Gatlet User Manual
Contents
1. link can be found in the upper right area after Welcome your name 2 amp 4 English User Name foo Password E Remember my login kogn j1 1 Login button Click on login to send username and password for authentication to the portal server Gatlet User Manual Page 4 MyProxy Portlet The MyProxy Portlet is the heart of Gatlet The access to grid resources is restricted to users that have a valid grid certificate Due to the fact that the portal will access grid resources on behalf of the user there must be a mechanism to share the user s grid certificate It s absolutely forbidden to save the private key of the user on the portal But this key is needed to access the grid So there must be another approach to delegate the user s rights to the portal The user has the ability to upload a short lived proxy certificate which is derived from his grid certificate to a MyProxy server The uploaded proxy is secured by aname and password which are chosen by the user A good tool for creating and uploading a proxy is the Grid Proxy Manager which is a Firefox plugin that has access to all certificates stored in the user s browser A resource e g the portal that knows the name and the password under which a proxy is stored on a MyProxy server can download a copy of it and therefore gets access to the grid on behalf of the user The MyProxy portlet of Gatlet implements the usage proxy certifica2. UNIVERSITY OF ULM KARLSRUHE INSTITUTE OF TECHNOLOGY Gatlet User Manual A user manual for Gatlet based grid portals Stefan Bozic Bastian Boegel 14 02 2011 Geben Sie hier das Exposee f r das Dokument ein Das Exposee ist meist eine Kurzbeschreibung des Dokumentinhalts Geben Sie hier das Exposee f r das Dokument ein Das Exposee ist meist eine Kurzbeschreibung des Dokumentinhalts A A e 3 Wei omenage a id 3 A A AN 3 WIIENLERIOKCEREIN Caterina diia 3 With Username and Password cccccccsssssssseecccccuceeessseeccccesseeesseeeecceessauesseeeeeesessauauseeeeeeeessaaagassss 4 MIRE O a ee ee 5 FIle BROWSER Poeta ee AEA E E ent 6 GTA 6 al pat Ol 9 f 1 010721 0 PDIET ee O A 7 Grid PTP DOWAlOAG Applet nee 8 Wep UBl030 22 2 2 228322 en ollas 9 Web DOWNIOS detona arenes E a a 9 Jo b SubmitPortet Globus 2 2 cn 10 VO Definition ac da 10 SEIECHRESOUrEE and QUEUE een 11 SOIC ECU CUS arde oran sii 11 JOD MONILOLIRE POrtlet ass N Eee 12 Submitted Jobs VIEW N A ON 12 JOD SUG VIEW nee ehe ee 13 MANO WG LOU een ee Renee 13 Tab Runtime ae RE 13 Tab FE ee ee Seele 14 STO aaa 15 SEIECERESOUFGE VIEW aaa 15 SSHTEFM ABBIEL VIEW aan Ie locked bt 15 A a 16 GUS POr dado 16 Appendix A GatletJoBstates nia 16 Gatlet User Manual Page 2 First Steps with Gatlet Welcomepage A grid portal based on Gatlet and GridSphere provides aWelcomePage to all visitors The page shows a welcome text and a short instruction about what ha
3. ad 4 1 File label Shows the path of the selected file on the GridFTP resource 2 Browse button A click on this button will open a file browser of the user s file system Select a directory where the downloaded file should be stored 3 Progress bar Shows you the status of the copy process Gatlet User Manual Page 8 4 Download button A click on this file starts the download The button is disabled until a directory has been selected Web Upload There are several causes that will make the usage of the GridFTP Upload Applet impossible The most common reason is that no Java Runtime is installed on the user s computer Furthermore there is a firewall in the user s network or on the GridFTP resource that forbids acommunication over the GridFTP port In these cases there is a workaround for uploading files via the portal server This approach is slower than the applet Also the size of the uploaded file is limited 1 MB to save portal resources A portal server should not be use as a distributer for storage resources In the just specified causes a click on the Upload button in the File Browser portlet willopen the Web Upload view which is similar to the upload applet Gatlet File Browser Portlet GridFTP Web Upload Upload file Resource opus Path fzk dgridlocalhome dgbw0195itemp 1 File 2 New File Name 3 Only needed if not the same as the uploaded file Upload4 Back 5 1 Path label Shows the target pat
4. cation issues a proxy certificate is used The user must only select the resource he wants to connect to Select Resource View When switch to this portlet the user has to select the interactive resource he wants to connect to Gatlet SshTerm Portlet Resource GSISSH bwGRiD Central Storage KIT bworid se scc kitedu cor 1 1 Filter button A click on this button will change the SSHTerm Applet View After selecting an interactive resource this view contains the SSHTerm Applet which will automatically connects to the interactive resource The connection establishment will take some time in cause of downloading the applet libraries from the portal and updating the CA certificates and revocation lists on the client The applet offers a lot of additional functionality You will get an overview of the features in the help section of the SSHTerm applet Gatlet SshTerm Portlet File Edit View Tools Proxy Help Ce 54 A a 29 0924 75 Last login Thu Mar 10 13 06 27 2011 from 1l4l 52 6 45 ee ee FIT TFT IT FF ee FF FF FF FF FF FT FF FT FF FT TI IF IT FF TFT FF FF FF FT FF FF FF IT FF IF T IF FT TI FF CHAREST ETAT NEC Cluster bwGRild Esslingen 84 eee eee eee eee eae TFT THF HF FF FT TH HF FF FF FH FF TH FH FH FF FF TI TI TI TH TH FH FH FH FF FT TH Ao ooo A HH General Information http ws bw grido de D Grid User Support http dgas d grid der Local User Support dqrid supporthhs esslingen de For hel
5. ces is supported too The list of resources a user can connect to depend on the VOs that are allowed on the GridFTP server and the VOs the user belongs to Gatlet File Browser Portlet One file directory successfully deleted 1 Resource juggle 2 Show Resource Resource othello Show Resource Resource othello Path home zidt0087 SONO Resource juggle Path home bworid dgbw0195 E Fl globus E Icgjm Fl ssh E output F portal E sandbox F testi authority bash_history classpath Jesshst Project nd profile local nw _ PI MAKT AT X MAKT AT X MWXT XT X MWXT XT X M n MWH nw MW T I mue MW T I Nov 12 09 00 Jul 21 16 26 Sep 9 15 32 Oct 22 15 28 Jul 8 17 08 Aug 3 10 08 Oct 22 14 40 Feb 10 13 49 Feb 10 13 50 Aug 19 16 15 Feb 11352 65 Aug 19 16 26 Nov 12 09 00 Apr 25 09 03 E bin A public_html PWI XI X wy PWXF XF X MWXT XT X 55 Feb 10 1450 23 Feb 10 1450 6 Feb 10 1450 23 Feb 10 14 50 17 1 Message Field Shows messages to user E g ifthe deletion of a file folder was successful 2 Resource selector This selector contains a list with GridFTP servers that are available to the user When the user change the selection the portlet is automatically connecting to the home directory of the user on the selected resource 3 Show resource In case of JavaScript is disabled the user has to press this but
6. e are for instance the job name and the resource Also the requirements to the computing resource like wall time and processors per node will be shown here Gatlet Job Monitoring Portlet Details Runtime Files Id 150 Name NWChem Job Testkoln Resource Globus bwGRiD Ulm scheduler PBS Queue user Process count 1 Node count 1 Processors pernode 1 Job type single Max CPU time min Max Wall time min 86400 Maximum Memory ME Command bin bash c source job control script Command Arguments sandbox Directory fusers dgrid ulbworpT ulbw0195 portal jobs WWChem Job TestKoeln_150 Refresh 3 1 Back button A click on this button will change to the Submitted Jobs View 2 Filter button A click on this button will trigger the portal to refresh the status of the job Tab Runtime This tab presents the jobs dynamic runtime information to the user This information depends on numerousness parameters and will be updated whenever the user triggers a job refresh either on this view or the Submited Job View Runtime parameters are for instance the current state of the job the destination host where the job will be executed or the start and stop time Gatlet User Manual Page 13 Gatlet Job Monitoring Portlet Details Parameter Laufzeit Dateien Job Id https fkojos rzuni ulm de 8443 ws rf services ManagedExecutableJobService fff21540 4653 11e0 a9ef ce86230164f9 Status DONE _ SUCCESS Exi
7. e file size 11 Download button A click on this button will download the selected file s from the current folder There are 2 download modes available Direct download from the resource via applet This is the preferable way to download files NOTE To use the download applet there must be a JRE 6 installed on the user s computer Web download via the portal This is the fallback strategy and not preferable because it consumes web server resources and therefore is limited in downloadable file size 12 Show Content button A click on this file will show the content of a file directory Id a file is selected it will be downloaded from the resource and shown in a new window If a folder is selected the file browser will make a change directory to this folder Only one file directory must be selected 13 Select all button A click on this button will select all files and directories in the file browser 14 Deselect all button A click on this button will deselect all files and directories in the file browser 15 Copy left to right button A click on this button will copy the selected files directories from the left resource to the selected folder on the right resource Directories will be copied recursively 16 Copy right to left button A click on this button will copy the selected files directories from the right resource to the current folder on the left resource Directories will be copied recursively 17 File Browser Window Show
8. fill in the job name and script that should be executed Job Name GlobusTestJob1 1 Bash Script 2 Next Requirements Clear fields 1 Job Name A name for the job 2 Bash Script Enter a bash script into the textbox Gatlet User Manual Page 10 3 Next button A click on this button will validate the user input If no error is detected the workflow continues with Select Resource and Queue mask 4 Clear Fields button Removes the value from Job Name and Bash Script Select Resource and Queue In this workflow steps the user can specify the job requirement in more detail For instance he can define parameters like the wall time max memory or the processors per node that his job needs Gatlet Job Submit Portlet Step 2 Select Resource and Queue Please select a resource from the list and press the select Button Then select one ofthe displayed queues from that resource and press the submit button to start the job Ifthe following parameters are not defined the server default is used Maximum wall time d hh mm ss Maximum memory per job MiB Number of nodes Processors per node e g 7 00 00 for 7 days default 1 hour e g 4096 for 4 GiB default 1024 MiB e g 5 for 5 nodes default 1 node 2 9 8 for 8 cores per node default 1 core per node Back to step 1 1 Back button A click on this button will change to the Job Definition step of the workflow select queue P Submit au
9. h of the file on the GridFTP resource 2 Browse button Click on this button to open a file browser of the user s file system Select a file to upload The file size is limited by the portal administrator 3 New File Name Specify a name for the uploaded file on the GridFTP resource 4 Upload button A click on this button starts the upload The button is disabled until a file has been selected 5 Back Button A click on the button will change to the File Browser Web Download Similar to the Web Download there are causes when the GridFTP Download Applet cannot be used A click on the download button will start a download of the selected files via the portal This download via portal is slower than the applet Also the size of the downloaded file is limited 1 MB to save portal resources A portal server should not be use a distributer for storage resources Gatlet User Manual Page 9 Job Submit Portlet Globus Gatlet includes a portlet for submitting bash scripts to Globus resources To submit a bash sript job the user has to follow a workflow shown in the picture below The single steps are explained in the following sections Job Definition Back Select Resource and Queue Select Queue Back Select Queue l Submit automatic queue selection Submit Job Definition In this step the user defines the base data for the grid job Gatlet Job Submit Portlet Step 1 Job Definition Please
10. hange to the Select Resource and Queue step of the workflow Gatlet User Manual Page 11 2 Submit button A click on this button will submit the job to the selected queue Job Monitoring Portlet The Job Monitoring Portlet is the central place to get details of the submitted jobs Submitted Jobs View The job table shows some common job information like the name state and submission date Click on the column header to change the order of the jobs The filter section will help the user to find previously submitted jobs In the last column of the job table the user find some action buttons that are assigned to each job The visibility of the refresh and stop button depends on the status of the current job Only jobs that are not ina final state DONE ABORTED CANCELED will have these two buttons NOTE The refresh stop and details action will take long because the portal must connect to the Globus resource to complete the action Gatlet Job Monitoring Portlet Submitted Jobs Job id Job name Job state Filter Jobld AL y Filter 4 GlobusTestJob2 gt4 fzk gridka de PBS dgiseq DONE_SUCCESS MEZ 2011 02 14 16 02 Details Entfernen 3 gLiteTestJob2 https wms c kit gridka de 7443 glite_wms_wmproxy_server UNKNOWN Aktualisieren3 Stop 4 Details Entfernen 7 2 gLiteTestlob1 _ https wms darid gridka de 7443 glite_wms_wmproxy_server SCHEDULED MEZ 2011 02 14 16 01 Aktualisieren St
11. initial on the middleware CLEARED output sandbox was transferred to the user or removed due to the timeout Gatlet User Manual Page 16
12. op 1 GlobusTestJob1 gt4 fzk gridka de PBS dgiseq DONE_SUCCESS MEZ 2011 02 14 16 01 Details I Entfernen 1 Remove selected 7 Refresh selected 8 This can take awhile 10 y 1 Filter Jobld button A click on this button will trigger a search for a special job 2 Filter button A click on this button will filter the user s jobs for a name or state 3 Refresh button A click on this button will call the portal to refresh the status of the job 4 Stop button A click on this button will terminate a scheduled or running job 5 Details button A click on this button will change to the Job Detail View 6 Remove button A click on this button will remove the job permanently from this view The job is not deleted and accessible via its id 7 Remove selected button A click on this button will remove the selected jobs permanently from this view The jobs are not deleted and still accessible via their ids 8 Refresh selected A click on this button will call the portal to refresh the status of the selected jobs Gatlet User Manual Page 12 Job Detail View The Job Detail View gives the user information about a single job that has been submitted with the portal The view is abstract and used to show the most common attributes of different middlewares To improve the view the job information has been group onto 3 tabs Tab Parameter The parameter tab shows the static job parameters that have been chosen by the user Thes
13. p please read BY GRID S type man bw grid Huge 125 256TE storage available in Earlsruhe See man bu grid Frontends are sfr l and grid l jobs can be submitted on both SHOME has a LOOMB quota please use workspaces for all data In addition to th default queue there is also a queue called cell which offers access to two FowerXlell based 05225 NEWS 2011 03 06 cluster online again 2011 03 30 central storage Karlsruhe not available until 4011 04 01 r i FF TFT I TH FH FH FH TFT a FH TFT FH TFT TH ee FH esbwOl Segrid l ps PID TTY TIME CMD 30695 prs 00 00 00 hash 30734 pta Information Starting of applet during 20 sec Gatlet User Manual Page 15 SRM Portlet This porlet allows access to SRM resources such as dCache or Castor It provides several common file operations on the storage resource See the file Browser Portlet for a detailed description of the actions GLite Portlet Appendix A Gatlet Job states Gatlet supports Globus and gLite and each middleware come with its own set of job states To provide the user a middleware independent view on his jobs Gatlet is hiding the specific states by transferring them to a Gatlet job model See the table below which states are supported by Gatlet PRE_SUBMIT initial state SUBMITTING Gatlet is preparing to submit the job SUBMITTING ABORTED Gatlet was unable to submit the job INITIAL Job has been submitted by Gatlet and has the state
14. s the files and directories that are located in the current folder on the selected resource GridFTP Upload Applet The GridFTP Upload Applet is a comfortable tool to copy files from the user s local file system to a remote GridFTP storage resource The applet creates a direct connection to the GridFTP server That avoids interaction with the portal and consequently save resources on the portal Additional a direct data transfer is much faster and not limited in the size of files Gatlet User Manual Page 7 GridFTP Upload Applet File Browse 1 J Fo 2 oad 3 1 Browse button Click on this button to open a file browser of the user s file system Select a file to upload The file size is only limited by the target system 2 Progress bar Shows you the status of the copy process 3 Upload button A click on this button starts the upload The button is disabled until a file has been selected GridFTP Download Applet The GridFTP Download Applet is a tool for copying data from a GridFTP storage resource directly to the users file system Like the upload applet there is a direct connection between the user s computer and the GridFTP resource That avoids interaction with the portal and therefore saves resources on the portal Additional a direct data transfer is much faster and not limited in the size of files GridF TP Download Applet File fhome dgbw0195 temp GridBean Demo taz 1 Destina Browse 2 0 3 Downlo
15. s to be done to get an user account for the portal English C3 D Welcome to D Grid Portal In a joint initiative with German research and industry the Federal Ministry of Education and Research BMBF is funding the development of D Grid Log in If you want to log in you need a DFN grid user certificate installed in your browser and you must be member of a Virtual Organization VO If you dont have a DFN grid user certificate or you are not member of a VO please consult the documentation on the D Gnd User Fonal After you have imported that certificate into your Firefox browser only Firefox is supported and you have become a member of a VO you can login with your DFN grid user certificate by accessing pipes gndbrowser d ord de 8443 ardsphere and clicking on login in the upper right corner NAT oe Federal Meestry ot Education Karwuhe Institute of Technology and Research 1 Login Link Click on this link to login to the portal Login With grid certificate Gatlet based grid portals usually supports user login with DFN grid certificates To use this feature the portal provider has to store the distinguished name DN of the user s grid certificate on the portal On the other hand the user has to import his certificate in his web browser During the login process the portal will ask automatically for your grid certificate Diese Website verlangt dass Sie sich mit einem Zertifikat identifizieren gridbro
16. t Code 0 Ausf hrender Rechner Abschickzeit Fri Mar 04 12 39 01 CET 2011 Startzeit Stopzeit CPU Zeit min 1 Back button A click on this button will change to the Submitted Jobs View 2 Filter button A click on this button will trigger the portal to refresh the status of the job Tab Files The Tab Files shows the working directory of the current job The user has the ability to execute common file operations in this directory See the file Browser Portlet for a detailed description of the actions Details Parameter A portal_job_607731 E HOMO cube gz E LUMO cube gz gridjob b gridjob b 1 gridjob c gridjob db 1 Back button A click on this button will change to the Submitted Jobs View 2 Filter button A click on this button will trigger the portal to refresh the status of the job Gatlet User Manual Gatlet Job Monitoring Portlet Resource GridFTP bwGRID Ulm Path users dgrid ulbworpt ulbw0195 portal jobs NWCh em Job TestKoeln 150 DOCOSOMNE TWX 4096 299607 492360 15576 15576 23352 713434 138619 Mar 4 12 39 Mar 4 12 39 Mar 4 12 39 Mar 4 12 39 Mar 4 12 39 Mar 4 12 39 Mar 4 12 39 Mar 4 12 39 Page 14 SSH Term Portlet The SSH Term Portlet allows user to open a ssh client embedded in the browser to an interactive grid resource This portlet is using an the SSH term Applet hence a Java Virtual Machine is required on the users computer For authenti
17. tes as a Single Sign On SSO mechanism to grid resources The user enters the access data to the proxy only one time in the portlet After this the portal can automatically download new instances of the proxy when accessing the grid Gatlet MyProxy Portlet MyProxy Settings MyProxy Server myproxy Irz muenchen de myproxy irz muenchen de 1 MyProxy User Name foo bar 2 MyProxy Password AE 3 Virtual Organisation for gLite Services dgtest 4 Save 5 Remove 1 MyProxy Server Defines the server where the user has been uploaded the proxy certificate 2 MyProxy User Name The name under which the user has stored the proxy on the server 3 MyProxy Password The password which protects the proxy on the server 4 Virtual Organization Is needed to create a VOMS proxy certificate when using gLite 5 Save button Click on the save button to store the entered data on the portal The portal will instantly try to download a proxy from the MyProxy server to validate the user s data 6 Remove button Click on the remove button to delete the MyProxy data from the portal Gatlet User Manual Page 5 File Browser Portlet For accessing GridFTP resources Gatlet provides the File Browser Portlet The portlet supports a set of common actions cd rm less upload download etc that a user can execute on files and directories The portlet allows accessing 2 GridFTP resources at the same time A file transfer between these resour
18. tomatic queue selection 2 Select queue button A click on this button will change to the Select Queue step of the workflow 3 Submit button A click on this button will submit the job to a Globus resource that is automatically determined by Gatlet Select Queue The table shows all queues that are assigned to Globus resources which match to the user s VOs The user can manually select a queue or delegate the decision to Gatlet which will automatically select a suitable queue Gatlet Job Submit Portlet Step 3 Select queue Please select the queue in that the job should run gt Automatic Queue Selection Cluster bwGRiD Ulm PBS user normal 2240 1 638 186 452 0 00 05 01 7 00 00 00 Cluster bwGRiD Esslingen PBS user single node 1464 27 0 0 0 0 00 01 00 1 00 00 00 Cluster bwGRiD Esslingen PBS user multi node 1464 27 48 13 35 0 00 01 00 1 00 00 00 Cluster bwGRiD Freiburg PBS user single node 1304 113 41 7 34 0 00 15 00 8 00 00 00 Cluster bwGRiD KIT PBS user single node 1120 9 23 11 12 0 00 01 00 1 00 00 00 Cluster bwGRiD KIT PBS user multi node 1120 9 42 6 36 0 00 01 00 1 00 00 00 Cluster bwGRiD Mannheim PBS batch single node 2464 44 126 56 70 0 00 01 00 5 00 00 00 O Cluster bwGRiD Tuebingen PBS user tue short 1720 45 13 8 5 0 00 01 00 3 00 00 00 Cluster bwGRiD Tuebingen PBS user tue long 1720 45 433 203 230 0 00 01 00 31 00 00 00 Back to step 2 1 Submit 2 1 Back button A click on this button will c
19. ton to connect to the selected resource 4 Home button Pressing this button will change the view to the home directory of the user 5 Refresh button A click on this button will refresh the list of files shown in the portlet 6 Rename button Select one or more files or directories which you want to rename The portlet will switch to an edit mode where you can assign new names 7 Delete button Select one or more files or directories which you want to delete The portlet will switch to confirmation dialog where the deletion must be confirmed by the user Gatlet User Manual Page 6 NOTE Only empty directories can be deleted by the portlet 8 Change Directory button A click on this button will change to the selected directory NOTE Exactly one directory has to be selected 9 Make directory button A click on this button will make a new directory in the current folder The portlet will switch to an edit mode where the user can enter the name of the new directory 10 Upload button A click on this button will upload a file to the current folder There are 2 upload modes available Direct upload via applet from the browser to the selected resource This is the preferable way to upload files NOTE To use the upload applet there must be a JRE 6 installed on the user s computer Web upload via the portal This is the fallback strategy and not preferable because it consumes web server resources and therefore is limited in uploadabl
20. wser d grid de 443 Organisation GermanGrid Ausgestellt unter GermanGrid W hlen Sie ein Zertifikat das als Identifikation vorgezeigt wird Details des gew hlten Zertifikats Ausgestellt auf CN Stefan Bozic OU KIT O GermanGrid C DE Seriennummer 26 28 G ltig von 01 07 2010 13 01 59 an 31 07 2011 13 01 59 Verwendung eines Zertifikatsschl ssels unterzeichne Non repudiation Schidssel Verschlisselung Daten Verschlisselung E Mail stefan bozic kit edu Ausgestellt von CN GridKa CA O GermanGrid C DE Gespeichert in Software Sicherheitsmodul Diese Entscheidung merken Abbrechen 1 Certificate Select box Select the suitable grid certificate from the list 2 OK Button Click on the OK button to submit the certificate data to the server Gatlet User Manual Page 3 If the certificate is accepted by the portal a message will be shown Login with certificate CN Stefan Bozic QU KIT O GermanGrid C DE 1 1 Login button Finally click on the button to login to the portal With Username and Password If you want to access your portal account without your DFN grid user certificate e g from another computer or browser you can set a password for your account after logging in with your DFN grid user certificate Please use Profile Change Password available only if you are logged in to change your password Please see Profile Profile settings to find out your local User Name in the portal The Profile
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