User's Manual: The RTGrid Portal
Contents
1. mc uk School of Compar Science Unversity Wakes UK 7 Cheek this be agree Do the terres cave Coppegre 2008 try argus Schoo Computer Cast Urivorsty Cord of Mecical Papua Vebncre nousta Figure 1 3 The sub panels Account Administration Resources Profiles and Experiments UK LT User s Manual The RTGrid Portal Version 2 0 Chapter 2 Installation Prerequisite packages to be installed are identified by the package name a URL from which they can be downloaded and an appropriate command for installing the package on systems that support Yum 1 Install and start MySQL server The RTGrid system requires a MySQL database server to be installed on the host system For further details on the installation of MySQL visit http dev mysql com The Yum installation command is as follows Syum install mysql mysql server 2 Create the RTGrid database After starting the MySQL server create the RTGrid database by running the following command as superuser Sdatabase dbinit_RTGrid2 sh user Sdatabase dbinit_RTGridPortal sh user where lt user gt is the username that will run the portal 3 Install other prerequisites The Experiment Manager requires the following packages a Python http www python org Syum install python MySQLdb http sourceforge net projects mysql pyth2. Schoo of Computer Science University Wales UK Figure 5 6 Viewing user group details Menu Group details Back to group list Create user m Last update time Apr 18 708 Fri 2 53 Creation time Apr 18 708 Fri 1 10 PM Ust groups Descripton List owned groups user group slows users to share access to administration related tasks Oriy users with Set preferences inistrator status should be allowed to join ths group Help Log out scmgy Refresh Members of this group sempdi Patrick Downes p downes bcs cardiffac uk School of Computer Science Cardiff University Wales UK Ir semjpg Jonathan P Giddy p gidoytbcs cf ac uk School of Computer Science University Wates UK songy Gagerine Yalkhom ac uk School of Computer Science Cardiff University Wales UK Dee Figure 5 7 Modify user group details User s Manual The RTGrid Portal Version 2 0 5 6 5 7 16 CHAPTER 5 ADMINISTRATION Listing the user groups owned by a user After a user group has been created the administrator who created the group owns the group By clicking on the List owned groups link on the action menu panel on the left all of the groups that are currently owned by this user will be listed Viewing or modifying user group details Details of a user group can only be modified by its owner or the administrator
3. ctae uk Wenn e Soence Contre Cam Vases UK sem gry Gagetre Yatrors uh of Compete Science Ureversty Wies UK W V Nore Delete 1293 Figure 5 2 Listing the users The next 10 users or the previous 10 users if available can be listed by clicking on the gt gt or lt lt previous link on the top right hand corner of the list header In the users list icons are used to identify the type and status of each of the users These icons and their meanings are as follows YW Inactive user without administrative privileges Active user without administrative privileges T amp K Inactive user with administrative privileges Active user with administrative privileges User s Manual The RTGrid Portal Version 2 0 5 3 5 4 CHAPTER 5 ADMINISTRATION 13 Only active users are allowed to use the RTGrid services For a user to become active he or she must first agree to the terms and conditions under which the RTGrid services have been provided Modifying user details In order to modify the details of a given user click on the row which corresponds to the user on the users list This will display the user modification dialog box as shown in Figure 5 3 Menu User details lt lt Back to user list Create use T Username scmjpg Real Name Jonathan P Giddy Create group List users List groups Email ID
4. resource manager provides interfaces for sutemitting jobs to Apr 21 08 Mon 3 50 PM ul Cardiff Condor This resource interface allows users to submit jobs to the Cardiff Apr 21 06 Mon 3 49 a Oxford NGS Gridi This resource manager provides interfaces for submitting jobs to Apr 21 08 Mon 3 44 PM tresh Select Al None Delete 1 3013 Figure 6 2 Listing resources State This summarises the current state of the resource Name The name of the resource which briefly describes the resource Description The description provides more detail about the resource This is used to provide in depth detail about the resource and its settings Last modified The date and time when the resource was last modified A check box appears in each row if the user can control the resource This may be used to select a subset of the listed resources Selected resources can be deleted by pressing the Delete button on the list header To summarise the current state of the resource four types of icons are used These icons are The locked icon is used to identify resources that are currently not usable by any user except for the owner A resource is locked when none of the groups are granted use access LJ The unlocked icon is used to identify resources to which jobs be submitted by any user who is a member of the groups that have been granted use access In order to unlock resource at least one group must be granted 5
5. 06 Fri 644 PM Set AR None Start Stop Delete 1 202 Figure 8 3 Listing experiments Associated with each of the displayed experiments are the following details Status This summarises the current execution status of the experiment It is divided into two parts a the first part displays the phase the experiment is currently in for instance Executing or Not Yet Started The second part displays the progress in that phase for instance Pending Failed etc Name The name of the experiment which briefly describes the experiment Description The description provides more detail about the experiment This is used to provide in depth detail about the experiment and its settings Last modified The date and time when the experiment was last modified User s Manual The RTGrid Portal Version 2 0 8 4 8 5 42 CHAPTER 8 EXPERIMENT MANAGEMENT A check box appears in each row if the user can control the experiment This may be used to select a subset of the listed experiments Selected experiments can be started stopped or deleted by pressing the Start Stop or Delete buttons on the list header Listing experiments owned by a user In order to list all of the experiments that are owned by a user click on the List owned link on the action menu Contrary to the listing described in Section 8 3 this will only list experiments that are currently owned by the user Hence some of the expe
6. lt Option gt lt Control gt The description of the choice control is very similar to that of the selection control The only differences are in the type attribute which is set to CHOICE and the column attribute which specifies the number of columns to be used for displaying the options Note here that the minimum and maximum number of columns that are allowed is one and four respectively Assortment control The assortment control allows a user to select a set of values from a given set of choices The main difference between this control and the rest is that it allows multiple values for a given parameter An assortment control is specified as follows lt Control type ASSORTMENT column 4 gt lt Label gt Select favourite fruits lt Label gt lt Name gt Fruits lt Name gt lt Choice gt lt Label gt Apple lt Label gt lt Value gt 1 lt Value gt lt Checked gt YES lt Checked gt lt Choice gt lt Choice gt lt Label gt Orange lt Label gt lt Value gt 2 lt Value gt User s Manual The RTGrid Portal Version 2 0 36 CHAPTER 7 PROFILE MANAGEMENT lt Choice gt lt Choice gt lt Label gt Mango lt Label gt lt Value gt 3 lt Value gt lt Checked gt YES lt Checked gt lt Choice gt lt Control gt The description is quite similar to that of the choice control except for the value AS SORTMENT for the type attribute In addition to specify an optio
7. 2525222 538 555946 6 39 52 an eperen uos Ee es oe 41 8 3 Listing experiments accessible to a user 41 8 4 Listing experiments owned by 42 85 Viewingexperiment details oc 2 eee R a Rs 42 86 Modifying experiment details 43 eea oe ae A a n 203 44 iv Chapter 1 Introduction 1 1 Overview The portal is the visual front end of the RTGrid system It is implemented with JSR 168 com pliant portlets deployed over a Gridsphere portal container Each of the portlets displayed on the portal communicates with the underlying web services the back end of the RTGrid system to perform service requests received from the portal users An overview of the relationships between the main components of the RTGrid system is shown in Figure 1 1 User account User account a lt Experiments T Experiments Experiment Profiles C Profiles x x 5 Resources E Resources Administration Administration Service Request Response SOAP Layer Figure 1 1 Components of the RTGrid system 1 2 Accessing the portal In order to access the RTGrid portal visit the following URL https hhost comsc grid cf ac uk
8. CHAPTER 8 EXPERIMENT MANAGEMENT 45 Archive Archives the given directory which generates a compressed file with the contents of the directory The experiment home directory cannot be archived since it is the root directory Please note that when a directory is archived the compressed file also appears in the same directory next to the directory just compressed Extract Extracts the contents of an archive file The archive formats that are cur rently recognised by the RTGrid system zip tar tgz tar gz tar bz2 jar Note that jar archives cannot restore file permissions If file permissions are signifi cant use the tar or zip formats Of course in this case the files should have been created by using the appropriate file permission restoration switches turned on User s Manual The RTGrid Portal Version 2 0
9. Value gt lt Option gt lt Option gt lt Label gt Gamma lt Label gt lt Value gt Gamma lt Value gt lt Option gt lt Option gt lt Label gt Delta lt Label gt lt Value gt Delta lt Value gt lt Option gt lt Control gt Control column 2 type ASSORTMENT gt lt Label gt Checkbox lt Label gt lt Name gt Checkbox lt Name gt lt Choice gt lt Label gt Alpha lt Label gt lt Value gt Alpha lt Value gt Checked NO Checked lt gt lt Choice gt lt Label gt Beta lt Label gt lt Value gt Beta lt Value gt lt Checked gt YES lt Checked gt lt Choice gt lt Choice gt lt Label gt Gamma lt Label gt lt Value gt Gamma lt Value gt User s Manual The RTGrid Portal Version 2 0 34 CHAPTER 7 PROFILE MANAGEMENT lt lt Checked gt YES lt Checked gt lt Choice gt lt Control gt Extension gt A profile extension is a list of controls that are defined by the profile creator These controls correspond to HTML fragments which are automatically generated upon parsing the XML de scription In the current version there are four controls that are available for use in a profile extension They are Text control The text control is the simplest of all the controls It displays a form field where the experiment creator can enter values This control may be used for receiving information that must be provided explicitly by the user
10. p giddy cf_ac uk List owned groups Affiliation School of Computer Science Cardiff University Wales UK Check this if the user should have administrative rights Save Delete Figure 5 3 Modifying user details In the user modification dialog box the information that can be modified is displayed as editable fields the rest are left as normal text In order to save any changes press the Save button To cancel any changes click lt lt Back to user list link To delete the user from the RTGrid system press the Delete button Saving changes to user details and deleting users from the RTGrid system require user confirmation Creating a new user group Only administrators are allowed to create a new user group create a new user group click on the Create group link on the action menu panel on the left The create user group dialog box as shown in Figure 5 4 will be displayed in the contents panel The create user group dialog box displays all of the fields that are required in order to create a new user group These fields are Group The group name is used to identify a user group It must be a unique al phanumeric word without any white spaces in between characters for example admin Description The description field provides further details about the group User s Manual The RTGrid Portal Version 2 0 14 CHAPTER 5 ADMINISTRATION Menu Create ne
11. tar gz tar bz2 jar Note that jar archives do not restore file permission information If file permissions are significant use the tar or zip formats Of course in this case the files should have been created by using the appropriate file permission restoration switches turned on 7 8 The components of a profile A profile consists of two main components 1 the set of executable objects that are invoked by the experiment manager at each of the stages of the experiment and their relevant data and 2 the profile extension which allows specialisation of the profile by providing an interface for passing experiment specific parameters This relationship is shown in Figure 7 8 Depending on the current state of the experiment the experiment manager executes spe cific scripts which are defined in the profile The profile extension specialises these scripts by providing interfaces for passing experiment specific parameters to these scripts By supplying the appropriate parameters the behaviour of the execution may be changed from that which User s Manual The RTGrid Portal Version 2 0 30 CHAPTER 7 PROFILE MANAGEMENT gt pre sh c z gt lt Z gt Experiment gt runsh gt gf t hd X Done Manager m ui H E Su Lu I 2 E qa n post sh gt PROFILE
12. 8000 gridsphere A login page similar to the one shown in Figure 1 2 will be displayed After logging into the portal the user must first subscribe to the The RTGrid Portal group This is done by going to the Welcome panel where the corresponding group is selected and saved in the Configure group membership section Once this is done the The RTGrid Portal panel will appear on the portal shown in Figure 1 3 CHAPTER 1 INTRODUCTION User Name F my bgn Forget yout passwort 2006 fremas try Crispus Beos at Came Soerce Cant f Urn Depatrur of Mecical Papua Veliscre nouta w Figure 1 2 Login page of the RTGrid portal Corot UK In the RTGrid panel as shown in Figure 1 3 five sub panels are displayed These are 1 Ac count 2 Administration only available to administrators 3 Resources 4 Profiles and 5 Ex periments Each of these sub panels deals with a specific aspect of the RTGrid system For example the Experiments sub panel will only deal with viewing and controlling all the experi ments that are currently accessible to the user In addition the Experiments sub panel will also allow creation of new experiments nane venom Wetcore The Portal Accnunt Adrinatration Roses Profies Uwe deteta Menu 721 Laat ioga Username sCmay Mesi Gagatne
13. A text control is described in the following manner lt Control type TEXT gt lt Label gt Number of particles lt Label gt lt Name gt numParticles lt Name gt lt Size gt 10 lt Size gt lt Default gt 1000 lt Default gt lt Control gt Here the type attribute of the control element lt Control gt is set to TEXT for text con trols Then we specify the label lt Label gt tag which will be displayed next to the input field The lt Name gt tag specifies the string to be used as the parameter name while gener ating the name value pair see Figure 7 9 The lt Size gt tag specifies the size in number of characters of the input field Finally the lt Default gt tag is used to specify a default value for this field The specified default value will be shown when the profile extension is displayed Selection control The selection control allows the user to select a value from a list of possible values The possible values are displayed in a drop down menu A selection control is described in the following manner Control type SELECTION gt lt Label gt Select a city lt Label gt lt Name gt City lt Name gt lt Default gt 1 lt Default gt lt Option gt lt Label gt Cardiff lt Label gt lt Value gt 1 lt Value gt lt Option gt lt Option gt lt Label gt Edinburgh lt Label gt lt Value gt 2 lt Value gt lt Option gt lt Option gt lt Label gt London lt Label gt l
14. C Alpha Beta C Gamma Delta Checkbox Alpha Beta Gamma Figure 7 10 When a profile is selected in the create experiment panel the corresponding profile extension if it has been defined is displayed to the user User s Manual The RTGrid Portal Version 2 0 32 CHAPTER 7 PROFILE MANAGEMENT lt NameValue gt lt Name gt Text lt Name gt lt Value gt Hello lt Value gt lt NameValue gt lt NameValue gt lt Name gt Param lt Name gt lt Value gt Hello lt Value gt lt NameValue gt lt NameValue gt lt Name gt Billy lt Name gt lt Value gt Hello lt Value gt lt NameValue gt lt NameValue gt lt Name gt Selection lt Name gt lt Value gt Gamma lt Value gt lt NameValue gt lt NameValue gt lt Name gt Radio lt Name gt lt Value gt Delta lt Value gt lt NameValue gt lt NameValue gt lt Name gt Checkbox lt Name gt lt Value gt Beta lt Value gt lt Value gt Gamma lt Value gt lt NameValue gt lt Parameters gt 7 8 2 Writing a profile extension The profile extension extends a given profile by allowing parametric specialisation As we have seen in Figure 7 9 an XML description is used to express the extension For example the XML description for the extension shown in Figure 7 10 is as follows lt xml version 1 0 lt Extension gt lt Control type TEXT gt lt Label gt Text lt Label gt lt Name gt Text lt
15. Figure 7 8 The main parts of a profile and how the experiment manager uses them is specified in the template Where such specialisations are not necessary the profile extension may be left undefined The profile extension Although the profile scripts can capture most of the simulation invariants it may be desirable to allow users of the profile to change certain parameters for example the profile may allow a user to specify the number of particles etc To provide the profile creator with such flexibilities a profile extension is used A profile extension is nothing but an XML file which describes a set of controls which should be displayed to the user of the profile when the profile is selected from the drop down menu in the experiment creation panel For any given profile only one profile extension is allowed If the uploaded profile extension is valid a preview will be displayed Figure 7 3 shows a valid profile extension after it has been uploaded If there are warnings or errors they will be highlighted In Figure 7 9 we summarise the flow of data between the Profiles sub panel and the Experi ments sub panel A profile extension XML description is uploaded while creating a new profile If the XML file is valid the extension is stored into the root directory associated with the profile shown in the file browser When a user selects this profile on the experiment creation panel con trols which correspond to the extension are
16. If the user is not the owner clicking on the row which corresponds to a given user group on the group list will display a read only dialog box as shown in Figure 5 6 This dialog box displays all of the information that can be view by normal users If the user owns the user group clicking on the row which corresponds to the group on the group list will display the user group modification dialog box as shown in Figure 5 7 In the user group modification dialog box the fields that can be modified are displayed as editable fields the rest are left as normal text In order to save any changes press the Save button To cancel any changes click on lt lt Back to group list link To delete the user group from the RTGrid system press the Delete button Saving changes to user group details and deleting user groups from the RTGrid system require user confirmation User s Manual The RTGrid Portal Version 2 0 Chapter 6 Resource management The resource management portlet allows administrators to create and manage distributed re sources that are accessible to the RTGrid system These resources can be used by any user when a new simulation experiment is created In the following sections we will discuss the various actions that can be performed from this portlet After an action has been performed the portlet will display any information related to that action for instance error messages etc on top of the contents panel 6 1 Adding
17. In order to list all of the profiles that are accessible to a user due to group membership click on the List accessible link on the action menu panel on the left This will display the first 10 profiles as shown in Figure 7 4 sorted in descending order of their modification time so that the most recently updated profiles are displayed first The next 10 profiles or the previous 10 profiles if available can be displayed by clicking on the next gt gt or lt lt previous link on the list header Associated with each of the displayed profiles are the following details User s Manual The RTGrid Portal Version 2 0 26 CHAPTER 7 PROFILE MANAGEMENT Menu Profile Itsting reste Prom Select All None Delete 1 2012 Status Name Description Last modified ru Test profile 1 This is a test profile Apr 22 06 Tua 11 52 AM 2 Profiet By using this profie user able to test the Apr 18 06 Fit 5 21 Select None Delete 1 2042 Re Figure 7 4 Listing profiles Status This status of the profile Name The name of the profile which briefly describes the profile Description The description provides more detail about the profile This is used to provide in depth detail about the profile and its settings Last modified The date and time when the profile was last modified A check box appears in each row if the user can delete the profile This may be used to selec
18. a new resource Only administrators are allowed to create a new resource To create a new resource click on the Create resource link on the action menu panel on the left The create resource dialog box as shown in Figure 6 1 will be displayed in the contents panel Menu Create new resource Create resource Name Oxford NGS Grid etie Job Manager gnid compule 108 Description This resource manager provides interfaces for submitting jobs to me Oxford NOS Gna node F resource This user group allows users to share tasks that are related the management of distributed resources By f users This user group allows Users 10 Shara tasks That ane in allowed fo non adeinietrnaeve users qs amn This user group allows users 10 share access to administration related tasks Onfy users with administrator Create Cancel Figure 6 1 Creating a resource The create resource dialog box displays all of the fields that are required in order to create a new resource These fields are 17 18 CHAPTER 6 RESOURCE MANAGEMENT Resource name The resource name is used to identify a resource in the RTGrid system Although it is not necessary that this string be unique it is advisable to choose a unique name since resource names are used when listing available resources during the experiment creation phase see Figure 8 1 Job Manager This field specifies the Unifo
19. displayed to the user as shown in Figure 7 10 This is achieved by translating the XML description and generating the corresponding HTML fragments which are then displayed inside a form to the user If the controls have default values they are displayed to the user The user may either accept these settings or change the values Once the experiment is created the HTML form is parsed to generate another XML description where the name value pairs are stored as shown below Finally the profile uses this name value XML description to retrieve values for each of the parameters that are specified in the profile extension See Section 8 6 for further details about these XML files xml version 1 0 encoding UTF 8 Parameters User s Manual The RTGrid Portal Version 2 0 CHAPTER 7 PROFILE MANAGEMENT 31 XML XML L Database YES NO valid ARIES HTML parse amp Display HTML m Create load y upioa Create ext xml HTML to XML 2 oo t Profile Creation Experiment Creation Figure 7 9 Profile extension and their relationship with the experiments Resource Oxford NGS Grid2 Profte Profile 1 ABows you to test the installation v Profile extension has been generated Profite extension Text Hano Param Melo 00 Selection Gamma 7 Radio
20. e g 367075 3 0 4 Download the UK e Science CA signing policy from http www grid support ac uk content view 182 244 and store it in the certificates directory e g 367b75c3 signing policy 3 8 Testing the globus installation Run the following command grid proxy init hours 168 out userproxy pem This will prompt you to enter the passphrase which you supplied while extracting the PEM files from PKCS12 see section 3 4 If successful a proxy file with the specified lifetime should be created in the current directory You can run the following command to check the lifetime of this proxy certificate grid proxy info f userproxy pem This proxy certificate should be uploaded to the RTGrid portal when using resources that require a GSI certificate for authentication User s Manual The RTGrid Portal Version 2 0 CHAPTER 3 INSTALLING GLOBUS User s Manual The RTGrid Portal Version 2 0 Chapter 4 Account management The account management portlet allows a user to manage their user account All the details that are specific to a user are made available to that user through this portlet In the following sections we will discuss the various actions that can be performed from this portlet After an action has been performed the portlet will display any information related to that action for instance error messages etc on top of the contents panel 4 1 Viewing and modifying user details To view or
21. may also need to install Visual 2008 redistributables Set path for the OpenSSL commands set path C OpenSSL bin path 2 Extract the public key openssl pkcs12 in 12 clcerts nokeys out usercert pem You will be prompted to enter the passphrase protecting the certificate see section 3 3 3 Extract the private key openssl pkcs12 in 12 nocerts out userkey pem You will be prompted to enter the passphrase protecting the certificate see section 3 3 You will also be prompted to enter a new passphrase for protecting the extracted private key Please note that the certificate file extracted from the browser in section 3 3 could be a PFX file if exported from Internet Explorer 3 5 Store your certificate Copy the extracted PEM files to the globus directory e Windows cd SHOMEPATHS mkdir globus e Linux mkdir globus User s Manual The RTGrid Portal Version 2 0 CHAPTER 3 INSTALLING GLOBUS 7 3 6 Change access permissions for better security Linux only cd globus chmod 644 usercert pem chmod 600 userkey pem S C x chmod 700 globus 3 7 Install the CA certificate and signing policy 1 Create a directory certificates inthe globus directory 2 Download the UK e Science CA certificate file from http www grid support ac uk content view 182 244 and store it in the certificates directory 3 Download the Certificate file for UK e Science CA
22. the user must first update the type of credential which he or she wishes to use To do this first select the credential type and press the Update button Once the credential type has been updated successfully any interfaces related to that credential type will be displayed as shown in Figure 6 5 Resource details lt lt Back to resource list Credential management Credential Upload GSI credential grid proxy nit Update Please upload new proxy file Proxy fe Browse Upload Resource detalls Name Condor Poot Job Manager conaor Last update time Apr 21 08 Mon 3 49 PM Creation time Apr 18 08 1 08 PM Figure 6 5 Credential management panel There are two ways for supplying a credential MyProxy credential By using this module the user requests the RTGrid system to obtain the required credential from a MyProxy server This feature is currently not implemented User s Manual RTGrid Portal Version 2 0 22 CHAPTER 6 RESOURCE MANAGEMENT GSI proxy file By using this module the user will upload a GSI credential proxy file from the local file system On Globus systems a proxy file may be generated by using the following command grid proxy init hours 10 out proxy pem In order to upload a GSI credential proxy file select the proxy file by clicking on the Browse button Then press the Upload button to upload the proxy fi
23. 2 PM r Tha group csat for stewing macurcus wih users Apr 2 06 Tew 11 O2 PM Refresh r admin This gosp is samt by miminisirsiors to share mimiisirntion tasks 22 00 Tom 11 01 PM Select AL Wore 1 5013 Figure 5 5 Listing the user groups 5 5 Listing the user groups In order to list all of the user groups that are currently active within the RTGrid system click on the List groups link on the action menu panel on the left This will display the first 10 user groups as shown in Figure 5 5 sorted in descending order of their last modification date so that the user groups which were modified most recently are displayed first The next 10 user groups or the previous 10 user groups if available can be listed by clicking on the next gt gt or lt lt previous link on the top right hand corner of the list header User s Manual The RTGrid Portal Version 2 0 CHAPTER 5 ADMINISTRATION 15 Menu Group details Back to group Create user em Last update time Apr 21 08 Mon 2 51 PM Ust users Creation time Apr 18 08 Fil 1 10 PM Description List groups List owned groups user group allows users 10 share access To administration related tasks Only users with ir strator status should be allowed to join this group Set preferences Help Log Refresh Members of this group Gagatine Yakrom
24. Apr 22 08 Tue 11 51 Description is a test profile Profile extension preview E Param Hao SS Figure 7 6 Modifying profile details me Upload Delete Archive e Dec 20 07 Thu 10 11 AM Delete Archive 12 bytes Dec 20 07 Thu 10 11 AM Delete Edit 12 bytes Dec 20 07 Thu 10 11 Delete Edit Apr 22 06 Tue 1 51 e Delete Extract Figure 7 7 The file management panel User s Manual The RTGrid Portal Version 2 0 CHAPTER 7 PROFILE MANAGEMENT 29 1 This shows the actions that are allowed on the current working directory They uploading a new file into the current working directory b deleting the current working directory and c archiving the current working directory into a compressed archive file this also saves the file permissions 2 This shows the current working directory relative to the profile home directory The dis played information is the path from the home directory to the current working directory If the depth of the path is more than five only the five closest components to the current working directory are displayed The rest are replaced with an ellipsis Clicking on the path component link sets the current working directory to that directory 3 This displays the contents of the current working directory Each file or directory is listed in a row Where file types are k
25. Name gt lt Size gt 30 lt Size gt lt Default gt Hello lt Default gt lt Control gt lt Control type TEXT gt lt Label gt Param lt Label gt lt Name gt Param lt Name gt lt Size gt 30 lt Size gt lt Default gt Hello lt Default gt lt Control gt lt Control type TEXT gt lt Label gt Billy lt Label gt lt Name gt Billy lt Name gt lt Size gt 30 lt Size gt lt Default gt Hello lt Default gt lt Control gt Control type SELECTION gt lt Label gt Selection lt Label gt ncoding UTF 8 User s Manual The RTGrid Portal Version 2 0 CHAPTER 7 PROFILE MANAGEMENT lt Name gt Selection lt Name gt lt Default gt Gamma lt Default gt lt Option gt lt Label gt Alpha lt Label gt lt Value gt Alpha lt Value gt lt Option gt lt Option gt lt Label gt Beta lt Label gt lt Value gt Beta lt Value gt lt Option gt lt Option gt lt Label gt Gamma lt Label gt lt Value gt Gamma lt Value gt lt Option gt lt Option gt lt Label gt Delta lt Label gt lt Value gt Delta lt Value gt lt Option gt lt Control gt lt Control column 2 type CHOICE gt lt Label gt Radio lt Label gt lt Name gt Radio lt Name gt lt Default gt Delta lt Default gt lt Option gt lt Label gt Alpha lt Label gt lt Value gt Alpha lt Value gt lt Option gt lt Option gt lt Label gt Beta lt Label gt lt Value gt Beta lt
26. SH s IMPORTANT Please note that the above commands will keep existing entries in the database To rebuild the database from scratch run the following before running dbmake_RTGrid2 py dbclean sh If you wish to populate the database with some test users and profiles run the following Spython pop py Start the portal To start the portal run the following prefix libexec rtportal start Start the experiment manager To start the Experiment Manager run the following prefix libexec rtmaster The Experiment Manager may also be started as a daemon by running the following Snohup lt prefix gt libexec rtmaster gt rtmaster log 2 gt 61 amp Check the installation To verify the installation please visit the following URL https lt HOSTNAME gt 8000 The RTGrid login page should now be displayed on the browser User s Manual The RTGrid Portal Version 2 0 Chapter 3 Installing Globus 3 1 Download and extract Globus 1 Goto http www globus org toolkit downloads 2 Download the latest Java WS Core Binary Installer 3 Extract the binary installer if the file downloaded in step 2 is compressed 4 Rename the directory to gt 4 3 2 Set environment variables 1 Set the environment variable GLOBUS LOCATION to the unpacked distribution e Windows set GLOBUS_LOCATION c gt4 Unix Linux setenv GLOBUS LOCATION home directory gt4 or export GLOBUS LOCATION home direc
27. User s Manual The RTGrid Portal Conformal Radiotherapy on the Grid THE RTGRID PROJECT funded by the EPSRC under grant number EP C538641 1 and OMII UK under the ENGAGE Engaging research with e Infrastructure initiative School of Computer Science Department of Medical Physics Cardiff University Velindre Hospital Queen s Buildings Velindre Road Whitchurch 5 The Parade Roath Cardiff CF14 2TL Cardiff CF24 3AA Last update March 26 2009 Contents 1 Introduction oe he Se ea ee 12 SONS TE PCA 4e ow bee OT e RR RR GR e 2 Installation 3 Installing Globus 31 sod extract Globus o es rom mm ge 32 Setenvirontment variables socer eio o e RR Ch 33 Extract GSI certificates from your browser 3 4 Extract public and private keys from the PRCSI2 25 SONS OR OR EH OEE ew 3 6 Change access permissions for better security Linux 3 Install the CA certificate and signing policy 2 3 8 Testing the globus installation 2 22 2 2 4 4 Account management 51 Viewing and moditying user details 222222224 o Ryo 42 Changing the login password s o sasssa nomu wee edent 43 Viewing the licensing terms 425229 9 ok e eee 5 Administration Ad Creaunganew lt d Ge HRS 5 2 the ASA REESE a 5 3 Modifying userde
28. above When the details of a profile are displayed the current XML description of the profile extension will be loaded automatically and displayed in the Profile extension XML field Uploading a new profile extension Last modified META INF Apr 22 08 Tue 11 51 Delete Archive RTGIidDBWSTest java 8KB Apr 22 08 Tue 11 49 AM Delete Edit f extension 1 KB Apr 22 08 Tue 11 52 AM Delete Edit jj hello Dec 20 07 Thu 10 11 AM Delete Archive testarchive tar gz 154 bytes Apr 22 08 11 54 Delete Extract a Figure 7 12 Editing profile extension by uploading The profile extension XML description is stored in the profile home directory as extension xml as shown in Figure 7 12 Simply uploading a new extension xml file with the new XML description of the extension will over write the existing profile extension file Another way of editing the profile extension is to click on the Edit button which corresponds to the profile in the file management panel This will load the extension xm1 file for online editing To remove an existing profile extension simply delete the extension xml file by clicking on the Delete button in the file management panel Naming the profile extension XML description as extension xml is simply a conven tion used by the RTGrid system It is therefore important to note that by default RTGrid assumes that any file in the profile home directory with the na
29. access Q The active icon is used to identify resources that are ready for use Depending on the type of the resource certain user specific parameters may have to be set before the resource is used i e authentication Once the relevant parameters have been set the resource becomes active and therefore usable Currently the user must specify the credential type to activate a resource see Section 6 7 The inactive icon is used to identify resources that are not ready for use In order to activate a resource the user must first set the user specific parameters see Section 6 7 Please note that in the experiment creation dialog box see Figure 8 1 only resources which are unlocked accessible to the user and activated by the user are listed Listing resources owned by a user In order to list all of the resources that are owned by a user click on the List owned link on the action menu panel on the left Contrary to the listing described in Section 6 3 this will only list resources that are currently owned by the user Hence some of the resources that are not shared with any other user group will appear in this list although they may not appear in the accessible list User s Manual The RTGrid Portal Version 2 0 20 CHAPTER 6 RESOURCE MANAGEMENT Menu Create Resource List owned List accessible Set preferences Help Log out scmjpg Refresh Menu Create Resource Ust owned Lit accessible Set pr
30. ation dialog box as shown in Figure 7 5 User s Manual Tbe RTGrid Portal Version 2 0 CHAPTER 7 PROFILE MANAGEMENT 27 Profile details lt lt Back to profile List File management Last modified Set preferences Apr 22 08 Tue 11 51 AM Read only vaut RTGridDBWSTest Java 8 KB Apr 22 46 Tue 11 49 Read only Refresh extension xml 1 KB Apr 22 08 Tue 11 52 Read only y Dec 20 07 Thu 10 11 AM Read only a testarchive tar gz 184 bytes Apr 22 08 Tue 11 54 AM Read only y uk Apr 22 08 Tue 11 51 AM Read only Profile details Name Test profile 1 Last update time Apr 22 08 Tue 11 54 AM Creation time Apr 22 08 Tue 11 51 Description is a test profile Profile extension preview Text Param elo Figure 7 5 Viewing profile details The details of the profile are divided into two main parts a the File management panel and b the general details about the profile The final management panel is used to browse and perform file management actions on the profile directory Files can be deleted edited or new files uploaded The general details section provides general details about the profile for instance the profile name creation time last modification time etc 7 6 Modifying profile details Users who have been granted edit access may edit the details of a given profile by clicking on the ro
31. d the portlet will display any information related to that action for instance error messages etc on top of the contents panel Creating a new profile To create a new profile click on the Create profile link on the action menu panel on the left This create profile dialog box as shown in Figure 7 1 will be displayed in the contents panel The create profile dialog box displays all of the fields that are required in order to create a new profile These fields are Profile name The profile name is used to identify a profile in the RTGrid system Al though it is not necessary that this string be unique it is advisable to choose a unique name since profile names are used when listing available profiles during the experiment creation phase see Figure 8 1 Description This field describes the profile in detail Access permission This field identifies the list of user groups which should be granted access to this profile Ultimately all of the members of the selected groups will be granted access to this profile See Section 7 2 for further details Profile files This field allows a user to upload files that are required by this profile All of the files that have been uploaded successfully using this field will be associated with the new profile and they will be stored in the unique directory allocated to this profile In this field all of the files that have been uploaded successfully will also be displayed as shown in F
32. e home directory to the current working directory If the depth of the path is more than five only the five closest components to the current working directory are displayed The rest are replaced with an ellipsis 7 Clicking on the path component link sets the current working directory to that directory 3 This displays the contents of the current working directory Each file or directory is listed in row Where file types are known an appropriate icon is displayed The file name is displayed next to this icon Clicking on the file name results in one of two actions if the component is a file it will display the file download dialog box for downloading that file if the component is a directory the current working directory will be set to this directory For a file component the size of the file is displayed next following which the last update time is displayed Finally the actions that are allowed to this component are listed Depending on the component type file or directory the appropriate actions will be displayed in the actions list These actions are Delete Deletes the file or directory When directories are deleted by pressing the Delete button all of the contents will also be deleted recursively Edit Opens the file for online editing Online editing is not allowed for files that are larger than 1MB The Edit button will therefore not appear in this case User s Manual The RTGrid Portal Version 2 0
33. ed in the contents panel Menu Change web services password User details Username scmgy Change password Old password User licence New password out scmgy Re type new password Change Cancel Figure 4 2 Changing the login password The change password dialog box displays the following fields Username The username which identifies the user in the RTGrid system Old password The old password which is to be changed New password The new password which replaces the old password Re type new password Confirm the new password To make the changes press the Change button to cancel press the Cancel button 4 3 Viewing the licensing terms Every user of the RTGrid system must agree to the licensing terms under which the RTGrid services have been provided To view these licensing terms click on the User license link on the action menu panel on the left This will display the licensing terms The user can either Agree or Decline the agreement by pressing the appropriate button If the user declines the agreement he or she will be logged out of the RTGrid system To agree to the terms simply log into the RTGrid system and the licensing terms will be displayed to the user The user can now agree to the terms and continue using the services provided by the RTGrid system User s Manual The RTGrid Portal Version 2 0 5 1 Chapter 5 Administration The administration portlet allows admi
34. eferences Help Log out scmgy Refresh Resource details lt lt Back to resource list Credential management Credential Type GSI credential required Update Resource details Name Oxford NGS Grid2 Last update time Apr 21 08 Mon 3 50 PM Creation time Apr 21 108 Mon 3 50 Job manager globus ngs oerc ox ac uk Jobmanager pbs resource manager provides interfaces for submitting jobs to the Oxford NGS Grid node Figure 6 3 Viewing resource details Resource details lt lt Back to resource list r Credential management Credential Type No GS credential required cj update r Resource details Name loxtors NGS Graz Job Manager WINGS oerc ox ac uk Jobmanager pbs Last update time Apr 21 08 Mon 3 50 Creation time Apr 21 08 Mon 3 50 PM Description resource manager provides interfaces for submitting jobs to the Oxford NGS Grid node Access permissions This user group allows users to share tasks that are related to the This user group allows users to share tasks that are in general allowed to This user group allows users to share access to administration related resource F F users F admin Figure 6 4 Modifying resource details User s Manual The RTGrid Portal Version 2 0 CHAPTER 6 RESOURCE MANAGEMENT 21 6 5 Viewing resource details Users who have been granted read access may view the detail
35. igure 7 2 Uploaded files may be deleted by pressing the Delete button If a file that is being uploaded has the same filename as one of the files in the uploaded list the existing file is always over written Profile extension This allows a user to upload a XML description of a profile extension By using profile extensions users are allowed to pass experiment specific parameters to the simulation template To upload a profile extension select the XML description file by pressing on the Browse button and press the Upload button to upload the extension If 23 24 CHAPTER 7 PROFILE MANAGEMENT Menu List owned List accessible Set preferences Help Log out scmgy Refresh Create profile lt lt Back to profile list C O Description rce This user group allows users to share tasks ihat are related Lo the management resu Ir uses This user group allows users to share tasks that are in general allowed to LIES GE This user group allows users to share access to administration related tasks Profien Upload Prof eextension XML Browse Upload Create Cancel Figure 7 1 Creating a profile Browse Uploaded profile files Figure 7 2 Uploading profile files User s Manual The RTGrid Portal Version 2 0 7 2 7 3 CHAPTER 7 PROFILE MANAGEMENT 25 the profile extension is valid a preview of the p
36. is ume 00 chare tests ihat 50 the mantenance of he system and 05 componant mocutes divin ced Tas group used for ehuing tasks which sequine advanced nowiedge of the undertyieng eystem P protie Thus gapis umm for shaving templates or profies with otser onem resource Ths group weed for sheeting riounces wif usen F admin Tha group by to share ncrm ristration seine tame Figure 8 5 Modifying experiment details Only owners are allowed to update access permissions of a given experiment This means that although users may be able to edit experiment details as a result of their membership to a group that has been granted edit access they will not be allowed to edit the access permissions The owner therefore has the highest priority over experiments owned by them With regard to the simulation parameters the relevant details are stored in two files which reside in the experiment home directory The first file extension xml is an XML descrip tion of the profile extension that was used to supply parameters to the simulation template This is similar to the profile extension in the profile management portlet The main difference between the two however is that the extension xml file in the experiment directory also User s Manual The RTGrid Portal Version 2 0 8 7 44 CHAPTER 8 EXPERIMENT MANAGEMENT saves the parameters
37. its any member of that group to modify the details of the given experiment If a group is granted edit access the RTGrid system will also automatically grant read access no edit access without read access Control By granting control access to a user group the owner of the experiment permits any member of that group to control the given experiment Controlling the experiment includes stopping the experiment restarting the experiment etc If a group is granted control access the RTGrid system will also automatically grant read access no control access without read access 8 3 Listing experiments accessible to a user In order to list all of the experiments that are accessible to a user due to group membership click on the List accessible link on the action menu panel on the left This will display the first 10 experiments as shown in Figure 8 3 sorted in descending order of their last modified time so that the most recently updated experiments are displayed first The next 10 experiments or the previous 10 experiments if available can be displayed by clicking on the next gt gt or lt lt previous link on the list header Menu Listing experiments Select None Sixt Stop Delete 1 202 Last modified NOT YET STARTED Test the installation Tris experiment wil teal framework has Apr 22 08 Tue 21 PM YET STARTED Experiment 1 Check This experiment allows a user to check the instalation This Apr 10
38. le If a valid credential was uploaded successfully the credential management panel will display the remaining lifetime of the proxy file as shown in Figure 6 6 Resource detalls lt lt Back to resource list Credential management Credential Type Upload GS credential grid peoxy init Update Remaining lifetime 59 minutes 49 seconds Delete Proxy Browse upload Resource details Name Oxford NGS Grid2 Job Manager potus nigs oerc ox ac uk jobmanager pbs Last update time Apr 21 08 Mon 3 50 PM time Are 21 TW Moni CAO Figure 6 6 Credential remaining lifetime Users can delete an existing proxy by pressing the Delete button or renew the proxy by uploading a new one When a proxy is renewed the old proxy file will be over written Please note that although a given resource may be shared by many users resource credentials are managed separately for each of the users Thus resource credentials are user specific Users Manual The RTGrid Portal Version 2 0 7 1 Chapter 7 Profile management This profile management portlet allows users to create and manage simulation templates which we call profiles in the RTGrid system These profiles can be used by a user for deriving simula tion experiments by using the template specification In the following sections we will discuss the various actions that can be performed from this portlet After an action has been performe
39. ls of an experiment under execution Figure 8 4 Viewing experiment details The details of the experiment are divided into three main parts a The current phase and status of the experiment b The job statistics which includes information on the number of jobs and their percentages that have been Submitted Running Done etc and also the detailed status of each of the jobs displayed as a job list and c The static information which User s Manual The RTGrid Portal Version 2 0 CHAPTER 8 EXPERIMENT MANAGEMENT 43 describes the experiment and its settings this information does not get updated once the experi ment has begun executing its jobs 8 6 Modifying experiment details Users who have been granted edit access may edit the details of a given experiment by clicking on the row which corresponds to that experiment This will display the experiment modification dialog box as shown in Figure 8 5 Experiment Mare perenne of pegas Oerer CIPgy Y Moon Last Apr 23 08 Wer 0 00 AM CrestentSme Apr 23 U8 wed 0 00 AM Desacriptiar Ths expeersent domons simaation in progress Resource Oxford NOS Node 2 Peofte Experiment parametara Test Poom eto DAN Gamma 7 Ro C Checkton Apma 12 Beta Gama Ths group
40. me extension xml isa profile extension User s Manual The RTGrid Portal Version 2 0 38 CHAPTER 7 PROFILE MANAGEMENT User s Manual The RTGrid Portal Version 2 0 8 1 Chapter 8 Experiment management The experiment management portlet allows users to create and manage simulation experiments In order to understand the following sections the user must first understand access control see Chapter 5 resource management see Chapter 6 and the concepts underlying simulation templates see Chapter 7 In the following sections we will discuss the various actions that can be performed from this portlet After an action has been performed the portlet will display any information related to that action for instance error messages etc on top of the contents panel Creating a new experiment To create a new experiment click on the Create experiment link on the action menu panel on the left The create new experiment dialog box as shown in Figure 8 1 will be displayed in the contents panel The create new experiment dialog box displays all of the fields that are required in order to create a new experiment These fields are Experiment name An experiment name is a short description of the experiment Al though it is not necessary that this string be unique it is advisable to choose an experiment name that is unique Description This field describes the experiment in detail Resource This field is used t
41. modify the user details click on the User details link on the action menu panel on the left The user details dialog as shown in Figure 4 1 will be displayed in the contents panel Menu User details Last login Thu May 15 16 03 36 BST 2008 Change password Username scmgy User licence Real Name Gagarine Yaikhom 10 cf ac uk Refresh Affiliation chool of Computer Science ardiff University ales UK Check this to agree to the licensing terms _Save Figure 4 1 Viewing or modifying user details The user details dialog box displays the following user details Last login This is the time and date when the user last logged in This is a read only field 9 10 4 Username The username which identifies the user the RTGrid system Real Name The real name of the user Email ID The email ID which will be used for any communications related to the usage of the RTGrid system Affiliation The institution the user is currently associated with Administrative status Check this to agree to the RTGrid user terms and conditions The user license can be viewed by clicking on the User license link on the action menu 4 2 Changing the login password To change the login password click on the Change password link on the action menu The change password dialog as shown in Figure 4 2 will be display
42. n we now use the lt Choice gt element instead There is no lt Default gt tag for specifying default value In stead we use the lt Checked gt tag with value YES to select those choices that must be selected by default More than one choice can be selected at once 7 8 3 Edit profile extension There are two ways in which a profile extension can be added edited or deleted from a profile once it has been created Editing online The first approach involves editing the profile extension XML online In order to add a new profile simply add the XML description of the extension in the Profile extension XML field as shown below Profile extension preview gt Text Param Hello Billy Selection Rado C Alpha Beta C Gamma Deita Checkbox Alpha Beta I gt i Gamma Profile extension XML xml version 1 8 encodings UTF 8 Extension Control type TEXT Label Text lt Label gt Name Text Nane 12e 30 S12e Default HWelloc Default lt Control gt Control types TEXT lt Label gt Paran Label lt Nane gt Paran lt Name gt lt 5 gt 309 lt 51 gt Figure 7 11 Editing profile extension User s Manual The RTGrid Portal Version 2 0 CHAPTER 7 PROFILE MANAGEMENT 37 In order to modify an existing profile simply edit the XML description in the Profile exten sion XML field as shown
43. nistrators to create and manage users and user groups By using users and user groups the RTGrid system controls access to resources profiles simulation templates and experiments In the following sections we will discuss the various actions that can be performed from this portlet After an action has been performed the portlet will display any information related to that action for instance error messages etc on top of the contents panel Creating a new user Only administrators are allowed to create a new user To create a new user click on the Cre ate user link on the action menu panel on the left The create user dialog box as shown in Figure 5 1 will be displayed in the contents panel Menu Create a new web services user Create user Create user Create group Real Name 18 9 3 List users List groups Affiliation List owned groups Set preferences Help Log out scmgy Refresh Emann Password Re type password This user should be granted administrative permissions Create Cancel Figure 5 1 Creating a new user The create user dialog box displays all of the following fields 11 12 CHAPTER 5 ADMINISTRATION Username A username is used to identify a user of the RTGrid system It must be a unique alphanumeric word without any white spaces in between characters for example rtgriduser Once a user has been created
44. nown an appropriate icon is displayed The file name is displayed next to this icon Clicking on the file name results in one of two actions if the component is a file it will display the file download dialog box for downloading that file if the component is a directory the current working directory will be set to this directory For a file component the size of the file is displayed next following which the last modified time is displayed Finally the actions that are allowed to be performed to this component are listed Depending on the component type file or directory the appropriate actions will be displayed in the actions list These actions are Delete Deletes the file or directory When directories are deleted by pressing the Delete button all of the contents will also be deleted recursively Edit Opens the file for online editing Online editing is not allowed for files that are larger than 1MB The Edit button will therefore not appear in this case Archive Archives the given directory which generates a compressed file with the contents of the directory The profile home directory cannot be archived since it is the root directory Please note that when a directory is archived the compressed file also appears in the same directory next to the directory just compressed Extract Extracts the contents of an archive file The archive formats that are cur rently recognised by the RTGrid system are zip tar tgz
45. o choose the distributed resource where all the jobs associ ated with the simulation experiment must be submitted Profile This field is used to choose the profile simulation template that is to be used to create the new experiment After a profile has been selected a profile extension that is associated with that profile will be displayed The user can either accept the default values or specify new ones Access permission This field identifies the list of user groups which should be granted access to this simulation experiment Ultimately all of the members of the selected groups will be granted access to this experiment See Section 8 2 for further details Experiment files This field allows a user to upload files that are required by this experi ment All of the files that have been uploaded successfully using this field will be associated with the new experiment and they will be stored in the unique directory allocated to this experiment 39 40 CHAPTER 8 EXPERIMENT MANAGEMENT n List owned Wome List accessible Description Set preferences Help Log out scmgy Refresh Resource Oxford NGS 2 Profile Select a Please select a profile Access permission D eB resource This user group allows users to share tasks that are related to the m users This user group allows users to share tasks that are general alowed to m Ev qu admin Th s user group allows users
46. on y Syum install MySQL python 4 Configure the installation To configure the installation run the following commands from the RTGrid source tree root configure prefix lt prefix gt where lt prefix gt is the installation directory If the file configure does not exists it may be created by running the following command Smake Makefile in bootstrap For the above command to work Autoconf must be installed For further details on Auto conf please visit http www gnu org software autoconf The installation command using Yum is as follows Syum install autoconf 5 Build the RTGrid system To build the RTGrid system run the following Smake CHAPTER 2 INSTALLATION 6 10 Install the RTGrid system To install the newly built RTGrid system into the installation directory run the following Smake install During the installation process you will be prompted to a accept the Gridsphere licence b confirm if you wish to install the Gridsphere documentation IMPORTANT If you are installing the RTGrid system for the first time or want to start with a fresh installation run the following command Smake fresh Please we warned that this will wipe clean the existing Gridsphere portal database Create or update the RTGrid database To create or update the MySQL database used by the RTGrid system run the following cd database python dbmake RTGrid2 py
47. riments that are not shared with any other user group will appear in this list although they may not appear in the accessible list Viewing experiment details Users who have been granted read access may view the details of a given experiment by clicking on the row which corresponds to the experiment This will display the experiment information dialog box as shown in Figure 8 4 Menu Experiment details Back to experiment list Experiment state eate riment ht owned t accessible EXECUTING EXPERIMENT gt gt EXECUTION gt gt Running 0 00 Set preferences Jeb progress Hel State jobs Percentage out Pending E 17 Submitted 2 9 Stagng in Sammod Staging in 2 9 Running Penang Running 3 13 Staging out 4 m 2 4 Staging out Done cleanup 2 4 Feed Failed cleanup 2 4 Stopping Done 2 9 Done cleanup JR Failed 2 a Total 23 Job Details mrunmng zT TNI 10 Running Apr 22 08 Tue 4 21 11 StagingOut Apr 22 706 Tua 4 21 PM 12 StagingOut Apr 22 706 Tue 4 21 PM 13 Stopping Apr 22 08 Tue 4 21 14 Stopping Apr 22 08 Tue 4 21 15 Done Apr 22 08 Tue 4 21 PM Rane 22 4 94 Experiment details Name Dummy Experiment Owner scmgy Gagarine Last update time Apr 22 08 Tue 4 20 PM Creation time Apr 5 08 Tue 3 30 PM Description s a dummy experiment which demonstrates the vanous detai
48. rm Resource Identifier URI for contacting the resource manager associated with this resource For instance the job manager for the Oxford NGS Grid is globus grid compute oesc ox ac uk jobmanager pbs Description This field is used to describe the resource in detail Access permission This field identifies the list of user groups which should be granted access to this resource Ultimately all of the members of the selected groups will be granted access to this resource See Section 6 2 for further details Once all of the above fields have been specified the new resource can be created by pressing the Create button To cancel resource creation press the Cancel button Please note that all of the above fields may be altered after the resource has been created 6 2 Sharing a resource There are three ways in which an owner can share resources Read By granting read access to a group the owner permits any user who is a member of that group to view the resource details Edit By granting edit access to a group the owner of the resource permits any member of that group to modify the details of the given resource If a group is granted edit access the RTGrid system will also automatically grant read access no edit access without read access Use By granting use access to a group the owner of the resource permits any member of that group to use the given resource for running simulations When a group is granted use acce
49. rofile extension will be displayed as shown in Figure 7 3 To discard a profile extension press the Discard button Profite extension XML Browse Upload Discard Profile extension preview Text Hello Paran Hello Billy Selection Gamma x Radio C Aipha Beta C Gamma Deta Alpha F Beta Gamma Figure 7 3 Uploading profile extension Once all of the above fields have been specified the new profile can be created by pressing the Create button To cancel profile creation press the Cancel button Please note that all of the above fields may be altered after the profile has been created Sharing a profile There are three ways in which an owner can share profiles Read By granting read access to a user group the owner of the profile permits any member of that group to view the profile details Edit By granting edit access to a user group the owner of the profile permits any member of that group to modify the profile details If a group is granted edit access the RTGrid system will also automatically grant read access no edit access without read access e Use By granting use access to a group the owner of the profile permits any member of that group to use the profile for creating new simulation experiments If a group is granted use access the RTGrid system will also automatically grant read access no use access without read access Listing profiles accessible to a user
50. s of a given resource by clicking on the row which corresponds to the resource This will display the resource information dialog box as shown in Figure 6 3 The details of the resource are divided into two main parts a The user specific credential management panel where the user set user specific parameters for activating the resource and b the common details of the resource 6 6 Modifying resource details Users who have been granted edit access may edit the details of a given resource by clicking on the row which corresponds to the resource This will display the resource modification dialog box as shown in Figure 6 4 Only owners are allowed to update access permissions of a given resource This means that although users may be able to edit resource details as a result of their membership to a group that has been granted edit access they will not be allowed to edit the access permissions The owner therefore has the highest priority over resources owned by them 6 7 Resource credential management Some resource managers require user authentication in order to validate job submissions to resources under their control To fulfill this requirement every resource is associated with a credential management module When a user with use access views the details of a given resource the interfaces that are related to credential management appears on the top see Figure 6 3 In order to activate a resource which requires user authentication
51. ss the RTGrid system will also automatically grant read access no use access without read access Please note that in the experiment creation portlet see Figure 8 1 only active resources that are accessible to a user either resources which the user owns or resources with use access set to true will be available in the drop down menu By controlling the use access to resources administrators can control the users who are allowed to run simulations on certain resources depending on the current state of the resources say testing out a new resource before granting general access to normal users 6 3 Listing resources accessible to a user In order to list all of the resources that are accessible to a user due to group membership click on the List accessible link on the action menu panel on the left This will display the first 10 resources as shown in Figure 6 2 sorted in descending order of their modification time so that the most recently updated resources are displayed first The next 10 resources or the previous 10 resources if available can be displayed by clicking on the next gt gt or lt lt previous link on the list header Associated with each of the displayed resource are the following details User s Manual The RTGrid Portal Version 2 0 6 4 CHAPTER 6 RESOURCE MANAGEMENT 19 Menu Resource listing Select Al None Delete 1 3013 State Grouprame Description Last updated L Oxford NGS Grid2
52. t a subset of the listed profiles Selected profiles can be deleted by pressing the Delete buttons on the list header To summarise the current status of the profile two types of icons are used These icons are e EB The locked icon is used to identify profiles that are currently not usable by any user except for the owner A profile is locked when no group has been granted use access e ES The unlocked icon is used to identify profiles that are usable Simulation experiments can be derived from these profile In order to unlock a profile at least one of the groups must be granted use access In the experiment creation portlet see Figure 8 1 only profiles that are accessible to a user either profiles which the user owns or profiles with use access set to true will be available in the drop down menu 7 4 Listing profiles owned by a user In order to list all of the profiles that are owned by a user click on the List owned link on the action menu panel on the left Contrary to the listing described in Section 7 3 this will only list resources that are currently owned by the user Hence some of the resources that are not shared with any other user group will appear in this list although they may not appear in the accessible list 7 5 Viewing profile details Users who have been granted read access may view the details of a given profile by clicking on the row which corresponds to the profile This will display the profile inform
53. t Value gt 3 lt Value gt lt Option gt lt Control gt User s Manual The RTGrid Portal Version 2 0 CHAPTER 7 PROFILE MANAGEMENT 35 Here same as the text control we specify the type by setting the type attribute to SE LECTION Then we specify the label and the name of the parameter Next we specify the default value if any Note here that this value must match the value of one of the supplied options Each option that should be displayed to the user is specified with an lt Option gt element which has the elements 1 the label to be displayed in the drop down menu and 2 the value to be returned if selected Choice control The choice control is similar in functionality to the selection control because it allows the user to select a value from a set of possible values The main difference is primarily in the manner in which the values are displayed all the possible values for the choice control are displayed with radio buttons A choice control is described as follows lt Control type CHOICE column 4 gt lt Label gt Select a greek alphabet lt Label gt lt Name gt Alphabet lt Name gt lt Default gt 2 lt Default gt lt Option gt lt Label gt Alpha lt Label gt lt Value gt 1 lt Value gt lt Option gt lt Option gt lt Label gt Beta lt Label gt lt Value gt 2 lt Value gt lt Option gt lt Option gt lt Label gt Gamma lt Label gt lt Value gt 3 lt Value gt
54. tails bs s os oS he ee RO ESO KO we d o User Og Sk ee ew Bw we 55 Lutte DF groups usu aT s a RE SK 5 6 Listing the user groups owned 57 Viewing or modifying user group details 6 Resource management 6 1 Addinganew resource 22 22 ace doe e OR RR hae e WC Gl Mu AM NE Lacs qoe do om arbem care qe 63 Listing resources accesible to a uer ec ea o RR 9 OR dE 6 4 Listing resources owned by a user 65 os o ccs ane Ww Se acer HME bce 66 Modifying resource details 2 2 2 2 4 67 Resource credential management 7 Profile management ii NN NACA 8 AL Crain ee PONS uic ees ewe Sud scs Andes SSS 23 HEC UD Ir o PLI Ew ES 25 7 3 Listing proties accessibleto 4 ust i so soe RR 55 5 25 7 4 Listing profiles owned by a user 26 75 Vi WS 5 1 5 A rm 26 TO Moses I oie dhe A Gee GR o Rd 27 PF Sle maar panel oux Bo hh a oe C a ud eS 27 78 es goii ow RR cce oe s 29 741 es x boe 30 242 6 646 6 sees we EDO Rm e 32 783 Editproble estensione us cu boob RR pom mL Oe 36 Experiment management 39 EI Creating anew 2 52
55. that were supplied to the extension when the experiment was created The second file parameters xml is an XML representation of the parameters as name value pairs Contrary to the extension xml file this only contains the experiment parameter name and its values File management panel The file management panel as shown in Figure 8 6 allows a user to browse and perform certain actions on the files and directories that are associated with a given experiment File management Fie Browse Upload Delete Archive eh BEAM exec Last dosxyznrc exe S87 KB Mar 5 08 Wed 4 26 Delete Edit dosxyznrc INTEL exe 587 KB Mar 5 08 Wed 4 26 Delete Edit dosxyznrc exe 430KB Mar 5 08 Wed 4 26 PM Delete Edit IbBEAM_Clinac21CDb_photon so 1MB Ma 5 08 Wed 4 26 PM Delete Edit libBEAM Oncort electron 1 MB Mar 5 08 Wed 4 26 PM Delete Edit Figure 8 6 The file management panel The file management panel has three main parts 1 This shows the actions that are allowed on the current working directory They are a uploading a new file into the current working directory b deleting the current working directory and c archiving the current working directory into a compressed archive file which also saves the file permissions 2 This shows the current working directory relative to the experiment home directory The displayed information is the path from th
56. the assigned username cannot be changed If the username is already in used the RTGrid system will alert the user Real Name The real name of the user for example Peter Smith Affiliation The institution the user is currently associated with Email ID The email ID which will be used for any communications related to the usage of the RTGrid system Password A temporary password which will be given to the user once the user has been created successfully It is important for the user to change this temporary password as soon as they log in for the first time Re type password Re type the temporary password Administrative status Check this if the user should be granted administrative privileges Once all of the fields have been specified the new user is created by pressing the Create button To cancel user creation press the Cancel button Please note that the field marked with cannot be changed after the user has been created 5 2 Listing the users In order to list all of the users that are currently registered with the RTGrid system click on the List users link on the action menu panel on the left This will display the first 10 users as shown in Figure 5 2 sorted in descending order of the last modification date so that the users who s details were modified most recently are displayed first Listieg users Select Were Delete 20 Erre Lost updated sanj aaan Gy
57. to share access 10 administration related Experiment nie Browse Upload Create Figure 8 1 Creating an experiment In this field all of the files that have been uploaded successfully will also be displayed as shown in Figure 8 2 Uploaded files may be deleted by pressing the Delete button If a file that is being uploaded has the same filename as one of the files in the uploaded list the existing file is always over written Experiment file Browse Upload Uploaded experiment files rtgridws 0 1 jar application java archive 37 KB Delete testarchive tar gz application x gzip 184 bytes Delete RTGridDBWSTest java text x ava Delete Figure 8 2 Uploading experiment files Once all of the above fields have been specified the new experiment can be created by pressing the Create button To cancel experiment creation press the Cancel button Please note that all of the above fields may be altered after the experiment has been created except for those that are marked with an User s Manual The RTGrid Portal Version 2 0 CHAPTER 8 EXPERIMENT MANAGEMENT 41 8 2 Sharing an experiment There are three ways in which an owner can share experiments Read By granting read access to a user group the owner of the experiment permits any member of that group to view the experiment details Edit By granting edit access to a user group the owner of the experiment perm
58. tory gt gt4 2 Add GLOBUS_LOCATION bin to the path environment variable e Windows set path path GLOBUS_LOCATION bin Unix Linux setenv PATH SPATH GLOBUS LOCATION pbin or export PATH SPATH SGLOBUS_LOCATION bin It is advisable to set these environment variables permanently Details on managing environ ment variables in Windows is available here http vlaurie com computers2 Articles environment htm 3 3 Extract GSI certificates from your browser Firefox 3 0 1 Goto Tools gt Options gt Advanced gt Encryption 2 Click on View certificates 3 Goto to Your certificates 6 CHAPTER 3 INSTALLING GLOBUS 4 Select the relevant GSI certificate 5 Click on backup 6 Save the certificate backup in PKCS12 format 7 Enter password for protecting the certificate backup file Internet explorer 7 1 Goto Tools Internet Options Content Certificates Personal Select the relevant GSI certificate Click on Export Select Yes export the private key and click next Default PKCS12 format is fine Click next Enter password for protecting the certificate backup file Supply filename for the certificate backup file Click on Finish 3 4 Extract public and private keys from the PKCS12 file 1 If you are using Windows download and install OpenSSL for windows http www slproweb com download Win320penSSL Light 0 9 8j exe You
59. w web services user group Create user ETITUENMNM Create grou group ri List users ist groups List owned groups et preferences Help Log out scmgy Refresh Select members Username Real name ID Afftiatior Jonathan P Giddy p giddyibes ct ac uk School of Computer Science University Wales UK Gagarine Yaiknom g yalkhom cs cf ac uk School of Computer Science Cardit University Wales UK Create Camel Figure 5 4 Creating a new user group Select members This field identifies the set of users who should become members of this user group It displays all of the users who are currently registered with the RTGrid system The members are selected from this list by checking the corresponding check boxes Once all of the above fields have been specified the new user group can be created by pressing the Create button To cancel user group creation press the Cancel button Please note that the field marked with an cannot be changed after the user group has been created Menu Liting user groups Select Al None Delete 1 5219 pag nghad This group weed 30 share tasis that aee seed the mamtenanoe of fe 22 00 Tve 11 0 PM ya f advanced Ths group weed tor sharing tacks which advanced knowledge cf 22 06 Tue 11 04 PM group t usad tor sharing or profes with oder Apr 22 08 Tou 11 0
60. w which corresponds to the profile This will display the profile modification dialog box as shown in Figure 7 6 Only owners are allowed to update access permissions of a given profile This means that although users may be able to edit profile details as a result of their membership to a group that has been granted edit access they will not be allowed to edit the access permissions The owner therefore has the highest priority over profiles owned by them 7 7 File management panel The file management panel as shown in Figure 7 7 allows a user to browse and perform certain actions on the files and directories that are associated with a given profile The file management panel has three main parts User s Manual The RTGrid Portal Version 2 0 28 CHAPTER 7 PROFILE MANAGEMENT Menu Create Profile List owned List accessible Set preferences Help Log out scmgy Refresh r File management Profile details lt lt Back to profile list File management 7 Browse upload mem SE 1 META ANE Apr 22 08 Tue 11 51 Delete Archive RTGHecDBWSTest java Apr 22 08 Tue 11 49 AM Delete J Edit J Iff extension xmi Apr 22 08 Tue 11 52 AM Delete J Edit hello Dec 20 7407 Thu 10 11 Delete Archivo testarchive tar gz Apr 22 08 Tue 11 54 AM Delete Extract Profile details Name Test profile 1 Last update time Apr 22 06 Tue 11 54 AM Creation time
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