a graph root root child1 child2 child3 child4 child Child2 child3 child4
28. mmand is then executed and its output is printed in standard output nu tot Need some work to handle long run and reading of the output on the fly if os path exists os path join scriptDir command command os path join scriptDir command print command command command shlex split command if silent False print Executing repr command in repr os getcwd n 50 n read_from None if lt in command read_from command 1 command command 2 p subprocess Popen command stdin subprocess PIPE stdout subprocess PIPE stderr subprocess PIPE if read_from p stdin write open read_from r read stdout_data if silent False print nXDRExecute StdQ0ut pn while True line p stdout readline if not line break if silent False print XDRExecute line rstrip sys stdout flush stdout_ data append line returncode p wait stderr_data p stderr read if always _print_err and not returncode if silent False print nXDRExecute tdErr pn print XDRExecute nXDRExecute join stderr_data split n if traite None 0 False Comme des retours negatif if returncode error Problem while running command join command n StdErr n stderr_data return join stdout_data 30 5 2 pluginScripts contents
29. n Large Eddy Simulation solvers 16 wate fo a optional e le ea T e ibnd3 bnd4 aj wa bnd5 Saar A Schild2 Ks an eo aram32 otrue param12 param22 false Figure 4 Three dynamic Figure 3 Path toward a invalid vertices a multiple ver parameter using the directed tree tex for the boundaries an structure A non validity is prop optional vertex for sin agated to the ancestors The gle two phase computa search for the non valid parame tions and an exclusive ter among 27 possibilities is high vertex whose children are lighted in 4 steps from the root mutually exclusive The tree model considered until now is static in the sense that no part of the graph can appear or vanish The actual setup of a solver is more dy namic the number of boundaries is not known in advance some equations are optional and some are mutually exclusive Consequently a supplemen tary property must be added to some vertices in order to allow the variety of setups illustrated in Fig 4 The exact property to add is discussed in the next section Operations on the tree model 3 3 1 Operations on the tree model Once a tree model is set its is possible to manipulate safely the solvers setups Two major operations are defined 1 the tree grafting operation is the addition of a tree B to a tree A by setting one node of A dependent of the root of graph B This opera tion is needed for the setup of cycled Fig 5 and coupled Fig 11 comput
30. nt industrialization methodology can be extended to the cou pling of legacy code by grafting the solvers tree to an application specific coupling tree as illustrated in Fig 11 Note that some exclusion require ments will be necessary impose temperature from fluid to solid and also temperature from solid to fluid for example will lead to exchange always the same quantity and no convergence A snapshot of the corresponding GUI is given on Fig 12 Parallel thermal solver developed at CERFACS 22 US 6 Phases av N ie AA Figure 11 Grafting operation for a CHT coupling setup a CFD solver coupled with a thermal solver Wish File Debug CIA TGM D complete cheris cas varam AAG aaan OD en Solution filename ain Desktop start h5 txt _ H 2 nz06 200 2 For coz0 2 chalo o 2 010 g mol OK 1788 6 kJ kg validate Figure 12 Snapshot of the C3SM graphical user inter face which must able to setup AVBP YALES2 AVSP simula tions as well as AVBP AVTP coupling with a reduced industrialization weight on academia with respect to the C3S project 23 4 Processes for the setup Python scripts The XML specifications must be completed with actions In OpenTEA these actions are done through Python gt 2 6 6 scripts The Numpy extension being now almost systematically associated to Python distributions on can use it safely within OpenTEA However if an
31. ossible to rely on environment variables however the debugging with become a bit harder the actual path is stored elsewhere and the environment variables of the python context of a subprocess can become extremely hard to control 5 2 1 More about XDR ssh_send This command encapsulated the action send this directory there using ssh Note that the actual transfer is done with a tar command before and after There is no temporary files the output of the tar is redirected to the ssh via a pipe def ssh_send host login distant directory local_directories_list options uu Uploads files to a server using ssh This creates a tar archive and pipes it through ssh to a tar xf on the distant side In short the command that we run is tar cf directoryi directory2 ssh distant_server tar xf C distant_directory with some additional safety won TODO check that we are on a platform where tar scp ssh actually exist TODO Check that local_directories_list is actually a list People will try with string and it does bad things with strings full host ssh_host host login if len local_directories_list 0 print No directories to be sent return print Sending and extracting archive commande ua pak ce At Ar evi kn E Gren Mery to ine lo cta lyndieelc t omnes ay leasite ae MURS ye ae Salah Binoy cee SS ANN era pee toe exch OL ERR taero T DEA ae ORANA UE iy Sia print ssh
32. oveDirectory script void An actual plugin for a distant execution will look like 32 class myplugin XDR Plugin def init__ self typePlugin initialisation by getting the data from the GUI testing the connexion and creating the distant folder XDR supported_applications tool_avsp52 tool_avbp621 def executeDistantCommand self command execDirectory appli flags print Plugin Running executeDistantCommand command in execDirectory appli INITS JHA hostname KALI pythonexec usr bin python TAIHA AA TEEPE AHA AHA AHA AHA PAH ETA AA AHA AHAA AHAA AAH AH a IHAA AAT TEEPE EEE ATT JHA 7 AVSP THA if appli tool_avsp52 avsp home home rolex QUIET_5 3 AVSP_HOME Temporary bug with axisym duplication in HIP v1 41 0 hip cur_ version home rolex HIP 1 40 1 hip 1 40 1 hostname avsptool plugin_avsp avsp_home hostname hip_cur _version pythonexec execDirectory command_exe avsptool switch_avsp _tools appli command THA AVBP JHA if appli tool_avbp621 avbp_home home rolex AVBP_V6 X AVBP_D6 2 1 avbptool plugin_avbp avbp_home hostname hip_cur _version pythonexec execDirectory command_exe avbptool switch_avbp _tools appli command PTT ATA AA TTP PAHA I ATTA AAA TTT TH THT TAA TTT ATT TH ca ia 7 PAHAA A AT AT TATA PTAA ETT if command exe startswith c3sm_a
33. rules The explicit reference to the French law and a French court in the Ce CILL licenses does not limit users who can still choose a jurisdiction of their choice by mutual agreement to solve any litigation they may experience The explicit reference to a French court will be used only if mutual agreement is not possible this immediately solves the problem of competence of laws 2 Installation Getting started 2 1 Requirements TclTk 8 5 Python 2 6 6 OpenTEA is currently using a graphical engine written in Tcl Tk 8 5 This limitation is motivated by use of the Themed Tk widgets native appear ance Tcl Tk 8 5 versions are almost always preinstalled on all flavours of Unix Linux distributions Using an older version of Tcl TK would bring the following dialog at the start of the GUI wish8 4 opentea tcl Error in startup script version conflict for package Tcl have 8 4 need 8 5 while executing package require Tcl 8 5 file opentea tcl line 4 OpenTEA is currently using the XDR python library a set of methods to give instant access to the memory of the GUI either for reading or writing This python library is customary for all Open TEA subprocesses The python versions must be over 2 6 6 one of the reasons is the format command which will fail on older versions The python versions must not be 3 or higher for they are not fully compatible with 2XX syntax Using the wrong version of python would br
34. solver with another easily The main drawback of this coupling methodology is that an adapted CHT framework is requested for the simulations especially on parallel ma chines The performances of such a coupling framework are linked to 1 the strategy to couple the solvers in an accurate and stable fashion and to 2 the exchange of information between the solvers in an efficient and scalable fashion when using a large number of processors Point 1 imposes to be able to extract and to impose information in the legacy codes during the computation at given times This work is done by collection of empty routines or User Defined Functions i e called at strategic places The success of point 2 relies on a coupling library able to e efficiently connect coupled geometric interfaces meshes or sub part of meshes of parallel solvers distributed on a large number of processors e produce high quality interpolations of exchanged data The OpenPALM coupler 1 co developed by CERFACS and ONERA tackles these issues It is used to control AVBP for the resolution of the fluid part and AVTP for the resolution of the conduction in solids In addition to the AVBP and AVTP parameters a set of coupling parameters has to be specified the frequency of meeting points for data exchange the number of meeting points the location where information need to be exchanged the type of information to exchange and some parameters for the interpolation The prese
35. sources Wish app Contents MacOS Wish Volumes c3sm c3sm tcl config Volumes myconfig xml plugins Volumes library DATA pluginscripts gt lt pluginsPath value Volumes library DATA pluginscripts gt lt libraryPath value Volumes library gt lt configPath value Volumes myconfig xml gt lt engine gt lt meta gt lt dataset gt First note that some nodes do not have any attribute at all Moreover the example block is only about the metadata content nothing is known about the validity or the default value The meta is essentially useful for debugging or datamining It is also used in Python scripts for some introspection matters see Sec 4 The XML file given to OpenTEA to create this application is lt model name basic title Simple Operation gt lt param name number_a title First number type double default 30 gt lt choice name operator title Operator type choice default addition gt lt option value addition title gt lt option value soustraction title gt lt option value multiply title x gt 10 lt choice gt lt param name number_b title Second Number type double default 12 gt lt info name result title Result type double gt lt desc gt This dialog triggers a simple computation lt desc gt lt docu gt How does it work section Graphical User Interface The XML file content is read by C
36. t lt config value gt lt gui value gt lt appearance value gt lt width value 1100 gt lt height value 1000 gt lt theme value aqua gt lt mode value multicolumn gt lt focusCorrection value 0 gt lt appearance gt lt paths value last gt lt lasitenyalie aye lt paths gt lt python value auto gt lt auto value gt lt python gt lt gui gt lt id value gt lt user value gt lt name value A Dauptain gt lt company value cerfacs gt lt cerfacs value gt lt company gt lt user gt lt id gt lt accounts value gt lt tool_plugins value distant_unix gt lt distant_unix value gt lt login value dauptain gt lt machine value babylon gt lt directory value wkdir cfdi dauptain gt lt nbprocs value 1 gt lt distant_unix gt lt tool_plugins gt lt accounts gt lt config gt lt meta gt lt dataset gt 2 2 2 Custom Installations A bit of flexibility is added when OpenTEA applications are used as pro duction tools They rely essentially on startup options e Explicit library position library To be used when several versions of the same library must coexist e Explicit plugins position plugins To be used when the plugins are NOT stored with the library folder 2 2 3 Hiding OpenTEA Adding private extensions The OpenTEA banner and logo are a default appearance
37. undaries conditions are mandatory but several nodes boundary conditions can exists A verbose mode supported only in Euler resolution is secured by the required parameter One can note that any choice or Xor implies the creation of an intermediate node which helps to store the choice result 3 3 5 Scattering files The description of a full solver in its entire complexity in one file is possible but heavy A alternative is scattering the solver description into smaller files 20 lt model name MySolver gt lt param name CFL type mandatory gt lt param name Vverbose type optional require equations Euler gt lt param name B C type mandatorymultiple gt lt param name passive scalar type optionalmultiple exclude species empty gt lt param name species type or gt lt choice name hydrogen gt lt choice name oxygen gt lt choice name water vapor gt lt choice name nitrogen gt lt param gt lt param name equations type Xor gt lt choice name Euler gt P lt choice name Navier Stokes gt Pag lt param gt lt model gt H2 mo M N Euler Figure 9 Example of an XML file with the Feature Modeling FM Figure 10 FM diagram associated notations to the XML FM file of Fig 9 As files are stored in a computer within an arborescence the tree structure of the arborescence can be used for in the description of the global tree using the
38. uto_ XDR error command was not understood command exe PATHE HHAH AHH SENDING DIRECTORY FAHA AHAHAHAH print Final composition of c3sm_archive print self dir2send XDR ssh_send self machine self login self distantDirectory self dir2send options TH THETA EXECUTING COMMAND PHA AT TT ATA sshCommand cd self distantDirectory execDirectory command_exe NB X allows here an interactive action output XDR ssh self machine self login sshCommand options X back to the initial directory os chdir local_directory return output def retrieveDirectory self directory local_directory os path abspath directory dist_directory os path basename local_directory Retrieve Directory if os path exists local_directory shutil rmtree local_directory scpCommand rsync a self login self machine self distantDirectory dist_directory os path dirname local_directory XDR execute scpCommand def removeDirectory self directory sshCommand bin rm rf self distantDirectory directory output XDR ssh self machine self login sshCommand options X 33 Several commands from the XDR library help to keep commands as sim ple as possible Note the XDR execute XDR ssh_send resp XDR ssh_retrieve commands which are all higher level commands than they look like Note also that in this plugin the path to the actual executables are totally explicit Il is also p
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