OASIS4-GUI User Guide
Contents
1. Figure 5 7 3 Boxes after loading components and NetCDF files 5 8 Coupling fields Once the different applications components and NetCDF files have been loaded you must define the connections between the coupling fields When clicking on the radio button Coupling fields on the top left pane c see the Figure 5 1 1 all the fields involved in the coupling appear in the left window see the Figure 5 8 1 Their names were obtained from the PMIOD XML files a Establishing a connection between a component and an input NetCDF file 24 When connecting the component ocn to the NetCDF file input_data_ocn nc the yellow bullets become red and the system opens a window to let the user characterize the connection between the coupling fields as illustrated on the Figure 5 8 1 eS File Settings Bl B B Aaa v Vecai yen aga Click with the left button C NetCDF files to select the output i my coupling field C Connections _____ Click with the left button to ocn select the correponding function received by the at data written in an output Ne input coupling field Insert a connection Source file jinput_data_ocn nc Source field input_data_ocn CF standard name Target component jocn Target field jinput_data_ocn CF standard name surface_net_downward_longwave_flux Minimal period 1 hours Exchange period 1 hours Target parame2. For example on a 64 bits Linux machine Tcl Tk 8 5 and libxml are not in the standard paths usr local lib and usr lib They are located in usr lib64 so it is not possible to use the automatic installation The different commands to install the source packages on such kind of machine are given below Be carefull that TclLib must be installed before Tclxml The directory lib is automatically created under the directory packages Installing Tclxml cd tclxml 3 2 configure prefix directory_of_mine oasis4 util gui packages exec prefix directory_of_mine oasis4 util gui packages make make install 2 3 Troubleshooting One problem commonly found on some systems is the absence of the telConfig sh file which results in the following error message configure WARNING Can t find Tcl configuration definitions The file in question is the configuration parameters of Tcl as installed on the system Usually the simplest way to get it is to download the linux package tcl devel from the Internet This package contains tclConfig sh tcl devel package comes in different releases as does tcl package Please first check the version of Tcl you have get_version tcl and then search the Internet for the corresponding tcl devel package version Be also careful that each Linux distribution has its own package format Some of them are becoming standard as the following RPM package originally from RedHat it is used on Fedora
3. Figure 5 5 1 Characteristics of the component ocn for the SCC file 19 You must enter the ranks on which the component will run You can also change the color of the box of the component by clicking with the left button of the mouse on the corresponding line Be aware that you have to edit all the components even if you do not change the ranks of the processes initilized by default at 0 to nbr_proc_appli 1 to be able to save the SCC XML file in the section 5 10 5 6 Input NetCDF files You can load existing input NetCDF files by using the menu File Load NetCDF Files These files can be restart files see OASIS4 User guide for their names or not In our example we have to load the NetCDF file input_data_ocn nc from which the component ocn will read its data see the creation of the AD and PMIOD files in the section 4 3 When using the menu File Load NetCDF Files a new window appears shown on the Figure 5 6 1 om File Settings w paa A A V View connections Applications and components C NetCDF files Coupling fields Load NetCDF files Directory space coquart OASIS4 GUI_3 2_installe Examples Browse Select file list File Mask nc Cancel Or enter new file name Figure 5 6 1 Loading the input NetCDF file for the component ocn 20 When clicking on the OK button another window appears with the characteristics of the file as illustrated on the Figure 5 6 2 Yo
4. There are the two directories in it tcllib 1 10 and Tclxml13 2 and the file TclxmlConfig sh In some non standard cases for example if Tcl Tk or libxml2 is not in the default location the automatic installation will not work on your system Therefore you may have to manually install the libraries 2 2 Manual installation of the libraries If you did not succeed to install automatically the libraries you can install them manually remembering that they must be located in the directory directory_of_mine oasis4 util gui packages lib Else they will not be found by the programs The installation of TclLib is done thanks to the script installer tcl with the options given below Installing TclLib cd package source tcllib 1 10 installer tcl no wait no gui no html no nroff no examples pkg path _ packages lib tcllib 1 10 no apps Tclxml uses the configure script You must check the appropriate options for your sytem Use the exec prefix and prefix to specify the destination directory lib is created automatically under this directory Use the enable threads switch if Tcl has been built with threads enabled Use the with tcl switch if Tcl configuration file tclConfig sh is not in a standard location Use the with xml2 config and with libxslt config switches to specify where are located the configuration files xml2 config and libxslt config of libxml2 and libxslt libraries if they are not in a standard location
5. I e Figure 5 1 1 oasis gui interface with our coupling example The main window consists of five planes a The canvas where a graphical representation of the current coupling is drawn b The menu and command buttons c The radio buttons selecting the type of elements listed in d d The list of elements participating to the coupling e The message bar where is displayed information related to mouse cursor position The user can control the width of the left panes c d by clicking on the slider appearing below the bottom right corner of pane c d The connections you created will disappear from the screen if you deactivate the View connections option 14 5 2 Description of the buttons bar a File Settings save of the scc and smioc files ane am gestion of input Connections and ouput NetCDF files load scc and load ad and smioc files pmiod files Figure 5 2 1 Buttons bar The first widget on the left on the Figure 5 2 1 can be used to load an already existing SCC XML file and its associated SMIOC XML files see also the section 5 10 The second one is used to load an application and its components AD and PMIOD XML files The third one is used to define new or to load existing NetCDF files The last one is used to save the SCC and SMIOC XML files at the same time see also the section 5 10 The two menus File and Settings will be described throughout the document 5 3 Loadi
6. application source You have then to define the output NetCDF restart file where the component ocn will write its data as plotted below on the Figure 6 2 see also the section 5 7 33 Applications and components C NetCDF files Coupling fields C Connections Edit Delete application component long name source application ocn ocean component Coupling field written in a restart file Load NetCDF files Directory space coquart OASIS4 GUI_3 2_installe Examples Mode_stand_alone Browse Select file list File Mask Or enter new file name ocn_restart_fnc_source ocn_rst 2001 01 01T00_00_00 nd Name of the restart file following OASIS4 rules k nc Figure 6 2 Defining the output restart file of the component ocn When connecting the component ocn to the NetCDF file you have to put the lag equal to zero see the Figure 6 3 below 34 Fie Settings S a a Aaa Leen Applications and components NetCDF files Insert a connection C Coupling fields Source component ocn S i Source field ocn_restart_fnc Edit CF standard name sea_surface_ temperature Minimal period 1 hours ocn_restart_fnc_sour lt Target file ocn_restart_fnc_source_ocn_rst 2001 01 01T00_00_00 nc Target field field CF standard name Exchange period Source parameters
7. this case each application has its own output files and the results are much simpler to analyze In MPI1 only the total number of processes here 3 is required on one line In MPI2 the names of the different hosts are required with the number of processors assigned to them 18 The total number of processes must stay lower or equal to the maximum number given in the AD XML file which is displayed in the second line of the form We recall that in this example the application source can only run on 1 or 3 processors We do not present any picture of it but you must do the same for the application target 5 5 Attributes of the components You must also define the attributes of the components that will appear in the SCC XML file You have first to select a component in the left window and then use again the Edit button If you edit the component ocn the following window appears on the Figure 5 5 1 E File Settings B amp a Applications and components C NetCDF files C Coupling fields C Connections V View connections long name atm target application atmosphere compa source application ocean component Edit component Name locn L yoi Long name ocean component 1 to 3 by step of 2 Number of Processes Ranks of Process io COE3CE Click inside with the left button to change the color of the box
8. Experiment dates and the Run dates included in these experiment dates see the OASIS4 User Guide 5 10 Saving and or loading a coupling configuration There are different ways to save the SCC and SMIOC configuration XML files 30 a By using the Save button see the section 5 2 or the menu File Save all In this case the SCC and SMIOC XML files are saved at the same time A window appears see the Figure 5 10 1 and you can choose the directory where you want to save these files Fie Settings z Sa pa iV View connections S i a aa Vee Applications and components C Coupling fields i Connections Edit Del 1 z ome application component long name ocn target application eo eo a atm atmosphere compa source application aa FL ocn ocean component ET directory where to save file scc xml Directory space coquart OASIS4 GUI_3 2_installe Examples E Mode_stand_alone E hd E z sd Figure 5 10 1 Saving the SCC and the SMIOC XML files b By using the file menu You can also save separately the SCC file and the SMIOC XML files by using the menu File Save SCC file or the menu File Save SMIOC files When saving the SCC XML file the geometry of the coupling in the main window is stored in the file Graphics xml 31 If you want to load an old configuration created with the interface you must have all the XML files AD PMIOD SCC a
9. Laure Coquart and Jean Marie Epitalon OASIS4 GUI User Guide Technical Report TR CMGC 10 36 SUC at CERFACS URA CERFACS CNRS No1875 France OASIS4 GUI User Guide Edited by L Coquart CNRS CERFACS J M Epitalon Consultant May 2010 1 TRO MU COM asucsssscisesashacecsasnsyeavsdebonesabivedaveseneastachavenya REEERE A OEE aS 3 2 T stalling the GATS sconnessi esaea R aaa aai aai Eia 4 2 1 Automatic installation of the libraries seseseeeseseeseesesesesressessrisresserserreesreserseresee 4 2 2 Manual installation of the libraries sosnsneenseneseenssesssesssseeesseesseesseesseressersssressrese 5 2 33 Troubl shootin g oretan neei ae ee er ee See s nnn E ee AE a E ERE 5 3 General characteristics of the User Interfaces seseseeeeeeseeseeseerrsreesersrerreesressrseresee 6 4 Running wizard tcl to create AD and PMIOD files eee eee eeeeeeneeceeeeeeeeeeeeeaeee 7 4 1 Characteristics of the app Cat OM ccs cose secetieeszeckaceacstudeecedhcaden aacenvizcusbartuunedeesteccaieces 7 4 2 Characteristics of each component included in the application eeeeeeeeeeees 9 4 3 Characteristics of each field of each component 0 0 00 eeeeeeeeeeeeceeeeeeteeeeetteeeeeneees 10 4 4 Saving the configuration files de bg ls ace eles enst data te ce dacee a dete deeded 12 5 Running oasis gui tcl to create SCC and SMIOC files eee eeeeeceseeeeeeeeeeeeeeeees 13 5 1 Description of the global graphical interface eee eeceeseeetecese
10. NetCDF file for the Cancel component atm Or enter new file name output_data_atm nd E ss E Fri Figure 5 7 1 Defining the name of the output NetCDF file for the component atm When clicking on the New button to validate your choice another window appears plotted on the Figure 5 7 2 where you must enter the name of the field contained in the NetCDF file 22 File Settings S a aa vaw connectens Applications and components C Coupling fields C Connections Edit Delete J Oo name io direction io mod cor input_data_ocn nc input losingle ocean component ie Edit NetCDF file Name joutput_data_atm nc I O direction joutput Access mode iosingle Suffix no Field name output_data atm Color Cancel Ok Figure 5 7 2 Characteristics of the output NetCDF file for the component atm By clicking on the NetCDF files item below the Applications and Components radio button the different NetCDF files involved in the coupling appear in the left window You can Delete them or Edit them if necessary Finally you obtain Figure 5 7 3 23 File Settings amp L H View Applications and components NetCDF files C Coupling fields output_data_atm nc output Click with the left button to select a NetCDF file
11. OpenSuse and Mandriva Debian package originally from Debian it is used on Debian and Ubuntu If nothing of the above works for you you can use the sample tclConfig h provided in this package in the directory package source To install everything in the standard locations you must be root or ask an administrator to do that for you Then depending on the location where you put this file you may install the libraries automatically or manually using the option of configure with tcl PATH If you did not succed to install the libraries neither automatically nor manually please contact Laure Coquart at CERFACS coquart cerfacs fr 3 General characteristics of the User Interfaces Online help is available for both wizard tcl and oasis gui tcl programs A box is displayed on the screen for each input required from the user For experienced users these online help may be deactivated by using the option silent on the command line when launching the programs see the sections 4 and 5 On every form presented to the user mandatory information is marked in red We describe and explain the two programs wizard tcl and oasis gui tcl through the creation of a coupling configuration step by step An application named source with one component ocn is coupled to an application named target with one component atm The component ocn reads data from an existing NetCDF file while the component atm writes data in a Ne
12. SIS4 GUI is based on Tclxml3 2 It is intended only for Linux Unix systems The utility sources are divided into four directories a gui main directory containing four Tcl Tk programs get version tcl install tcl wizard tcl oasis gui tcl and the other directories b gui package source directory with the libraries needed to run correctly the utility c gui IMAGES directory with the bipmaps used by the graphical interface oasis gul tcl d gui examples directory with the examples used to present and illustrate the document In the main directory the four programs are written in Tcl Tk version 8 4 If you run the program get version tcl you get the version of Tcl Tk installed on your computer The OASIS4 GUI interface requires version 8 4 or greater The program wizard tcl is used to create the AD and the PMIOD XML files which will be necessary to run the second program oasis gui tcl The program oasis gui tcl is used to generate the SCC and the SMIOC from the AD and PMIOD XML files as represented on Figure 1 1 By Ze AD JX ai SCC a i A AaS PMIOD SMIOC Figure 1 1 Functioning of the OASIS4 GUI The program install tcl installs automatically the libraries needed by the two programs wizard tcl and oasis gui tcl as described below in the section 2 1 The directory package source contains the source files of the Tcl packages needed for the execution These are written in C and Tcl Tk The directory Examples contains th
13. dialog based wizard helps you define your model application parameters so that XML configuration files are automatically generated at the end from your input XML files include Application Description AD file Potential Model Input Output Description PMIOD files Component jocn Component main attributes Description ocean component Simulated ocean 7 Default component yes v Number of processes 1 to 3 increment 2 Grids Add periodic J periodic K periodic grid_ocn true false Coupling fields input_data_ocn ocn_fnc_sent Add Previous Figure 4 2 1 Characteristics of the component ocn One component can not run on more processes than the number defined for the application For each component you must define all the grids that will be involved in the coupling with their directions of periodicity and then all the fields that can be exchanged It is recommended to declare the fields of a component in identical ordering as in the corresponding coupled component In our example there is only one grid grid_ocn periodic in the I direction for the component ocn This component reads data from a NetCDF file coupling field input_data_ocn and exchanges data with the component atm of the application target coupling field ocn_fnc_sent You go to the characteristics of each field of each component by clicking on Next You can always come back by using the Previous butt
14. e AD PMIOD SCC and SMIOC XML files that were created with wizard tcl and oasis gui tcl to present the interfaces below The first part of this document describes how to install on the computer the libraries contained in the directory package source The second part is dedicated to the description of the wizard tcl interface while the third part describes the oasis gui tcl program Finally we describe how to create the configuration files for a stand alone application see the OASIS4 User Guide for more details 2 Installing the libraries The libxml2 libiconv and libxslt are mandatory to run the interface OASIS4 GUL They are not provided with this package but you can download separately libxml2 and libxslt from xmlsoft org http xmlsoft org and libiconv from a GNU mirror site On Linux RedHat or Fedora you can check for libxm12 invoquing the command rpm q If Tcl Tk librairies and then the tclConfig sh configuration file are located in standard location as usr local lib or usr lib you should be able to install automatically the libraries Else you will have to manually install them see the section 2 2 2 1 Automatic installation of the libraries To install automatically you must type the following commands chmod u x install tel install tel At the end of the installation a new directory directory_of_mine oasis4 util gui packages lib is created containing the different libraries needed by the interface
15. eeeeeeeneecsaeenseeees 13 5 2 Description of the buttons Bats ccniedcscsticeta esd ceesniecreieadeeteeeteteieedeeseieseedeass 15 5 3 Loading the AD and PMIOD files oi ciczsacteesccschcidsensteredsiaiedeuscadduessadeosdeessbouaainapedevare 15 5 4 Attributes of the applications and components 00 eeeeeseesseceeeeeseeeeseeenaeenseeeees 17 5 Attributes of the COMI OMEDIUS scsi isese rE E 19 5 6 Amu NetCDF Ta 6 srs crease dorneta eadi eaa Eea NEEE i eee EESE EES EE 20 Sots Output NetCDF MS ssecsresioiaienien erinin esgere ia ase eig ass 21 5 8 Coupling fieldS posesnoincenaeioni nsi E aE E aena 24 5 9 Experiments SUIT AS ss pestiassosncenscengtncpessyies wesralen er A nae EE EET a EEE ERES ES 29 5 10 Saving and or loading a coupling configuration eeseseeseeeeeseeesesresrrererressreee 30 6 Whe minds standalone cajeticccsestincacerscactere ts resestsaclewveth dee dadedeaiecheanisaciaes vai a Ei 32 hy Acknowledgement 25 cccbps eceasesscetercvad besd ceucs enaiis E eaer asai 36 1 Introduction The OASIS4 Graphical User Interface helps OASIS4 user in creating the AD Application Description PMIOD Potential Model Input and Output Description SCC Specific Coupling Configuration and SMIOC Specific Model Input and Output Configuration XML files needed by OASIS4 to run a coupled model These files are described in details in the OASIS4_User_Guide pdf that you can find in the directory oasis4 doc in the sources of OASIS4 The OA
16. ff 4 value mandatory for restart files Time operation None Algebraic operation Mult by 1 Add 0 Non masked value scattering no Debug mode no 7 Statistics Masked off Non Masked off gt All off NetCDF field attributes Packing Scaling Adding Fill value Cancel Figure 6 3 Connection between the component ocn and its restart file When entering the Experiments settings you must put the number of processors of the driver to zero and put Run start date Run end date Experiment start date Your Experiment start date This date must also correspond to the one written in the name of the NetCDF restart file see the Figure 6 2 35 E File Settings EE a Q Lee Applications and components C NetCDF files Coupling fields C Connections Delete application component long name A source application ocean component Experiment settings Experiment name Creation of restart Long name Creation of restart by the ocean Start mode not_spawn Number of processes for OASIS driver 0 Year Month Day Hour Minute Second Experiment start date 2001 1 0 Experiment end date 2001 1 gt Run start date Run end date Figure 6 4 Experiments settings You finally save the configuration as for a coupling ca
17. nd SMIOC and Graphics xml in the same directory You can also load an existing SCC XML file if only the AD and PMIOD XML files are present in the directory 6 The mode standalone In this case the application is running alone without exchanging data with another component through the driver This particular mode can be used to create restart files with OASIS4 thanks to the routine prism_put_restart see the OASIS4 User Guide In the following we describe how to use the graphical interface to create the configuration files that will be used to create a restart file with OASIS4 for the component ocn of the application source We suppose that we have already created the AD and PMIOD XML files with the wizard tcl program see the section 4 You can find these files in the directory Examples Mode_stand_alone You must begin by loading the AD and PMIOD configuration XML files of the application source as shown below on the Figure 6 1 see also the section 5 3 32 File Settings S Bi a AB M View connections ai Applications and components C NetCDF files C Coupling fields C Connections Edit Delete application component long name start j Load Application Description files Directory space coq uart OASIS4 GUI_3 2_installe Examples Mode_stand_alone Browse Select file list File Mask ou _ad xml Figure 6 1 Loading the AD and PMIOD files for the
18. ng the AD and PMIOD files The first step is to load the XML files AD and PMIOD which have been created with the wizard tcl program before by using the menu File Load Application Descriptions You must choose the directory where the files are located and then select the AD files as shown on the Figure 5 3 1 below 15 NetCDF files C Coupling fields C Connections Edit Delete application component long name start Directory space coquart OASIS4 GUI_3 2_installe Examples Browse File Mask Select file list _ad xmi Figure 5 3 1 Loading the AD and PMIOD files The PMIOD XML files are automatically loaded when you load the AD XML files Once the AD and PMIOD XML files are loaded a box associated to each component appears in the canvas see the Figure 5 3 2 below 16 File Settings 5 a B Applications and components C NetCDF files application component long name l target application atmosphere compo source application ocean component lick with the left button o select Use the Edit button to edit an application or a omponent View connections Click with the left button to select and move around Double click with the left button to edit the component Input coupling field Click with the left button to hide the connections of the component Output coupling field Figure 5 3 2 Comp
19. oanp Symbolize the existence of data ocn input_data_ocn ne _ input T a regridding between the ot D i Get two components Figure 5 8 5 Graphical coupling configuration To be able to save the SCC and SMIOC configuration XML files you must fulfill the experiments settings that will be written in the SCC XML file as described now 5 9 Experiments Settings It is mandatory to fill up the experiment settings by using the menu Settings Experiment settings A new window appears as illustrated on the Figure 5 9 1 29 File Settings B S a Qa sea Applications and components C Coupling fields i Connections i atm input_data_ocn input _data_ocn nc Experiment settings Experiment name Ocn Atm coupling f Long name Ocena Atmosphere coupling Start mode not_spawn 7 Number of processes for OASIS driver Year Month Day Minute Second Experiment start date 2001 1 Experiment end date 1 Run start date Run end date Cancel Figure 5 9 1 Experiment settings The entry Experiment name is mandatory You have to precise the mode in which the application will be started spawn in MPI or not spawn in MPI from what is allowed in the AD XML file and the number of processes for the driver You must finally define the
20. od at which the coupling will be effectively performed 27 b Establishing a connection between a component and an output NetCDF file When connecting the atm component to the output NetCDF file output_data_atm nc the window Figure 5 8 4 appears File Settings B i a data_ocn input_dat ocn_fnc_sent ocn V View connections Insert a connection Source component atm Source field output_data_atm CF standard name Minimal period air_density 1 hours Target file output_data_atm nc Target field field CF standard name Exchange period Source parameters Lag Time operation Algebraic operation Non masked value scattering Debug mode Statistics None Mult by 1 fe ino Masked off gt Non Masked off All off NetCDF field attributes Packing Scaling Adding Fill value Cancel Figure 5 8 4 Connection between the component atm and the output_data_atm nc file The lag is only used in the stand alone mode for the creation of restart files see the section 6 and the OASIS4 User Guide Finally you get the graphical coupling configuration Figure 5 8 5 28 File Settings 6 a al aa M View connections Applications and components C Coupling fields Connections f from from component ne dain am A Sraa
21. on 4 3 Characteristics of each field of each component When clicking on Next the window on the Figure 4 3 1 appears corresponding to the first field input_data_ocn entered in the list of the component ocn 10 This dialog based wizard helps you define your model application parameters so that XML configuration files are automatically generated at the end from your input XML files include Application Description AD file Potential Model Input Output Description PMIOD files Component jocn Coupling field attributes Symbolic name input_data_ocn Description data read in an input NetCDF file Type single v CF Standard name surface_net_downward_longwave_flux vi Search list Intent input v Required yes v Gathering Scattering no 7 Units W m 2 Numeric datatype double Minimal exchange period 1 hours v Previous Next Figure 4 3 1 Characteristics of the field input_data_ocn When clicking on Next you will have to fill up the characteristics of the second field ocn_fnc_sent of the component ocn as shown on the Figure 4 3 2 This dialog based wizard helps you define your model application parameters so that XML configuration files are automatically generated at the end from your input XML files include Application Description AD file Potential Model Input Output Description PMIOD files Component locn Coupling field at
22. onents ocn and atm The boxes can be moved inside the window by using the left button of the mouse The coupling fields of the component are represented by the yellow bullets attached to the boxes The INPUT fields are at the top of each box while the OUPUT fields are at the bottom of the boxes Their number and their names have been obtained from the information given in the PMIOD XML files 5 4 Attributes of the applications and components You must define the attributes of the applications that will appear in the SCC XML file You first have to select an application in the left window and then 17 use the Edit button For example if you select and edit the application source you get the Figure 5 4 1 below E File Settings B a aa Applications and components C NetCDF files 3 Edit Application C Coupling fields eE ESSA Name source Number of processes 1 to 3 step 2 Edit Allowed start mode Either spawn or not spawn application jcomponent Executable name source arget Executable args arget atm Redirect stdout source ponies pes Hosts Add Name Nb processes Enter name 3 X V View connections Figure 5 4 1 Characteristics of the application source The name of the executable in red is mandatory The arguments needed by the executable are optional We recommend to keep yes for the Redirect stdout option as in
23. se except that you will have only one SMIOC XML file see the section 5 10 7 Acknowledgement We thank Moritz Hanke DKRZ Ren Redler Max Planck Institute and Sophie Valcke CERFACS who tested the GUI and re read this document for their remarks and improvements 36
24. t mode notspawn_or_spawn v Coupling mode coupled v Components Click with the right button to delete Next Figure 4 1 1 Characteristics of the application source The symbolic name in red is mandatory and must correspond to the argument appl_name entered in the routine prism_init of OASIS4 You must define the total number of processes on which the application can run In our case the application source can run only on 1 or 3 processors which is expressed by the increment value equal to 2 You must define the mode in which the application may be started notspawn for MPI1 spawn for MPI2 or notspawn_or_spawn if both may be used then the mode in which the application may run coupled standalone or coupled_or_standalone Finally you must enter the list of components included in the application These names must correspond to the argument comp_name entered in the routine prism_init_comp of OASIS4 In our example we only have one component ocn When clicking with the right mouse button in one particular line of the list a pop up menu appears that lets you delete the line Then by clicking on Next you will go to the characteristics of every component within this application 4 2 Characteristics of each component included in the application The window corresponding to the only component ocn defined in the application source of our example is shown Figure 4 2 1 OASIS 4 application definition wizard This
25. tCDF file The component ocn also send a coupling field to the component atm The application source can run on lor 3 processors while the application target can run on 1 2 or 3 processors In the last section 6 we finally present how to create the configuration files for the application source with the component ocn that will run in the stand alone mode see the OASIS4 User Guide for details 4 Running wizard tcl to create AD and PMIOD files The interface wizard tcl must be called before invoking the oasis gui tcl to create the AD and PMIOD XML files As there is one AD file per application wizard tcl must be launched for each application source and target of the coupling In the following we only present to creation step by step of the AD and PMIOD XML files of the source application In order to run the program wizard tcl just type wizard tcl silent 4 1 Characteristics of the application The first window that appears is about the characteristics of the application as illustrated on the Figure 4 1 1 below This dialog based wizard helps you define your model application parameters so that XML configuration files are automatically generated at the end from your input XML files include Application Description AD file Potential Model Input Output Description PMIOD files Application main attributes Symbolic name source Description source application Number of processes 1 to 3 increment 2 Star
26. ters Time operation None Closest time Algebraic operation Mult by i Non masked value gathering no Target debug mode no 7 Target statistics Masked off Non Masked off v All off E K f Figure 5 8 1 Connection between the component ocn and the input_data_ocn nc file Then you have a connection that appears in the main window and in the left plane as illustrated below on the Figure 5 8 2 25 File Settings ag ae K M View connections D t a aA Applications and components C Coupling fields 1 P yi canoa Double click with the left _ button to edit the connection Edit Delete i from component E Seo input_data_ocn input_data_ocn nc input ocean component 0 Click with the left button to select a connection Figure 5 8 2 Graphical connection Once you have selected a connection in the left window you can Edit or Delete it You can also double click on the graphical representation of it to edit it b Establishing a connection between two components When connecting the ocn component to the atm component a new window appears as on the Figure 5 8 3 26 File Settings S ti al AQ a Lae Insert a connection Applications and c C NetCDF files C Coupling fields Source field ocn_fnc_sent Source component Connec
27. tions CF standard name sea_surface_temperature Minimal period 1 hours Target component atm input_data_ocn input Si Target field jatm_fnc_recv CF standard name surface_temperature Minimal period 1 hours Exchange period 1 hours r Source parameters Lag Time operation None Algebraic operation Mult by 1 Add lo Non masked value scattering no Debug mode no Statistics Masked off v Non Masked off 7 All off Regridding 2D Bicubic w Options Target parameters Algebraic operation Mult by 1 Add 0 Non masked value gathering Ino Target debug mode no Target statistics Masked off Non Masked off gt All off Cancel OK e_ f 3 Ei Figure 5 8 3 Connection between the component ocn and the component atm You must enter the coupling period and define if there is a lag see the OASIS4 User Guide If the lag was equal to one the coupling field ocn_fnc_sent would be read from a restart file at the beginning of the experiment and you would have had to define it as in the section 5 8 a You must also define the Regridding type of interpolation with its options by clicking on the right Options button You can also add a scalar or multiply the target field by a constant By default there is no lag and then no restart files and no operation on the target field The exchanged period is the peri
28. tributes Symbolic name locn_fnc_sent Description function sent by the ocean to the atmosphere Type single 7 CF Standard name sea_surface temperature Search list Intent output v Gathering Scattering no vj Units K Numeric datatype double v Minimal exchange period 1 hours 7 Previous Next Figure 4 3 2 Characteristics of the field ocn_fnc_sent The description of all the characteristics needed for the exchanged fields can be found in the OASIS4 User Guide The CF standard names are read in the XML file cf standard name table xml provided with the utility and taken from the PCMDI Program for climate model diagnosis and intercomparison web site Be aware that the minimal period of exchanges is the time at which the calls to the routines of OASIS4 prism_put and prism_get are done in the component 4 4 Saving the configuration files When everything is fulfilled you have to save your AD and PMIOD XML files by clicking on OK as illustrated on the Figure 4 4 1 below The files are stored in the directory where you launched the wizard tcl and named accordingly to OASIS4 naming rules lt appl_name gt _ad xml and lt appl_name gt _ lt comp_name gt _pmiod xml 12 a This dialog based wizard helps you define your model application parameters so that XML configuration files are automatically generated at the end from your input XML files include Application Description AD file Potential Model Input O
29. u validate your choices by clicking on the OK button File Settings a a it NetCDF fil S w Edit NetCD e files Name input_data_ocn nc _ 7 1 0 direction input Applications and components NetCDF files Access mode iosingle 7 C Coupling fields Suffix no C Connections Time values unknown Edit if Color ok Cancel Input NetCDF file for the Directory space coquart OASIS4 GUI_3 2_installe Examples Browse component ocn eee file list File Mask ME Or enter new file name SL d E a EL J Figure 5 6 2 Characteristics of the input NetCDF file of the component ocn 5 7 Output NetCDF files You also define the output NetCDF files by using the menu File Load NetCDF Files You must enter in the window enter new file name the name of a new file that will be written during the run as shown on the Figure 5 7 1 21 File Settings GCI E aa Applications and components sla aia ea v View connections C Coupling fields C Connections Edit Delete name io direction io mod ane data_ocn nc input losingle ocean component Load NetCDF files Directory space coquart OASIS4 GUI_3 2_installe Examples Browse Select file list File Mask input_data_ocn nc E enc Name of the output
30. utput Description PMIOD files Validation Files to be created Note existing ones will be replaced source_ad xml source _ocn_pmiod xml Please click on OK to validate all the data you entered and generate the above XML files that describe the application and its components Previous OK Figure 4 4 1 Creation of the AD and PMIOD file for the source application 5 Running oasis gui tcl to create SCC and SMIOC files The Oasis gui is a tool that allows the user to graphically define a coupling configuration SCC and SMIOC XML files from the AD and PMIOD XML files created with the wizard tcl interface We will now describe the creation step by step of the coupling configuration and the associated SCC and SMIOC XML files corresponding to the AD and PMIOD XML files created above To run the interface oasis gui tcl type oasis gui tcl silent 5 1 Description of the global graphical interface The global interface representing our example of coupling when everything has been full filled is plotted on the Figure 5 1 1 13 File Settings Applications and components C Coupling fields c i application component long name oon rget target application ocean component rget atm atmosphere compo 9 ource source application ont ource ocn ocean component KE a d to control the width of the b c d planes pa pa b V View connec BEE aa lv Vie bid E
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