User's Manual - GForge
Contents
1. Local filesystem En E Remote connections CER file ff M7 Lyon Sophia Rennes Orsay Lille Nancy Filesystem home david Sfip home lyon dloureiro Gomi Da BR HAR ee I Ada piano Comi 2 kb gt bashrc 2 kb gt bashrc 23 bs gt scratch lyon dloureiro 13 kb gt AbiWord Profile a a 24 P DB 852 bs gt todo do I le Ga AbiSuite I z IM 57 bs gt DCOPserver_Endywion_ 0 AbiSuite IB 57 bs gt 0COPserver Endymion 0 o adobe ID 1 kb gt IcEauthority 5 kb gt bash_history 63 Trash IM 220 bs gt bash logout 119 bs gt Xauthority IM 414 bs gt bash_profile Ga adohe UB 847 bs gt bashrc adonthe11 a diet IM 65 kb gt bash_history emacs d B 220 bs gt bash logout BD 35 bs gt lesshst B 414 bs gt bash profile a ssh D D D B X 01d pwd yon d New pwd home lyon dloureiro Changing of directory from home lyon dloureiro to home lyon dloureiro on frontale nancy grid5000 fr Retrieving files list of home lyon dloureiro on frontale nancy grid5000 fr Retrieving files list of home lyon dloureiro on frontale nancy grid5000 fr DONE Retrieving files list of home lyon dloureiro on frontale nancy grid5000 fr Retrieving files list of home lyon dloureiro on frontale nancy grid5000 fr DONE che Figure 7 1 JFTP main interface For the2. User s Manual Version 1 1 1 Abdelkader AMAR David LOUREIRO Contents 1 Introductio 2 Requirements and installatio 2 1 Requirement 2 2 Installatio 2 2 1 Automatic installatio 2 2 2 Manual installatio 3_ Interface presentatio 4 Resources allocatio 41 Using OAR interfacel 5 Monitoring GRID 5000 6 The Ganglia module for GRUD 6 1 Ganglia short introductio 6 2 Ganglia plugi 7__JFTP Module for GRUD 7 1 Presentatio 8 Deploy your Kadeploy images Application settings 10 Troubleshooting NO B_ License of GRUD Q o BOBB A 22 23 24 26 26 26 27 27 29 List of Figures 2 1 Installation packages selection oo ea a a vr 5 22 Shortcuts configuration s cicl n er RES PSG REE Ree SS 6 2 3 GRID 5000 access configuration sc cc ss amo dnu na aaa aw aa 7 24 GRID 5000 clusters conficuration ss s amp er e aoao ehe e Ea ev e a 7 2 5 Configuration window First tab 8 26 Configuration window Second tab so e secs satoa dagaa auna ee 9 2 7 Configuration window Third tabl o sr sr ss ts ses 10 3 1 Maininterfaceof GRUDU siea eina a da m a ene a eia aaa f rr un DoS 12 3 2 Tip of the day f r GRUDU ceres amp amp 8 La a iea ba enia nka enh 13 4 1 Resources allocation frame Mainpanel 15 4 2 Resources allocation frame OAR pro
3. 1 0 27 APPENDIX A CONFIGURATION FILES e For each cluster name the name of the cluster xda the partition used by KaDeploy GRUDU User s Manual v1 1 0 28 License of GRUDU FREE SOFTWARE LICENSING AGREEMENT CeCILL This Agreement is a free software license that is the result of discussions between its authors in order to ensure compliance with the two main principles guiding its drafting firstly its conformity with French law both as regards the law of torts and intellectual property law and the protection that it offers to authors and the holders of economic rights over software secondly compliance with the principles for the distribution of free software access to source codes extended user rights The following bodies are the authors of this license CeCILL Ce CEA C CNRS I INRIA LL Logiciel Libre Commissariat iad l Energie Atomique CEA a public scientific technical and industrial establishment having its principal place of business at 31 33 rue de la Fi di Fration 75752 PARIS cedex 15 France Centre National de la Recherche Scientifique CNRS a public scientific and technological establishment having its principal place of business at 3 rue Michel Ange 75794 Paris cedex 16 France Institut National de Recherche en Informatique et en Automatique INRIA a public scientific and technological establishment having its principal place of business at Domaine de Voluceau Rocquencou
4. files A 1 Files used by GRUDU GRUDU uses several configuration files saved in the diet directory which is located at the root of your home directory e GRUDUApplicationProperties xml main configuration file containing the high level information e g5K xml this file contains the main information for the GRID 5000 connection manage ment e g5k_cfg xml this file corresponds to the grid description For each file the main content for the GRUDU usage will be described A 2 GRID 5000 configuration file GRUDUApplicationProperties xml lt application gt lt properties name tipOfTheDayShowOnStartup value false gt lt properties name tipOfTheDayFileOfTips value languages totd defaultGRUDUFileOfTips_eng xml gt lt properties name version value 1 1 0 gt lt application gt This files defines the application wide configuration iformation For the moment every elements are a properties with a name and a value For the moment there are three properties declared in that file e version the purpose of that property is obvious it corresponds to the version of GRUDU e tipOfTheDayShowOnStartup This property declares whether the tip of the day should or not be displayed on startup e tipOfTheDayFileOfTips This property defines the file from which the tips of the day should be taken 26 APPENDIX A CONFIGURATION FILES A 3 GRID 5000 configuration file g5k xml lt xm
5. is not altered and that no Articles are either added or removed herefrom This Agreement may apply to any or all software for which the holder of the economic rights decides to submit the operation thereof to its provisions Article 1 DEFINITIONS For the purposes of this Agreement when the following expressions commence with a capital letter they shall have the following meaning Agreement means this Licensing Agreement and any or all of its subsequent versions Software means the software in its Object Code and or Source Code form and where applicable its documentation as is at the time when the Licensee accepts the Agreement Initial Software means the Software in its Source Code and or Object Code form and where applicable its documentation as is at the time when it is distributed for the first time under the terms and conditions of the Agreement Modified Software means the Software modified by at least one Contribution Source Code means all the Software s instructions and program lines to which access is required so as to modify the Software Object Code means the binary files originating from the compilation of the Source Code Holder means the holder of the economic rights over the Initial Software Licensee s mean s the Software user s having accepted the Agreement Contributor means a Licensee having made at least one Contribution Licensor means the Holder or any or all other indivi
6. repartition summary for Grid 5000 10 al a so so jua S 70 E g so creat g so Granoble ldpot 20 Grenoble ICluster2 20 10 ol E Cape Sagi Azur Helios Oray Uile Nancy a Free m Moges percentage Figure 5 1 Grid 5000 view e The second view in FigureB2 corresponds to a site view A graph represents the different numbers of nodes for each different state ant the ones corresponding to your possible reser vation s A table presents these information in a different way Another table displays the reservation s realized on the site You can also display a Gantt chart of the different reservations of the cluster to know when you are able to reserve If you selected the Ganglia plugin at the installation step you also have a button bar on the right hand side of the frame that will be populated with a Ganglia information button 16 CHAPTER 5 MONITORING GRID 5000 allowing you to get low level information on every machines of the site data are instanta neous Grid5000 resources management tool Job description Avallable chars Pie Chart gt Status of Lyon Nancy Grenoble mossen 15m e Free Job e Dead Host Network CPUS Load A cru toed Disk Mem swap Y Figure 5 2 Site view v y Grid5000 resources management tool Ganglia Information capricorme lyon gri
7. to fulfill its obligations ii direct or consequential loss due to the Software s use or performance that is suffered by the Licensee when the latter is a professional using said Software for professional purposes and iii consequential loss due to the Software s use or performance The Parties expressly agree that any or all pecuniary or business loss i e loss of data loss of profits operating loss loss of customers or orders opportunity cost any disturbance to business activities or any or all legal proceedings instituted against the Licensee by a third party shall constitute consequential loss and shall not provide entitlement to any or all compensation from the Licensor Article 9 WARRANTY 9 1 The Licensee acknowledges that the current situation as regards scientific and technical know how at the time when the Software was distributed did not enable all possible uses to be tested and verified nor for the presence of any or all faults to be detected In this respect the Licensee s attention has been drawn to the risks associated with loading using modifying and or developing and reproducing the Software that are reserved for experienced users The Licensee shall be responsible for verifying by any or all means the product s suitability for its requirements its due and proper functioning GRUDU User s Manual v1 1 0 33 APPENDIX B LICENSE OF GRUDU and for ensuring that it shall not cause damage to either pe
8. MENT 12 1 Any or all person is authorized to duplicate and distribute copies of this Agreement 12 2 So as to ensure coherence the wording of this Agreement is protected and may only be modified by the authors of the License that reserve the right to periodically publish updates or new versions of the Agreement each with a separate number These subsequent versions may address new issues encountered by Free Software 12 3 Any or all Software distributed under a given version of the Agreement may only be subsequently distributed under the same version of the Agreement or a subsequent version subject to the provisions of article 5 3 4 Article 13 GOVERNING LAW AND JURISDICTION 13 1 The Agreement is governed by French law The Parties agree to endeavor to settle the disagreements or disputes that may arise during the performance of the Agreement out of court 13 2 In the absence of an out of court settlement within two 2 months as from their occurrence and unless emergency proceedings are necessary the disagreements or disputes shall be referred to the Paris Courts having jurisdiction by the first Party to take action Version 1 1 of 10 26 2004 GRUDU User s Manual v1 1 0 35
9. Main information At al Lyon Rennes Orsay Bordeaux Toulouse Lille Figure 4 2 Resources allocation frame OAR properties for the reservation After the reservation a status frame summarizes the information about the success or not of your jobs submission gt Reservation status frame AAD Start time Walltime OAR grid sub behaviour Queue Cluster Lyon Capricorne Reservation summary 2007 7 17 16 17 42 1 0 false default Reservation state OK Nodes number Quit Figure 4 3 Resources allocation frame Reservation status GRUDU User s Manual v1 1 0 15 CHAPTER 5 Monitoring GRID 5000 To monitor GRID 5000 three views can be displayed e The first view in Figure B T corresponds to the GRID 5000 view You can see the state of the grid in term of free occupied dead absent suspected possessed nodes for each site and for the entire grid Added to the states of the nodes you can also see which nodes you have reserved You can also see a table summarizing these information Finally you have a table of your reservation s on the grid Thanks to two buttons you can save your reservation s in a directory for a future use for example in the DIET Mapping Tool or with the XMLGoDIETGenerator Grid5000 resources management tool ese Available chants Stack Bar Chart gt Nodes
10. NDIX B LICENSE OF GRUDU Article 3 ACCEPTANCE 3 1 The Licensee shall be deemed as having accepted the terms and conditions of this Agreement by the occurrence of the first of the following events i loading the Software by any or all means notably by downloading from a remote server or by loading from a physical medium ii the first time the Licensee exercises any of the rights granted hereunder 3 2 One copy of the Agreement containing a notice relating to the specific nature of the Software to the limited warranty and to the limitation to use by experienced users has been provided to the Licensee prior to its acceptance as set forth in Article 3 1 hereinabove and the Licensee hereby acknowledges that it is aware thereof Article 4 EFFECTIVE DATE AND TERM 4 1 EFFECTIVE DATE The Agreement shall become effective on the date when it is accepted by the Licensee as set forth in Article 3 1 4 2 TERM The Agreement shall remain in force during the whole legal term of protection of the economic rights over the Software Article 5 SCOPE OF THE RIGHTS GRANTED The Licensor hereby grants to the Licensee that accepts such the following rights as regards the Software for any or all use and for the term of the Agreement on the basis of the terms and conditions set forth hereinafter Otherwise the Licensor grants to the Licensee free of charge exploitation rights on the patents he holds on whole or part of th
11. Sophia fc DARZ Y Rennes ES OAR2 Y Orsay OAR ov Bordeaux 0 OAR v Toulouse OAR Y Lille les D R Y Nancy OARZ Y Grenoble amp OAR Cr avec IzPack http www izforge com narun CO rr c den Y CS CS umer Figure 2 4 GRID 5000 clusters configuration GRUDU User s Manual v1 1 0 7 CHAPTER 2 REQUIREMENTS AND INSTALLATION When all these information will be filled out you will be able to write the configuration by clicking the Write configuration button This action will create the local hierarchy of files mandatory for GRUDU a directory called diet containing all the files for GRUDU will be cre ated in your home directory and the remote hierarchy of files mandatory for GRUDU approxi mately the same on the clusters of GRID 5000 2 2 2 Manual installation If you want to compile GRUDU sources you need to install the Java build tool Ant El You must have a cvs access to the GRUDU repository Then simply execute the following command ant GRUDU for the compilation If your login on your local machine differs from the login on the CVS specify it with the following option Duser your_cvs_login If the compilation succeeds you will get a new jar file GRUDU jar representing the program Launching GRUDU can be done like a typical jar file java jar GRUDU jar It is preferable that your first step with GRUDU is to configure it The configuration window contains three tabs the first cor
12. a aj LL wl Vv Pe PRAT YA o 606 isis s610 16127 1614 tele 1618 1670 1627 late System User as Job omar 17 3 sc CHAPTER 6 The Ganglia module for GRUDU 6 1 Ganglia short introduction Ganglia is a scalable distributed monitoring system for high performance computing systems such as clusters and Grids It is based on a hierarchical design targeted at federations of clusters It leverages widely used technologies such as XML for data representation XDR for compact portable data transport and RRDtool for data storage and visualization It uses carefully engi neered data structures and algorithms to achieve very low per node overheads and high concur rency The implementation is robust has been ported to an extensive set of operating systems and processor architectures and is currently in use on thousands of clusters around the world It has been used to link clusters across university campuses and around the world and can scale to handle clusters with 2000 nodes Ganglia is an open source project that grew out of the University of California Berkeley Mil lennium Project which was initially funded in large part by the National Partnership for Ad vanced Computational Infrastructure NPACI and National Science Foundation RI Award EIA 9802069 NPACI is funded by the National Science Foundation and strives to advance science by creating a ubiquitous contin
13. able for deployment i e reserved with the deploy type You can click on the checkboxes to select deselect the nodes If you want to select deselect all nodes you can click on the corresponding button on the right hand side of the frame Then you can select the image you want to deploy from the lists on the right hand side of the frame When you are done with the configuration you can click on the deploy button A new frame will be displayed corresponding to the log of the deployment with both standard output and error O Deploy your system pith Kudeploy 4 Clusters Selection Mode 5 pa G 2 Lvon Capricorne Select all hosts Select None E node 31 Ivon arid5000 fr node 39 lvon arid5000 fr Lyon Capricorne sid x64 nfs demo ramses node 42 won arid5000 fr I node 46 lvon arid5000 fr Lyon Sagittaire Sid x64 nfs diet 1 0 O node 50 Ivon arid5000 fr Sophia Azur sid x64 nfs demo ramses Sophia Helios sid x64 nfs diet 1 0 Sophia Sol sid x64 nfs demo ramses Rennes Parasol sid x64 nfs demo ramses A Rennes Paravent sid x64 nfs diet 1 0 d Rennes Tartopom A amo Rennes Paraquad Gid x64 nfs demo ramses Nancy sid x64 nfs demo ramses Deploy Cancel Figure 8 1 Kadeploy frame 22 CHAPTER 9 Application settings By clicking the application settings button the following frame appears O GRUDU Settings ADA Here are the settings of the GRUDU 4 GRUDU if F Genera
14. censor and the Licensee pursuant to a memorandum of understanding The Licensor disclaims any or all liability as regards the Licensee s use of the Software s name No warranty shall be provided as regards the existence of prior rights over the name of the Software and as regards the existence of a trademark Article 10 TERMINATION 10 1 In the event of a breach by the Licensee of its obligations hereunder the Licensor may automatically terminate this Agreement thirty 30 days after notice has been sent to the Licensee and has remained ineffective 10 2 The Licensee whose Agreement is terminated shall no longer be authorized to use modify or distribute the Software However any or all licenses that it may have granted prior to termination of the Agreement shall remain valid subject to their having been granted in compliance with the terms and conditions hereof Article 11 MISCELLANEOUS PROVISIONS 11 1 EXCUSABLE EVENTS Neither Party shall be liable for any or all delay or failure to perform the Agreement that may be attributable to an event of force majeure an act of God or an outside cause such as notably defective functioning or interruptions affecting the electricity or telecommunications networks blocking of the network following a virus attack the intervention of the government authorities natural disasters water damage earthquakes fire explosions strikes and labor unrest war etc 11 2 The fact that eit
15. configuration of the options for the Rsync transfert between GRID 5000 frontales you can click on the option menu and you will find the following frame where you can edit the Rsync options 20 CHAPTER 7 JFTP MODULE FOR GRUDU G Rsync options 000 Base options ol Archive mode all is conserved fs Compression of the data to transfer Updating the local remote files Deleting parameters Recursive work Skip files that are newer on the receiver Update destination files in place Append data onto shorter files Deleting files before transfer Deleting files during transfer Deleting files after transfer Ignoring symlinks that point outside the directory Skipping updating files that exist on receiver Make backup Make backup into hierachies base directory DIR Suffix for the backup Apply cancel Figure 7 2 JFTP rsync options GRUDU User s Manual v1 1 0 21 CHAPTER 8 Deploy your Kadeploy images KaDeploy is a fast and scalable deployment system for site and grid computing KaDeploy is the reconfiguration system used in GRID 5000 allowing the users to deploy their own OS on their reserved nodes For more information about how to create and manage KaDeploy images please refer to the documentation available on the GRID 5000 web page The Figure 8 1 shows the frame allowing you to deploy images on which you have rights The left hand side of the frame corresponds to sites and nodes avail
16. d the main node of each of his her reservations on GRID 5000 Deploy images through KaDeploy on the appropriate nodes Exchange files between the locale machine and GRID 5000 but also synchronize files be tween GRID 5000 frontends Log out Display the Help of GRUDU 11 CHAPTER 3 INTERFACE PRESENTATION 1 jerat khar a cluster cag i eneblec and where wy heve no eservaricrz a cluste ial eneblec and where weyd have one ar mc ur y 19 reservatior E E si i rn cello a cluste 7191 eneblec and where ou heve one OF mE welig Peservaricr Figure 3 1 Main interface of GRUDU Legend of FigureB 1 A Options toolbar left hand side 1 ao fF Q N N oa Button used to log in GRID 5000 When connected to GRID 5000 you will have a but ton to log out Button used to display the reservation frame Button used to update the GRID 5000 tree of sites and jobs Button used to display the configuration frame Button used to display a summary of the information about GRID 5000 and your reser vations Button used to display a terminal on the preferred access point you have defined Button used to display the KaDeploy frame for the deployment of images with user defined environments Button used to display the JFTP module for GRUDU This module allows the user to transfert data between your locale machine and GRID 5000 You can also transfert data between the GRID 5000 frontales B Options toolbar r
17. ded that said redistribution complies with all the provisions of the Agreement and is accompanied by a copy of the Agreement a notice relating to the limitation of both the Licensor s warranty and liability as set forth in Articles 8 and 9 and that in the event that only the Modified Software s Object Code is redistributed the Licensee allows future Licensees unhindered access to the Modified Software s full Source Code by providing them with the terms and conditions for access thereto it being understood that the additional cost of acquiring the Source Code shall not exceed the cost of transferring the data 5 3 3 redistribution OF DYNAMIC MODULES When the Licensee has developed a Dynamic Module the terms and conditions hereof do not apply to said Dynamic Module that may be distributed under a separate Licensing Agreement 5 3 4 COMPATIBILITY WITH THE GPL LICENSE In the event that the Modified or unmodified Software is included in a code that is subject to the provisions of the GPL License the Licensee is authorized to redistribute the whole under the GPL License In the event that the Modified Software includes a code that is subject to the provisions of the GPL License the Licensee is authorized to redistribute the Modified Software under the GPL License Article 6 INTELLECTUAL PROPERTY 6 1 OVER THE INITIAL SOFTWARE The Holder owns the economic rights over the Initial Software Any or all use of the Initial S
18. ds 000 CPU amp Load Load of the machine e The third view in figure 53 corresponds to the job view Here you can see the different information of the job such as the nodes of the reservation the job state the walltime etc If you selected the Ganglia plugin at the installation step you also have a button bar on the right hand side of the frame that will be populated with a Ganglia history information button allowing you to get an history on the low level information concerning the nodes of your reservation a Grid5000 resources management tool State R Resources numi ber T Scheculeo ume 2007 11 08 16 04 45 Command San tima 2007 11 08 16 04 58 Submit tme 2007 11 08 16 04 54 CPU set Name sloureira s7730 Ext Code Resubmit fob ic y po 27720 Type INTERACTIVE Launching Directory jriome Nonjcioureiro Reservation Schadulad valtime Loe denia Cee aa ress Lwalime 10 5 Y Owner alowraira GRUDU User s Manual v1 1 0 Figure 5 3 Job view Job description Grid5000 resources management tool Get fresh data Host Ccapricome S yon arid3900 fr a Metrics Butes sec Memory nro Swap Into a Metrics CAU Info History of the idle system user cpu occupation 160 5 so al
19. dual or legal entity that distributes the Software under the Agreement Contributions mean any or all modifications corrections translations adaptations and or new functionalities integrated into the Software by any or all Contributor and the Static Modules Module means a set of sources files including their documentation that once compiled in executable form enables supplementary functionalities or services to be developed in addition to those offered by the Software Dynamic Module means any or all module created by the Contributor that is independent of the Software so that this module and the Software are in two different executable forms that are run in separate address spaces with one calling the other when they are run Static Module means any or all module created by the Contributor and connected to the Software by a static link that makes their object codes interdependent This module and the Software to which it is connected are combined in a single executable Parties mean both the Licensee and the Licensor These expressions may be used both in singular and plural form Article 2 PURPOSE The purpose of the Agreement is to enable the Licensor to grant the Licensee a free non exclusive transferable and worldwide License for the Software as set forth in Article 5 hereinafter for the whole term of protection of the rights over said Software GRUDU User s Manual v1 1 0 LICENSE OF GRUDU 30 APPE
20. e inventions implemented in the Software 5 1 RIGHTS OF USE The Licensee is authorized to use the Software unrestrictedly as regards the fields of application with it being hereinafter specified that this relates to permanent or temporary reproduction of all or part of the Software by any or all means and in any or all form loading displaying running or storing the Software on any or all medium entitlement to observe study or test the operation thereof so as to establish the ideas and principles that form the basis for any or all constituent elements of said Software This shall apply when the Licensee carries out any or all loading displaying running transmission or storage operation as regards the Software that it is entitled to carry out hereunder 5 2 entitlement to make CONTRIBUTIONS The right to make Contributions includes the right to translate adapt arrange or make any or all modification to the Software and the right to reproduce the resulting Software The Licensee is authorized to make any or all Contribution to the Software provided that it explicitly mentions its name as the author of said Contribution and the date of the development thereof 5 3 DISTRIBUTION AND PUBLICATION RIGHTS In particular the right of distribution and publication includes the right to transmit and communicate the Software to the general public on any or all medium and by any or all means and the right to market either
21. figuration Misc il Kadeploy Paritition Kadeploy partition Lyon OAR Sophia COAR gt Rennes COAR Orsay COARI Bordeaux ES COAR Toulouse COAR Lille COAR D Nancy COAR2 Grenoble COAR Save Close Figure 2 6 Configuration window Second tab The third tar shown in figure 2 ZJjallows the user to configure the KaDeploy partition for every clusters independently GRUDU User s Manual v1 1 0 9 CHAPTER 2 REQUIREMENTS AND INSTALLATION Grid 5000 reservation tool configuration oo User configuration Misc Kadeploy Paritition Lyon Capricorne Lyon Sagittaire Sophia Azur Sophia Helios Sophia Sol Rennes Paraquad Rennes Paravent Rennes Parasol Rennes Paramount Orsay Gdx Orsay Netgdx Bordeaux Bordeplage Bordeaux Bordereau Bordeaux Bordemer Toulouse Violette Lille Chuque Lille Chti Lille Chicon Nancy Grelon Nancy Grillon Grenoble Idcalc Grenoble Idpot Figure 2 7 Configuration window Third tab GRUDU User s Manual v1 1 0 10 CHAPTER 3 Interface presentation GRUDU is composed of one principal frame shown in Figure B 1 From this frame the user will be able to Log in GRID 5000 Monitor GRID 5000 and his her reservations Have a terminal on the preferred access frontale the different sites an
22. h the jar file from a shell terminal with the following command MzPack is an installer s generator for the Java platform 2works on operating systems where the jar mime type is managed by java CHAPTER 2 REQUIREMENTS AND INSTALLATION java jar GRUDU_installer jar The installation is separated into two parts the installation of the software itself the jar file the libraries and the resource files and then its configuration locally and remotely Installation of the software The first one corresponds to the selection of the different packages you want to install Five packages are available e The base package contains the software and the mandatory libraries It is required e The JFTP module for GRUDU This module corresponds to a File Transfert Protocol module This module allows you to transfert data between GRID 5000 and your local machine but also between the frontales of GRID 5000 e The Ganglia module for GRUDU This module corresponds to a plugin retrieving data from Ganglia to display low level information about all the nodes of a site or the history of these metrics for the nodes of your jobs e The documentation package corresponds to the User s Manual and the JavaDoc of GRUDU e The source code of GRUDU O GRUDU 1 1 0 IzPack Assistant d installation oe S lection des paquets installer GRuxpu J S lection des modules installer 3 7 Note les paquetages gris s ne sont pas optionnels X Ba
23. her Party may fail on one or several occasions to invoke one or several of the provisions hereof shall under no circumstances be interpreted as being a waiver by the interested Party of its entitlement to invoke said provision s subsequently 11 3 The Agreement cancels and replaces any or all previous agreement whether written or oral between the Parties and having the same purpose and constitutes the entirety of the agreement between said Parties concerning said purpose No supplement or modification to the terms and conditions hereof shall be effective as regards the Parties unless it is made in writing and signed by their duly authorized representatives 11 4 In the event that one or several of the provisions hereof were to conflict with a current or future applicable act or legislative text said act or legislative text shall take precedence and the Parties shall make the necessary amendments so as to be in compliance with said act or GRUDU User s Manual v1 1 0 34 APPENDIX B LICENSE OF GRUDU legislative text All the other provisions shall remain effective Similarly the fact that a provision of the Agreement may be null and void for any reason whatsoever shall not cause the Agreement as a whole to be null and void 11 5 LANGUAGE The Agreement is drafted in both French and English In the event of a conflict as regards construction the French version shall be deemed authentic Article 12 NEW VERSIONS OF THE AGREE
24. ight hand side 9 10 JavaHelp dedicated to the Help of GRUDU Application settings of GRUDU C Legend of the colors used for the sites and jobs D Main panel where information are displayed Information about GRID 5000 the different sites and the jobs are displayed here GRUDU User s Manual v1 1 0 12 CHAPTER 3 INTERFACE PRESENTATION E GRID 5000 sites and jobs 11 Root node of the GRID 5000 sites and jobs tree This node allows you to display in formation about the grid When right clicking on this node you can either update the GRID 5000 view open a shell on your preferred access point or delete all your reservations on GRID 5000 12 Node corresponding to a site Information about the site i e the occupation of the nodes and the existing reservations on this site When right clicking on a site node you can either delete the reservations you have on the site or open a shell on the site frontale 13 Node corresponding to a job Information on the job are displayed in the information panel When right clicking on that node you will able to delete the corresponding reservation update the site view or open a shell on the main node of the corresponding job A tip of the day frame is shown if you want so at GRUDU startup and presents you some tips for the use of GRUDU You can enable disable the frame in the application configuration frame see 9 Tip of the Day O 0 Did you know When selec
25. in GRUDU User s Manual v1 1 0 31 APPENDIX B LICENSE OF GRUDU consideration of a fee or free of charge a copy or copies of the Software by means of any or all process The Licensee is further authorized to redistribute copies of the modified or unmodified Software to third parties according to the terms and conditions set forth hereinafter 5 3 1 REDISTRIBUTION OF SOFTWARE WITHOUT MODIFICATION The Licensee is authorized to redistribute true copies of the Software in Source Code or Object Code form provided that said redistribution complies with all the provisions of the Agreement and is accompanied by a copy of the Agreement a notice relating to the limitation of both the Licensor s warranty and liability as set forth in Articles 8 and 9 and that in the event that only the Software s Object Code is redistributed the Licensee allows future Licensees unhindered access to the Software s full Source Code by providing them with the terms and conditions for access thereto it being understood that the additional cost of acquiring the Source Code shall not exceed the cost of transferring the data 5 3 2 REDISTRIBUTION OF MODIFIED SOFTWARE When the Licensee makes a Contribution to the Software the terms and conditions for the redistribution of the Modified Software shall then be subject to all the provisions hereof The Licensee is authorized to redistribute the Modified Software in Source Code or Object Code form provi
26. in node of your reservation for the launch of the remote jar creating the history Grid5000 resources mana gement tool Goorfiguration gt 00 00 90 00 00 jin node of the reservation fopt jak1 6 0 Ge OM Es A 10 a p mi z8 E m O ES gt Job description Gamen data Host Metrics CPU Info History of the idle system user cpu occupation Figure 6 3 Ganglia plugin for the job view GRUDU User s Manual v1 1 0 19 CHAPTER 7 JETP Module for GRUDU 7 1 Presentation JFTP is an acronym for Java File Transfert Protocol JFTP is a graphical Java network and file transfer client At the origin JFTP is developed as a project under GNU GPL license You can find more information about the initial project atfhttp j ftp sourceforge net JFTP has been modify to corresponds to the needs of the GRUDU users Thanks to the mod ified JFTP you can transfer data between you local machine and GRID 5000 but also between GRID 5000 frontales 7 2 Interface The JFTP module presents three internal frames one for the local machine one for GRID 5000 with one tab per site and the last frame for the log of the module a JFtp The GRUDU module for File transfer on Grid 5000 Version oee File Options 1
27. it Toolkit java 804 swing swing swing swing yJ JPanel lt init gt JPanel java 64 swing yJ swing swing UlManager initialize UlManager java 1262 UIManager maybeInitialize UIManager java 1245 UIManager getUI UIManager java 851 JPanel updateUI JPanel java 104 Panel lt init gt JPanel java 87 JPanel lt init gt JPanel java 95 pplication settings SettingsPanelImplementation ttingsPanelImplementation java 13 pplication settings DIETInstallationSettingsPanel ETInstallationSettingsPanel java 32 24 at diet appl CHAPTER 10 TROUBLESHOOTING ication DDBApplicationConfiguration initializeSpecificSettingsPanelList DDBApplicationConfiguration java 49 at diet application ApplicationConfiguration loadConfiguration ApplicationConfiguration java 165 at diet application ApplicationConfiguration setApplicationContext ApplicationConfiguration java 118 at diet DietOffice main DietOffice java 834 Caused by java lang ArrayIndexOutOfBoundsException 1 at sun awt XllGraphicsEnvironment getDefaultScreenDevice X11GraphicsEnvironment java 178 at sun awt X11 XToolki 18 more Answer To so lt clinit gt XToolkit java 98 Ive this juste launch the installer or GRUDU on the other screen it should be the first display under Linux something like gt echo SDISPLAY 0 20 GRUDU User s Manual v1 1 0 25 APPENDIX A Configuration
28. l General settings of GRUDU Version of GRUDU 1 1 0 Tips of the day showed on start up Validate Close Figure 9 1 Application settings For the instance you can only define if you want the tip of the day frame to be displayed on startup 23 CHAPTER 10 Troubleshooting Some problems can appear during the installation or during the use of GRUDU Here are some solutions e Question I am under Gentoo and when I am launching the installer GRUDU I get the following error java Aborted xcb_xlib c 50 xcb xlib unlock Assertion c gt xlib lock failed Answer This problem come from the Java runtime you are using Simply run the follow ing peace of code in a console and you will be able to run your java application CFLAGS DNDEBUG emerge av1 libxcb e Question I have two screens and when I am launching the installer GRUDU java complains and the following exception is raised ava ava 1 ang Cl ava a ava a avax avax avax avax avax avax ja th fs O es es Cas ls A L t javax t diet a nit gt Se t diet a lt init gt DI p 9 AD DODODDDLDD VD MM OM WM WM p ct Exception in thread main java lang ExceptionInInitializerError j lang Cl ass forName0 Native Method ass forName Class java 164 wt Toolkit 2 run Toolkit java 821 ava security AccessController doPrivileged Native Method wt Toolkit getDefaultToolk
29. l version 1 0 standalone yes gt lt g5Sk gt lt preferredAccesPoint host acces lyon grid5000 fr fr gt lt username id myG5KLogin gt lt sshkey file thePathToMySSHKeyFile gt lt G5K Sites gt lt g5k gt This file defines the global information used to log in GRID 5000 The elements that are not used by GRUDU have been removed from the description Here are the parameters that should be supplied e preferredAccesPoint the node has an attribute named host This attribute have to be the name of one of the access frontales of GRID 5000 e username the node has an attribute named id that is the login of the user e sshkey the node has one attribute file which is the file storing the ssh private key A 4 GRID 5000 configuration file g5k_cfg xml lt g5Sk gt lt site id Lyon nable false batch_schedulers 0AR1 gt lt cluster name Lyon Capricorne xda gt lt cluster name Lyon Sagittaire xda gt lt site gt lt g5k gt This file describes the platform of GRID 5000 the properties of the sites id batch_scheduler etc but also the clusters of the sites with their deployment partitions Here are the parameters that should be supplied for each site e id Name of the site e enable true false defines whether the site is considered in the interrogation parts of GRUDU e batch_schedulers Name of the batch scheduler to use GRUDU User s Manual v1
30. oftware is subject to compliance with the terms and conditions under which the Holder has elected to distribute its work and no one shall be entitled to and it shall have sole entitlement to modify the terms and conditions for the distribution of said Initial Software The Holder undertakes to maintain the distribution of the Initial Software under the conditions of the Agreement for the duration set forth in article 4 2 6 2 OVER THE CONTRIBUTIONS The intellectual property rights over the Contributions belong to the holder of the economic rights as designated by effective legislation 6 3 OVER THE DYNAMIC MODULES GRUDU User s Manual v1 1 0 32 APPENDIX B LICENSE OF GRUDU The Licensee having developed a Dynamic Module is the holder of the intellectual property rights over said Dynamic Module and is free to choose the agreement that shall govern its distribution 6 4 JOINT PROVISIONS 6 4 1 The Licensee expressly undertakes not to remove or modify in any or all manner the intellectual property notices affixed to the Software to reproduce said notices in an identical manner in the copies of the Software 6 4 2 The Licensee undertakes not to directly or indirectly infringe the intellectual property rights of the Holder and or Contributors and to take where applicable vis ig vis its staff any or all measures required to ensure respect for said intellectual property rights of the Holder and or Contributors A
31. ork The ComboBox contains the different sites of GRID 5000 e your user name your GRID 5000 login e your ssh public key rsa or dsa for more information about ssh access with public private keys please refer to the GRID 5000 Wiki pages treating this subject at https www grid5000 fr mediawiki index php SSH GRUDU User s Manual v1 1 0 CHAPTER 2 REQUIREMENTS AND INSTALLATION GRUDU 1 1 0 IzPack Assistant d installation ee Configuration de GRUDU skupu Pal User configuration Misc Frontale d acc s pr f r e Lyon y Utilisateur Cl SSH priv e C Explorer Passphrase CEcrire ta configuration Cr avec IzPack http www izforge com FEEL T EREET TT Cr CO Figure 2 3 GRID 5000 access configuration The second tab of the panel consists in selecting the sites you want to enable in GRUDU e g the sites that will be considered when launching oarstat or oarnodes commands or when reserving machines In this tab you will also be able to define the partitions used by KaDeploy for the deployment of an image for more informations about the partitions you can specify please refer to the pages of the sites on the GRID 5000 Wiki or to the messages of the day displayed when you get connected to a site GRUDU 1 1 0 IzPack Assistant d installation ee Configuration de GRUDU GR rpU F User configuration Mise Kadeploy partition Lyon les OAR
32. perties for the reservation 15 4 3 Resources allocation frame Reservation statud 15 51 Grid SOOO VIE serias esa ke never ve drar dr net s BA Ad BGN A A hain 16 fh Arie At ne ap Meg A A 17 See Lee Tee sl ee eee ee eee ee ee eee eT er re er 17 19 19 19 TL JETP anain interaccion 20 72 JELE rsync option syste a A Ba ek ES RR he RE A AE ee ed 21 8 1 Kadeployv tramel lt 2 4 44 42 de dob bees oe ES ERS Se Se ee a 22 9 1 Application settingg ee 23 CHAPTER 1 Introduction If you encounter installation difficulties don t hesitate to send an email to grudu usr listes ens lyon fr If you find a bug in GRUDU please don t hesitate to submit a bug report on http graal ens lyon fr bugzilla If you have multiple bugs to report please make multiple submissions rather than submitting multiple bugs in a single report A mailing list concerning the development of GRUDU is also available at the following ad dress grudu dev listes ens lyon fr CHAPTER 2 Requirements and installation 2 1 Requirements Since GRUDU is dedicated to GRID 5000 computing infrastructure the first thing you need to use is a GRID 5000 account and an access to at least one site of those composing the platform For more information about how to access GRID 5000 please refer to the web page of GRID 5000 p GRUDU i is n in java and thus it can be ected on any Sitio that offers a recent ver
33. responding to the user parameters the second tab is relative to GRID 5000 sites and the last one allows you to define specific KaDeploy partitions for the sites clusters The figure2 5 represents the first tab of the configuration windows where we can found the following parameters e Preferred access point this is the GRID 5000 site GRUDU will use to access to all the platform Your account in this site must contain your private ssh key file e Username your GRID 5000 username e Private SSH key file your private ssh key file O Grid 5000 reservation tool configuration 00 User configuration Misc Kadeploy Paritition Preferred acces point C acces sophia grid5000 fr A Username dloureiro Private SSH key file shomejdavid sshfid dsa Browse D Password Save Close Figure 2 5 Configuration window First tab The second configuration tab shown in figure 6 allows the user to configure the following parameters Shttp ant apache org GRUDU User s Manual v1 1 0 8 CHAPTER 2 REQUIREMENTS AND INSTALLATION e Enabling Disabling a site by default all sites are disabled e KaDeploy partition for each site the same partition will be used for every clusters of that site e OAR batch Scheduler main version you can choose between oarl and oar2 a Grid 5000 reservation tool configuration 00 User con
34. rsons or property 9 2 The Licensor hereby represents in good faith that it is entitled to grant all the rights on the Software including in particular the rights set forth in Article 5 hereof over the Software 9 3 The Licensee acknowledges that the Software is supplied as is by the Licensor without any or all other express or tacit warranty other than that provided for in Article 9 2 and in particular without any or all warranty as to its market value its secured innovative or relevant nature Specifically the Licensor does not warrant that the Software is free from any or all error that it shall operate continuously that it shall be compatible with the Licensee s own equipment and its software configuration nor that it shall meet the Licensee s requirements 9 4 The Licensor does not either expressly or tacitly warrant that the Software does not infringe any or all third party intellectual right relating to a patent software or to any or all other property right Moreover the Licensor shall not hold the Licensee harmless against any or all proceedings for infringement that may be instituted in respect of the use modification and redistribution of the Software Nevertheless should such proceedings be instituted against the Licensee the Licensor shall provide it with technical and legal assistance for its defense Such technical and legal assistance shall be decided upon on a case by case basis between the relevant Li
35. rt BP 105 78153 Le Chesnay cedex PREAMBLE The purpose of this Free Software Licensing Agreement is to grant users the right to modify and redistribute the software governed by this license within the framework of an open source distribution model The exercising of these rights is conditional upon certain obligations for users so as to ensure that this status is retained for subsequent redistribution operations As a counterpart to the access to the source code and rights to copy modify and redistribute granted by the license users are provided only with a limited warranty and the software s author the holder of the economic rights and the successive licensors only have limited liability In this respect it is brought to the user s attention that the risks associated with loading using modifying and or developing or reproducing the software by the user given its nature of Free Software that may mean that it is complicated to manipulate and that also therefore means that it is reserved for developers and experienced professionals having 29 APPENDIX B APPENDIX B in depth computer knowledge Users are therefore encouraged to load and test the Software s suitability as regards their requirements in conditions enabling the security of their systems and or data to be ensured and more generally to use and operate it in the same conditions of security This Agreement may be freely reproduced and published provided it
36. rticle 7 RELATED SERVICES 7 1 Under no circumstances shall the Agreement oblige the Licensor to provide technical assistance or maintenance services for the Software However the Licensor is entitled to offer this type of service The terms and conditions of such technical assistance and or such maintenance shall then be set forth in a separate instrument Only the Licensor offering said maintenance and or technical assistance services shall incur liability therefor 7 2 Similarly any or all Licensor shall be entitled to offer to its Licensees under its own responsibility a warranty that shall only be binding upon itself for the redistribution of the Software and or the Modified Software under terms and conditions that it shall decide upon itself Said warranty and the financial terms and conditions of its application shall be subject to a separate instrument executed between the Licensor and the Licensee Article 8 LIABILITY 8 1 Subject to the provisions of Article 8 2 should the Licensor fail to fulfill all or part of its obligations hereunder the Licensee shall be entitled to claim compensation for the direct loss suffered as a result of a fault on the part of the Licensor subject to providing evidence of it 8 2 The Licensor s liability is limited to the commitments made under this Licensing Agreement and shall not be incurred as a result in particular i of loss due the Licensee s total or partial failure
37. se 6 88 MB JFTP module 444 53 KB Ganglia Analyzer module 377 77 KB Documentation de GRUDU 4 03 MB sources de GRUDU 1 57 MB Description Si vous souhaitez avoir la documentation de GRUDU vous devez cocher ce pack Espace total requis 6 88 MB Espace disque disponible 3 2 GB Cr avec IzPack http www izforge com CARES TE TT O Pr c dent suivan Quiter Figure 2 1 Installation packages selection If you have an Unix like operating system Linux or BSD variants or Windows the seventh panel will allow you to put shortcuts on your desktop and also in the program group if you want to GRUDU User s Manual v1 1 0 5 CHAPTER 2 REQUIREMENTS AND INSTALLATION O GRUDU 1 1 0 IzPack Assistant d installation oe Configuration des raccourcis GRuxpu R cr er les raccourcis E cr er un raccourci sur le bureau S lectionnez un groupe pour les raccourcis GRAAL Cr er un raccourci pour utilisateur courant GRAAL GRUDU Remise 0 Cr avec IzPack http www izforge com Etape 7 sur 12 O Pr c dent CO suivant Quiter Figure 2 2 Shortcuts configuration Configuring GRUDU After having installed GRUDU you should configure it The configuration panel is separated into two parts the first concerns the access to GRID 5000 In this tab you have to define e a preferred access point the external frontal that will be used to enter in the GRID 5000 netw
38. sion of the Java runtime At least 1 5 0 version or higher Currently GRUDU support only the Bourne shell so if your GRID 5000 account uses another shell type you need to change it This requirement is only for your GRID 5000 account and you still can use your preferred shell on your machine To allow GRUDU to access to all the platform you need to configure your account to authorize a direct access to the different sites To do so make sure all these conditions are fulfilled 1 you have your ssh key in every site each GRID 5000 site has its own NFS filesystem so you need to copy your ssh key at least the public one in your ssh directory 2 you have you public ssh key in the file SHOME ssh authorized_keys You can do this by such a command cat SHOME ssh id_rsa pub gt gt SHOME ssh authorized_keys 3 the following option should be present in your HOME ssh config file Host StrictHostKeyChecking no For more information about ssh access to GRID 5000 key manage ment or file exchange please refer to the documentation of GRID 5000 at 2 2 Installation 2 2 1 Automatic installation GRUDU is provided through a single installation jar file containing the GRUDU software the required libraries the source files and the documentation User Manual and JavaDoc This in stallation file has been created with IzPacH To launch the installer you can either double click on the installer jar fi or launc
39. the minutes of your reservation e Queue default deploy for KaDeploy or allow classic sshE e OARGridSub behaviour the user can specify if the reservation should be done with the OARGridSub behaviour i e when the user chooses to realize several reservations on dif ferent sites if one fails all the previous successful reservations are deleted e A script to launch The user can specify a script that will be launched in order to be executed on the reserved nodes The reservation will be stopped when the script ends 1You can allocate resources only on enabled sites 2When the mouse is over the site box a tooltip will tell you the repartition of the nodes you may want to reserve 3 specific for OAR2 but corresponds to default for OAR1 14 CHAPTER 4 RESOURCES ALLOCATION o Resources allocation first step Main Information Advanced oar properties Oo PES to Starting date 08 11 2007 Ja Starting hour ha y Ms Starting minute 22 ok Starting second 17 g Hour 15 A Grid 500098 ue a el E Queue Gi kk E LU o a OARGridSub behaviour B Script Executable to launch OK Cancel Figure 4 1 Resources allocation frame Main panel Concerning the second tab of the window presented on Figure 2 4 it allows the user to define the OAR properties that will be used for the reservation Resources allocation first step
40. ting a job in the tree you can see a lot of information such as the nodes used by this job or the walltime of your reservation etc R Show tips on startup Next Tip Figure 3 2 Tip of the day for GRUDU GRUDU User s Manual v1 1 0 13 CHAPTER 4 Resources allocation 4 1 Using OAR interface The most used operation is probably the resources allocation In GRID 5000 this operation can be done by the OAR system GRUDU provides an easy way to manipulate OAR either the OARI1 or OAR versions The resources allocation window on Figure 2 5 shows a map of France with GRID 5000 sites and jobs characteristics time queue oargridsub behaviour the script to launch These information are presented on the first tab of the window The second tab provides the definition of the properties for the different sites Since some sites include more than one cluster you have to click first on the site and then select the number of desired nodes for each cluster or you can specify that you do not care where they are located When selecting resources numbers the map displays the total number of re quested resources for each sit Jobs characteristics are e Time parameters date and reservation walltime The starting time can be specified manu ally or through the use of a calendar for the day and through boxes where you can specify the hour the minute and the second For the walltime you have to define the number of hours and
41. uous and pervasive national computational infrastructure the Grid Current support comes from Planet Lab an open platform for developing deploying and accessing planetary scale services You can find more information on the Ganglia Website at http ganglia sourceforge net 6 2 Ganglia plugin As Ganglia is installed on GRID 5000 the GRUDU users can have access to the information provided by the software inside GRUDU If you selected the ganglia plugin during the installation step of GRUDU there is two ways to use it e From the site information panels where you can have instantaneous low level information about every nodes of the site computation nodes but also frontends 18 CHAPTER 6 THE GANGLIA MODULE FOR GRUDU Nework CPUS Load A cpu a Disk Y Mem amp Swap Y Grid5000 resources management tool Caprera ian afi 0004 gt CPU amp Load us 150 Bas Bano hna 30 vas on Load of the machine Fite 5 vac F pr Figure 6 1 Ganglia plugin for the site view e From the job information panels where you can get the history of the low level information brought to you by Ganglia Concerning the generation of the history you have first to configure the history generation which means defining the period of data refreshing of the form hh mm ss the range of the chart same format the path to the java home on the ma
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