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The Advanced Resource Connector User Guide

1. For example ngresume s FAILED c my grid org lt jobid gt will resume all failed jobs on the Grid plus all jobs in any state on the cluster my grid org plus the job lt jobid gt 8 2 11 Auxilliary files ARC client keeps local job lists in two files SHOME ngjobs and SHOME arc history HOME ngjobs is a local list of the user s active jobs When a job is successfully submitted it is added to this list and when it is removed from the remote site it is removed from this list This list is used as the list of all active jobs when the user specifies a option to the various ARC user interface commands For information about how to reconstruct this file in case it is damaged or you relocate to a different workstation see section 8 2 1 about the ngsync command HOME arc history contains the jobIDs of the jobs the user has submitted together with the time of submission This file is purely informational In ARC lt 0 5 48 HOME nghistory Chapter 9 Data Management At this stage data management possibilities in an ARC enabled system are limited to basic operations such as simple one by one file copy and removal with eventual use of data indexing services to assist in arranging files in logical collections keep track of their replicas and simplify storage resource discovery 9 1 Working with files 9 1 1 ngls The ngls is a simple utility that allows to list contents and view some attributes of objects of
2. NORDUGRID NORDUGRID MANUAL 6 7 12 2010 THE NORDUGRID ARC USER GUIDE Advanced Resource Connector ARC usage manual Contents 2 Roadmap Cd 3 1 1 Download 3 1 2 Unpack s 0 20020044 3 1 3 Configure 3 2 System wide installation 3 2 1 Installation via repositories 3 2 2 Globus Toolkit 3 2 3 Download the client 3 24 Build 3 2 5 Install the client oe ead Oe hae 3 3 1 cliemt cOMf 3 3 2 srms conf 3 3 3 Deprecated configuration files 4 Grid Certificates 4 1 Quick start with certificates 4 1 1 Certificates in local standalone client a od Gees eee da A E ee N E te 4 2 Grid Authentication And Certificate Authorities 0202 00020004 AA 4 2 2 Certificate Authorities ee 4 2 3 Globus Grid certificates ee lr Beeline a x hi ee fun fe BIER BOA ease ot a oe ee ee a ee ee 4 2 6 Certificate Request o e aaa 4 2 7 Working with certificates examples 11 13 15 15 15 15 16 16 17 18 18 19 20 21 21 23 24 5 Getting Access to Grid Resources Virtual Organisations 5 1 NorduGrid Virtual Organisation i ee eee o ad eH 6 1 Logging Into The Grid 2 0 2 en 6 1 1 Proxy Handling Tips 000 6 2 First Grid test 244s sie e 64b 66444 249 o
3. The Queue Information module is accessible via links to queue names in the Cluster Information Sec tion 10 2 Job Information Section 10 4 User Information Section 10 5 and Attributes Overview Sec 10 6 modules 10 4 Job Information The Job Information module is activated on three different occasions To display a list of all running Grid jobs on a cluster To display a list of all queued Grid jobs on a cluster To show the full information on a given job Lists of running and queued jobs are accessible from the top Grid Monitor window Section 10 1 by clicking the corresponding fields marked 2 and 3 in Figure 10 1 As shown in Figure 10 4 such a list contains not only job names but also their respective owners status as returned by the Grid Manager execution time in case of running jobs and the submission queue zax Running jobs at iscf nbi dk O Force refresh Print Close 1 SpinS Run2 Z tra512_1r27 O Sylju sen INLRMS R 519 se Wi 2 SpinS Run3YMtra512_1r31 O SyljS4 sen INLRMS R 519 gridrong 3 SpinS Run71 tra256_01r71 O Sylju sen INLRMS R 510 gridlong Figure 10 4 Grid job list Most of the fields in a job list window are linked to the corresponding monitor modules giving access to more detailed information 1 Job name just like in the Queue Details window Section 10 3 the job name is linked to the Job Information window described below However
4. Unique yes Operators User input ftpThreads lt integer gt GM input Example ftpThreads 4 Defines how many parallel streams will be used by the GM during gsiftp and http s g transfers of files integer a number from 1 to 10 If not specified parallelism is not used ARC gt 0 5 12 ARC 0 6 ARC 0 8 Unique no Operators User input acl lt xm1 gt GM input Example acl lt xml version 1 0 gt lt gacl version 0 0 1 gt lt entry gt lt any user gt lt any user gt lt allow gt lt write gt lt read gt lt list gt lt admin gt lt allow gt lt entry gt lt gacl gt Makes use of GACL 19 rules to list users who are allowed to access and control job in addition to job s owner Access and control levels are specified per user any user tag refers to any user authorized at the execution cluster To get more information about GACL please refer to http www gridsite org xml a GACL compliant XML string defining access control list Following job control levels can be specified via acl write allows to modify contents of job data job directory and control job flow cancel clean etc read allows to read content of job data contents of job directory list allows to list files available for the job contents of job directory admin allows to do everything full equivalence to job ownership 56 CHAPTER 7 DESCRIBING GRID TASKS ARC 0 3 ARC 0 4 ARC 0 5 ARC
5. 3 3 CLIENT CONFIGURATION FILES 21 3 3 Client configuration files 3 3 1 client conf The default behaviour of ARC client can be configured by specifying alternative values for some parameters in the client configuration file The file is called client conf and is located in directory arc in user s home area If this file is not present or does not contain the relevant configuration information the global configuration files if exist or default values are used instead The ARC configuration file consists of several configuration blocks Each configuration block is identified by a keyword and contains the configuration options for a specific part of the ARC middleware The configuration file can be written in either of two different formats plain text or XML In the plain text format client configuration block starts with its identifying keyword inside square brackets client Thereafter follows one or more attribute value pairs written one on each line in the following format client attributel valuel attribute2 value2 comment line 1 comment line 2 attribute2 value3 In the XML format the configuration file consists of a single arc XML element Inside this element client configuration block appears as a separate XML element lt client gt This block in turn contains attribute value elements in the following format lt arc gt lt client gt lt attribute1 gt valuel lt attribute1 gt lt attribute
6. 8 2 10 ngresume In some cases a user may want to restart a failed job for example when input files become available or the storage element for the output files came back online or when a proxy is renewed with ngrenew This can be done using the ngresume command Make sure your proxy is still valid or when uncertain run ngrenew before ngresume The job will be resumed from the state where it has failed ARC 0 6 ARC 0 8 80 CHAPTER 8 JOB MANAGEMENT Options a all all jobs i joblist filename file containing a list of jobIDs c cluster textemname explicitly select or reject a specific site cluster C clustlist textemfilename list of sites clusters to select or reject s status statusstr only select jobs whose status is statusstr t timeout time timeout for queries default 40 sec d debug debuglevel debug level from 3 quiet to 3 verbose default 0 x anonymous use anonymous bind for queries default X gsi use GSI GSSAPI bind for queries v version print version information h help print help page Arguments job list of job IDs and or jobnames For descriptions of a i and s options see ngstat section For descriptions of the c C g G t and d options refer to the ngsub description in Section When several of the a i c C s and job command line options are specified the comand resumes ALL jobs that match either of the criteria logical OR
7. INLRMS E job is finishing in LRMS INLRMS 0 job is in any other LRMS state CANCELING KILLING job is being cancelled by user request EXECUTED job is completed in LRMS FINISHING FINISHING output files are being transferred FINISHED FINISHED job is finished FAILED job is finished with an error KILLED job is cancelled by user request DELETED DELETED job is removed due to expiration time Detailed information on job states can be found in the Information System manual 4 For ARC versions 0 3 and 0 4 most of the states may be prepended with the PENDING message if the job can not move from the state for example if the limit of jobs in the next state is reached That is PENDING PREPARING means that the job exited the PREPARING state and is pending transfer to the next state SUBMITTING The FINISHED state may be followed by an error message if the job failed starting with FAILURE string In ARC versions 0 5 and 0 6 new states are added instead to better describe the situaton If the q option is used ngstat returns the status of the sites and queues available rather than of the jobs submitted In this case the c and C options can be used to select or reject clusters for which the status should be returned For descriptions of the c C g G t and d options refer to the ngsub description in Section 8 2 4 ngcat It is often useful to monitor the job progress by checking what it prints on the standard outpu
8. all all jobs i joblist filename file containing a list of jobIDs c cluster textemname explicitly select or reject a specific site cluster C clustlist textemfilename list of sites clusters to select or reject s status statusstr only select jobs whose status is statusstr k kluster textemname explicitly select or reject a specific site cluster as re submission target K Klustlist textemfilename list of clusters to select or reject as re submission target g giisurl url URL of a central Information System server 8 2 WORKING WITH JOBS 77 G giislist filename list of GIIS URLs o joblist filename file where the job IDs will be stored dryrun add dryrun option to the xRSL dumpxrsl do not submit dump transformed xRSL to stdout keep keep files on gatekeeper do not clean t timeout time timeout for queries default 40 sec d debug debuglevel debug level from 3 quiet to 3 verbose default 0 x anonymous use anonymous bind for queries default X gsi use GSI GSSAPI bind for queries U unknownattr allow unknown attributes in job description pass them through v version print version information h help print help page Arguments job list of job IDs and or jobnames If the original job description contained input file locations specified as relative paths non URLs the command must be issued in the same directory as the original ngsub instruction It
9. list of job IDs and or jobnames When option j is used and several jobs have the same name ALL such jobs will be cancelled Job cancellation is an asynchronous process such that it may take a few minutes before the job is actually cancelled When a job is successfully killed it is erased from the remote site Use keep option to keep the output for eventual retrieval with ngget or ngcat For descriptions of a i and s options see ngstat section For descriptions of the c C g G t and d options refer to the ngsub description in Section When several of the a i c C s and job command line options are specified the comand kills ALL jobs that match either of the criteria logical OR For example ngkill s INLRMS R c my grid org lt jobid gt will kill all running jobs on the Grid plus all jobs in any state on the cluster my grid org plus the job lt jobid gt 8 2 7 ngresub Quite often it happens that a user would like to re submit a job but has difficulties recovering the original job description xRSL file This happens when xRSL files are created by scripts on fly and matching of xRSL to the job ID is not straightforward The utility called ngresub helps in such situations allowing users to resubmit jobs known only by their job IDs Only jobs where the gmlog attribute was specified in the job description can be resubmitted ARC 0 3 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Options a
10. Options d debug debuglevel debug level 0 some 1 more 2 a lot v print version information h short help Arguments get URL get Grid ACL for the object put URL set Grid ACL for the object URL object URL curently only gsiftp and sse URLs are supported 84 CHAPTER 9 DATA MANAGEMENT ACL document an XML file is printed to standard output when get is requested and is acquired from standard input when set is specified Usage examples are ngacl get gsiftp sel ndgf csc fi ndgf tutorial dirname filename ngacl set gsiftp sel ndgf csc fi ndgf tutorial dirname filename lt myacl 9 1 5 ngtransfer The ngtransfer command initiates direct transfer of data between 2 servers known as third party transfer ARC 0 3 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Options s source URL source file URL d debug debuglevel debug level 0 some 1 more 2 a lot v print version information h short help Arguments destination destination URL currently only se and gsi ftp are supported This command initiates file copy from multiple source instances to a destination URL Destination of gsi ftp type accepts only similar kinds of sources Destination can also be URL of an Indexing Ser vice In such a case real destinations with suitable protocols are chosen when available Requests are sent to the corresponding services servers to initiate file transfer from one of the sources Absence of s option is
11. e g as produced by uname a ARC gt 0 3 24 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Unique yes Operators User input nodeAccess inbound outbound GM input Example nodeAccess inbound Request cluster nodes with inbound or outbound IP connectivity If both are needed a conjunct request should be specified 7 1 TASK DESCRIPTION LANGUAGE XRSL 59 ARC 0 3 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Unique yes Operators User input dryRun yes no GM input Example dryRun yes If yes do dry run job description is sent to the optimal destination input files are transferred but no actual job submission to LRMS is made Typically used for xRSL and communication validation ARC 0 3 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Unique no Operators User input rsl_substitution lt string1 gt lt string2 gt GM input Example rsl_substitution ATLAS opt atlas Substitutes lt string2 gt with lt string1 gt for internal RSL use string1 new internal RSL variable string2 any string e g existing combination of variables or a path Use this attribute to define variables that simplify xRSL editing e g when same path is used in several values typically in inputFiles Only one pair per substitution is allowed To request several substitution concatenate such requests Bear in mind that substitution must be defined prior to actual use of a new variable string1 After the su
12. ngrc file Comments starts with NGDEBUG 1 NGTIMEOUT 60 NGDOWNLOAD tmp If the environment variables NGDEBUG NGTIMEOUT or NGDOWNLOAD were defined these took prece dence over the values defined in this configuration Any command line options override the defaults The file HOME nggiislist was used to keep the list of default GIIS server URLs one line per GIIS see giis attribute description above The file HOME ngalias was used to keep the list of site aliases one line per alias see alias attribute description above Chapter 4 Grid Certificates This Chapter is not an easy reading but the presented knowledge is essential for newcomers unfami lar with Grid Impatient readers can go to Section for quick instructions however it is strongly recommended to eventualy read the entire Chapter In a Grid environment such as the NorduGrid ARC users normally don t have local password protected accounts on computing resources they intend to use You should hold instead an electronic certificate which ensures unique authentication This Chapter gives some basic information on a what is a Certificate Authority and how to affiliate yourself with an appropriate one b Cc how to request user certificates how to use a certificate d why do you have to trust different Certificate Authorities and how to obtain their credentials Access control for the computing resources is a matter of local policy
13. site administrators retain full control of choosing which Grid user is allowed to use their resources Typically such local authorization process is done by mapping an accepted set of Grid users onto a set of local user accounts See Chapter 5 on how to get access to the Grid resources and other related information 4 1 Quick start with certificates This section is primarily intended for the Nordic countries Denmark Finland Iceland Norway and Sweden and Estonia residents current members of the NorduGrid collaboration Users from other places should modify instructions accordingly or read further for detailed information The amount of setup you have to do regarding certificates depends on the way you installed the client 4 1 1 Certificates in local standalone client Luckily the standalone client Section 3 1 comes with all the necessary pre requisits Continue to Sec tion to learn how to obtain a personal certificate 25 26 CHAPTER 4 GRID CERTIFICATES NorduGrid middleware External software CA certificates globus certrequest config globus config gpt gsoap SHIFT or CTRL click to select multiple packages Reset Getlatest nightly releases tags certificate_authorities nordugrid 0 20 2004 03 25 CET 13 57 13 Figure 4 1 Downloading NorduGrid Certificate Authority public keys Example shows packages for Debian Linux NorduGrid middleware External software CA certificates nigh
14. 0 5 ARC 0 6 ARC 0 8 Options a all all jobs i joblist filename file containing a list of jobIDs c cluster textemname explicitly select or reject a specific site cluster C clustlist textemfilename list of sites clusters to select or reject s status statusstr only select jobs whose status is statusstr t timeout time timeout for queries default 40 sec d debug debuglevel debug level from 3 quiet to 3 verbose default 0 x anonymous use anonymous bind for queries default X gsi use GSI GSSAPI bind for queries v version print version information h help print help page Arguments job list of job IDs and or jobnames Prior to using ngrenew be sure to actually create the new proxy e g grid proxy init valid 24 00 Here valid specifies for how long the proxy will be valid You can renew a VOMS extended proxy as well use voms proxy init For descriptions of a i and s options see ngstat section For descriptions of the c C g G t and d options refer to the ngsub description in Section When several of the a i c C s and job command line options are specified the comand renews proxies for ALL jobs that match either of the criteria logical OR For example ngrenew s FAILED c my grid org lt jobid gt will renew proxies of all failed jobs on the Grid plus of all jobs in any state on the cluster my grid org plus of the job lt jobid gt
15. 0 6 ARC 0 8 Unique yes Operators User input cluster lt string gt GM input Example cluster clusterl site2 org The name of the execution cluster string known cluster name or a substring of it Use this attribute to explicitly force job submission to a cluster or to avoid such The job will not be submitted if the cluster does not satisfy other requirements of the job Disjunct requests of the kind cluster clus1 cluster clus2 are supported To exclude a cluster use cluster clus3 ARC 0 3 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Unique yes Operators l User input queue lt string gt GM input Example queue pclong The name of the remote batch queue Use only when you are sure that the queue by this name does exist string known queue name While users are not expected to specify queue in job descriptions this attribute must be present in the GM side xRSL In fact this is primarily an internal attribute added to the job description by client tools after resource discovery and matchmaking Still users can specify this attribute to explicitly force job submission to a queue when specified explicitly by the user this value will not be overwritten by the ARC Client and an attempt will be made to submit the job to the specified queue If for some reason e g due to a client tool error queue is absent from the GM side xRSL GM on the selected cluster will attempt to submit the
16. 12 Running Grid jobs 4 Queued jobs 0 Queued Grid jobs 0 Mds validfrom 2002 11 17 20 05 43 Mds validto 2002 11 17 20 06 13 Job name Owner Status CPU min Memory KB 1 SpinS Run28 tra512_1r28 O Sylju sen FINISHED at 2002 11 17 16 25 40 N A N A 2 Spins Run29 tra512_1r29 O Sylju sen FINISHED at 2002 11 17 16 27 03 1439 N A 3 SpinS Run32 tra512_ir32 O Sylju sen FINISHED at 2002 11 17 16 35 40 1439 N A 4 SpinS Run69 49256_01r69 O Sylju sen FINISHED at 2002 11 17 16 37 15 1439 N A 5 SpinS Run70 256_01r70 O Sylju sen FINISHED at 2002 11 17 16 41 40 1439 N A 6 SpinS Run77 tra512_01r77 O Sylju sen FINISHED at 2002 11 17 16 39 40 1439 N A PA SpinS Run80 tra512_01r80 O Syljy sen FINISHED at 2002 11 17 16 41 40 1439 N A 8 SpinS Run81 tra512_ 01r81 O Sy sen FINISHED at 2002 11 17 16 41 40 1439 N A 9 SpinS Run84 tra512_01r84 O Sylju sen FINISHED at 2002 11 17 16 41 40 1439 N A 10 SpinS Run85 tra512_01r85 O Sylju sen FINISHED at 2002 11 17 16 43 40 1439 N A aa SpinS Run87 tra512_01r87 O Sylju sen FINISHED at 2002 11 17 16 47 28 1439 N A 12 SpinS Run103 tra1024_01r103 O Sylju sen INLRMS R 539 434456 13 SpinS Runi02 trai024_01ri02 O Sylju sen INLRMS R 541 434456 14 SpinS Run82 tra512_01r82 O Sylju sen INLRMS R 514 102652 15 SpinS Run86 tra512_01r86 O Sylju sen INLRMS R 514 102644 Figure 10 3 Grid queue details The Queue Details module provides the list of the queue attributes and of all the jobs scheduled run
17. Example cache yes Specifies whether input files specified in the inputFiles should be placed by default in the cache or not This does not affect files described by the executables which will be placed in the session directory always If not specified default value is yes Cached files can not be modified by jobs by default If your job has to modify input files please use the readonly no URL option for those files This option does not affect whether or not the file is cached ARC 0 3 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Unique yes Operators User input outputFiles lt string gt lt URL gt GM input Example outputFiles local_to_job dat gsiftp sel uo no stored dat local_to_job dat rc rc1 uc dk set1 stored_and_indexed dat local_to_job_dir List of files to be retrieved by the user or uploaded by the GM and indexed registered in a data indexing service e g Globus RLS or Fireman string filename local to the Computing Element CE If this string ends with a backslash and lt URL gt is empty the entire directory is being kept at the execution site If however this string ends with a backslash but the lt URL gt starts with gsiftp or ftp the whole directory is transfered to the destination URL destination URL of the remote file see Section 7 1 1 if void use the quotes the file is kept for manual retrieval Note that this ca
18. Having defined your private database Section B 4 you can attempt to install any RPM package by doing the following Here command line parameters have the following meaning i perform an installation procedure v print extra information h print progress bar with hash marks Keep in mind that if you didn t define a default database in HOME rpmmacros you ll have to append dbpath HOME myrpmdb or whatever is your private database location to the directive Most likely however such a simple installation instruction will fail There are two main reasons a RPM packages attempt to install themselves in locations defined by their creators not by you How to get around this is described in Section b RPM checks for other software needed by the package dependencies in your private database however most likely such software was not installed by you and can not be found in your database How to deal with this is described in Section B 6 Upgrading RPM Packages If you happened to have a package installed and simply want to upgrade it issue the following instruction Here command line parameters have the following meaning U upgrade the installation v print extra information h print progress bar with hash marks Since this operation needs to access a database you either have to have the default database location specified in the HOME rpmmacros file or to append dbpath HOME myrpmdb or whatev
19. Having such a personal RPM database allows you to perform more complex operations with RPM packages without resorting to simple unpacking and manual installation To simplify your life even further do the following This will create a file rpmmacros in your HOME directory and add there the line specifying the database location In this example home yourname myrpmdb should be substituted with your RPM database path This will instruct RPM to use always your personal database Tf you don t want to use this feature for example if you have several databases take care to append to each RPM instruction which refers to such a database e g package installation or removal It may be useful to copy the system wide database into your own one RPM does not provide any tool for database synchronization yet thus you have to do it hard way Here var 1ib rpm is a typical default location of the system wide database it could be different though on different systems Having thus your private database initialized with the existing system information may help you in dealing with dependencies see Section B 8 but only for a while since any system wide upgrades will not be registered in your database and there is no way to synchronize RPM databases in a clever manner On some systems you should use gt instead of gt gt if the file rpmmmacros did not exist before B 5 INSTALLING AN RPM PACKAGE 107 B 5 Installing an RPM Package
20. MIIC6zCCA1SgAwIBAgICAPAWDQY JKoZIhvcNAQEEBQAWTZENMASGA1UEChMER3 Jp ZDESMBAGA1UEChMJTm9yZHVHcm1kMSowKAYDVQQDEyFOb3 JkdUdyaWQgQ2VydGlm aWNhdGlvbiBBdXRob3 JpdHkwHhcNMDMWNTIxMTkzOTA3WhcNMDQWNTIwMTkzOTA3 WjBQMQOWCwYDVQQKEwWRHcm1kMRIwEAYDVQQKEw10b3JkdUdyaWQxEjAQBgNVBAsT MF IxDTALBgNVBAoTBEdyaWQxEj AQBgNVBAoTCU5vcmR1R3JpZDEUMBIGA1UECxML cXVhcmsubHUuc2UxFzAVBgNVBAMTDkK94YW5hIFNtaXJub3ZhMIGfMAOGCSqGSIb3 DQEBAQUAA4GNADCBiQKBgQC5qAKyKGv0 6G7VC2CnICXWAwvKFX961AcyKeT5zxg 1DXUVx1hrLnHGKh9t1UZxGONCT1UTQ W4FVo5EPSpdsHI1MOyoVUF HNIglI1 TNj AgMBAAG j gdQwgdEwCQYDVROTBAIWADAsBg1 ghkgBhvhCAQOEHxYdT3B1b1NTTCBH ZW51cmF0ZWQgQ2VydG1maWNhdGUWHQYDVROOBBYEFLmvMBnYA8Bjee0mtDzmE84y 2fCiMHcGA1UdI wRWwMG6AFBgFwPwLObc69GWSC tZoV HiMTwoVOkUTBPMQOwCwYD VQQKEwWRHcm1kMRIwEAYDVQQKEw10b3JkdUdyaWQxK jAoBgNVBAMTIU5vcmR1R3Jp ZCBDZXJOaWZpY2F0aW9uTEF1dGhvcm10eYIBADANBgkqhkiG9w0BAQQFAAOBgQC1 VPU8sBArpPAoZKgWOmM7C7EZBQ2xKMAU uJqWcAHPqGEReGbghCBIwIsQP3onT2Y SqFWQSHM5gXBZ6sWGw YrAiGfURgsSsYZwSa9Bs6mJcANxNU8SHioyY1ingJwVJMDr 1xc00tWbHZpekWMe9QG8gn 0UKdXz1TKUS9Cx mBZw Save such text in Check the information stored in the certificate Now you can use this certificate as your electronic passport on the Grid and elsewhere Read Chapter 5 and apply for access to Grid resources and then go to Chapters 7 and 8 to learn how to work on Grid 4 2 Grid Authentication And Certificate Authorities Instructions given in Section 4 1 refer to the NorduGrid Certificate Authority as the body that is appoi
21. Obtain a personal certificate To obtain a personal certificate do Follow carefuly the instructions Select the appropriate Authority from the list NorduGrid hash 1f0e8352 or Estonia hash 566bf40f Enter the password called passphrase and memorize it If asked enter the two letter country code EE for Estonia or hit Return Enter Grid for Level 0 Organization Name or hit Return If asked enter NorduGrid for Level 1 Organization Name or hit Return Enter your domain typically the string which follows in your official e mail address e g cd uit fi Enter your name using strict Latin alphabet characters e g Goran Mueller Enter your official e mail address This procedure will create a new directory called globus in your home directory and generate sev eral files there If you already have this directory make sure it is empty or rename it before issuing grid cert request e g to globus old Send the certificate request to the corresponding Certificate Authority NorduGrid CA if you are a Nordic country resident Same instructions are valid for the Estonian certificates replace simply NorduGrid with Estonia in all the strings 28 CHAPTER 4 GRID CERTIFICATES Now you only have to wait within 2 working days you will receive an e mail containing your public certificate signed by the proper authority Find the part of the message that looks like
22. Section 8 2 11 If you are using several different machines to submit jobs make sure to issue ngsync command Section 8 2 1 after changing the machine to synchronise the list of known jobs ngstat can not return information about jobs that have been erased The jobs are normally erased by the sites if they were not retrieved within 24 hours after job end 72 CHAPTER 8 JOB MANAGEMENT A standard output produced by ngstat is rather short informing the user only about the job status Use ngstat 1 to receive the complete job information as stored in the system The s option can be used to select jobs in a specific state For finished jobs the s option will match FINISHED or FAILED depending on whether the job finished successfully or not These options can be repeated several times For example to check the status of jobs being on a particular stage of execution e g only running jobs use ngstat s INLRMS R Diferent sites may report slightly diferent job states depending on the installed software version A summary of essential job states is ARC 0 3 ARC 0 4 ARC 0 5 ARCO 6 Description ACCEPTING job has reached the site ACCEPTED ACCEPTED job submitted but not yet processed PREPARING PREPARING input files are being retreived PREPARED input files are retreived SUBMITTING SUBMITTING interaction with LRMS ongoing INLRMS Q INLRMS Q job is queued by LRMS INLRMS R INLRMS R job is running INLRMS S job is suspended
23. U O is a owt ected aneaetan ae Commands rarere Eki eee eee eee ees NPCS E E E aktioadd actions 34 Urb an A diya Maes EE as wed User Interface 0 00 61 USEF INTOPMALION dota dine see dinars Gd dh dada User Interface 0 ccc ser Sl Mae be ee deka eA eee vV Virtual Organization 0 0 0 008 VO A E dinate MANISES id ia a W Web Blc da X X509_USER_PROXY 00 cece eens XRSL attribute DC eee dada architecture 0 cece eee eens AL PUMENGS oi ai benchmarks 00 0c cece eee eens Calleri dida Cluster ccc cece eee COUNT satis si cpu LM rr a credentialserver AA ad aha rrio ia a diyR fi soria Mie Ae dae been environment 66 cee ee eens executable 00 ccc cece cece executables 0 000 cece cece ee eee ees ftp Thr ddg rici cee rsr orcas od TIN or ste at ace asec ot att reas Seat Ate doe aa End Tie eiii beaten panera inputFiles cece eee eee eee ett JON MO civic ros ede Fad AAA tana eben ety nen JOU jos ttl aa ie bhai era lifeTime 0d dada edd es INDEX middleware 0c ccc cece cece eee ooo NOCCACCESS 2 cece eee eee OPSYS kates ae Wen Aldea eee raw aerate nes wallTime 0 ccc cee cece eect ee eee attributes user side 1 cece eee eet e eee 123
24. detailed list of queue attributes and corresponding jobs can be obtained by clicking on a queue name see Queue Details module description Section 110 3 the most essential parameters are listed already in the Cluster Description module They are queue name queue status queue length minimal and maximal number of CPUs assigned to a queue if available and number of running and queued jobs Since queues can be shared between Grid and local users the total number of jobs is shown with the number of Grid jobs in parentheses The Cluster Description module is linked from most other modules except List of Users clicking on the domain name of a cluster opens the Cluster Description window 10 3 Queue Details In the Grid Information System the nordugrid queue objectclass is described by a set of queue specific attributes and has two sub trees nordugrid job and nordugrid authuser This structure reflects the fact that users are not implicitly authorized to submit jobs to any queue However the list of users allowed to a specific queue is a fairly static information and thus is beyond the scope of the Grid Monitor 6 NorduGrid Queue Details Netscape Queue dque at fire ii uib no Force refresh Print Close Distinguished name nordugrid queue name dque nordugrid cluster name fire ii uib no Mds Vo name local o grid objectClass Mds nordugrid queue Queue name dque Queue status active Running jobs
25. executable attribute had the value bin echo A very important thing to understand is that the Grid Manager always expects the file specified by the executable attribute to be at the execution machine not the user s machine This means that if a user wants to submit a job executing an own tool say_hello and specifies in the xRSL text executable say_hello the Grid Manager will attempt to execute a file say_hello in the temporary session directory local to the job Naturally this file will not appear there by magic Instead the User Interface prior to job submission will interpret such a request as if a user has the executable file say_hello in the current directory at the submission machine and will upload the file to the destination Absence of the leading slash makes the User Interface assume that the file in question resides locally in the path relative to the current directory So far so good but what if the executable resides not in the current directory but elsewhere on your computer or even better at a remote location If this is the case you have to instruct the User Interface how to get the file by using the inputfiles attribute amp main executable of the task executable say_hello arguments for the main executable arguments Hello again where does the executable reside inputfiles say_hello file home john bin say_hello standard output will be redirected to this file stdou
26. expression runTimeEnvironment envi runTimeEnvironment env2 You can use gt or lt operators job will be submitted to any suitable site that satisfies such requirements and among the available at the sites runtime environments the highest version satisfying a requirement will be requested in the pre processed xRSL script Runtime environment string interpretation is case insensitive If a runtime environment string consists of a name and a version number a partial specification is possible it is sufficient to request only the name and use gt or gt operators to select the highest version ARC 0 3 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Unique no Operators l gt lt gt lt User input middleware lt string gt GM input Example middleware nordugrid arc 0 5 99 7 1 TASK DESCRIPTION LANGUAGE XRSL 53 Required middleware version Make sure to specify full name and version number string Grid middleware name The site to submit the job to will be chosen by the ARC Client among those advertising specified middleware Usage is identical to that of the runTimeEnvironment Use the gt operator to request a version equal or higher ARC gt 0 3 21 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Unique no Operators ll Il v A Vv Il A ll User input opsys lt string gt GM input Example opsys FC3 Required operating system string Opera
27. host file name with a full path An URL can be used in a standard form i e Or to enhance the performance it can have additional options For a metadata service URL construction is the following For the Smart Storage Element service the syntax is For the SRM service the syntax is Versions 1 1 and 2 2 of the SRM protocol are supported The default service_path is srm managerv2 when the server supports v2 2 srm managervl otherwise The URL components are location lt location_name_in_RC gt option option host port IP address of a server DN Distinguished Name as in LDAP of an RC collection lfn Logical File Name LFN url URL of the file as registered in LFC RLS Fireman service_path End point path of the Web service file local to the host file name with a full path The following options are supported for location URLs 44 threads lt number gt cache yes no renew copy readonly yes no secure yes no blocksize lt number gt checksum cksum md5 adler32 no exec yes no preserve yes no pattern lt pattern gt guid yes no overwrite yes no protocol gsi gssapi spacetoken lt pattern gt autodir yes no CHAPTER 7 DESCRIBING GRID TASKS specifies number of parallel streams to be used by GridFTP or HTTP s g default value is 1 maximal value is 10 indicates whether the GM should cache the file default for input files is yes renew forces a download of the file ev
28. into cache p use passive transfer does not work if secure is on default if secure is not requested n do not try to force passive transfer i show progress indicator u use secure transfer insecure by default r recursion_level operate recursively if possible up to specified level 0 no recursion R number how many times to retry transfer of every file before failing t time timeout in seconds default 20 f if the destination is an indexing service and not the same as the source and the destination is already registered then the copy is normally not done How ever if this option is specified the source is assumed to be a replica of the destination created in an un controlled way and the copy is done like in case of replication Using this option also skips validation of completed transfers T do not transfer file just register it destination must be non existing meta url Arguments source source URL destination destination URL This command transfers contents of a file between 2 end points End points are represented by URLs or meta URLs For supported endpoints please refer to Section ngcp can perform multi stream transfers if threads URL option is specified and server supports it Source URL can end with In that case the whole fileset directory will be copied Also if the destination ends with it is extended with part of source URL after last thus allowing users to skip the destination f
29. j will assign your job name to the local directory with the output files be careful not to call all the jobs same name when using this option Ul does not clean up such download areas so please take care of doing this yourself A default value for the download directory other than the current working directory can be set by the first existing of 8 2 WORKING WITH JOBS 75 1 downloaddir option in client section in HOME arc client conf 2 downloaddir option in common section in HOME arc client conf NGDOWNLOAD option in HOME ngrc ARC lt 0 5 48 downloaddir option in client section in ARC_LOCATION etc arc conf 3 4 5 downloaddir option in common section in ARC_LOCATION etc arc conf 6 downloaddir option in client section in etc arc conf 7 downloaddir option in common section in etc arc conf If your job produces many small output files consider archiving them into a single file Transfering a lot of small files at a time may temporarily consume all TCP ports allocated for data transfer on some servers resulting in an error When the job result is retrieved the session directory is erased from the execution machine and the job ID is removed from your list of submitted jobs If you however want to keep the job for a while use the k option Beware that the job results will be removed by the Grid Manager at the execution machine 24 hours after job completion independently of whether you retrieved the results
30. jobs from your local list of jobs ngjobs file if they can not be found in the information system and you are confident they are not needed anymore For descriptions of a i and s options see ngstat section For descriptions of the c C g G t and d options refer to the ngsub description in Section When several of the a i c C s and job command line options are specified the comand cleans ALL jobs that match either of the criteria logical OR For example ngclean s FAILED c my grid org lt jobid gt will clean all failed jobs on the Grid plus all jobs in any state on the cluster my grid org plus the job lt jobid gt 8 2 9 ngrenew Quite often the user proxy expires while the job is still running or waiting in a queue In case such job has to upload output files to a Grid location Storage Element it will fail By using the ngrenew command users can upload a new proxy to the job This can be done while a job is still running thus preventing it from failing If a job has failed in file upload due to expired proxy ngrenew can be issued whithin 24 hours or whatever is the expiration time set by the site after the job end which must be followed by ngresume The Grid Manager will then attempt to finalize the job by uploading the output files to the desired location In ARC versions prior to 0 6 ngrenew automatically resumed jobs failed in upload 8 2 WORKING WITH JOBS 79 ARC 0 3 ARC 0 4 ARC
31. many attributes as specified by a user request eventualy applying the user selection criteria lol Anribute List Name Jobs total amount 1 Cluster lscf nbi dk 1 2 Cluster seth hpc2n umu se 69 3 Cluster login 3 monolith nsc liu se 426 4 Cluster grendel it uu se 14 6 5 Cluster farm hep lu se 31 6 Cluster ingvar nsc liu se 6 7 Cluster fire ii uib no 39 Figure 10 7 ARC objects grouped by attribute Figure shows a typical result of the Attributes Overview query in this example the nordugrid cluster attribute Jobs total amount was queried and a comparative list of results returned The Resource field 100 CHAPTER 10 THE GRID MONITOR indicated by the tag 1 depends on the nature of the attribute and can be either of cluster name linked to the Cluster Description module cluster name and queue name linked to the Cluster Description and Queue Details modules respec tively job ID string see ref 3 for details linked to the Job Information module 10 7 Match it yourself The Match it yourself display tool is a customizeable interface to the Attributes Overview module Sec tion 10 6 It allows users to chose which attributes of an object to display optionally applying filters While the other Monitor windows display a pre defined set of data this module gives an advanced user the possibility to build a customized request to the Information System An example use case for
32. package Ex E O 26 10 1 The Grid Monitor sisas hada date Bay Ree PA De ea ee eee es 94 10 2 ARC enabled cluster details 0 2 2 ee 95 bee ee Eee eis Pee ely ee ek ee oo oe 96 10 4 Grid Job USO 2 2 24 2 hoe ebe5 a a be sha ead Gb a auree all 97 Peta bh dS a hehe A ade GRE Mod e tA eee es 98 ae ot a we Get Re hee cane ee eee Gus wees ee Se es Be ee eee 99 bod Bune eva ia goa amp ee ee ek ae we ear tee ee 99 Poth odie nie sh Pile ely el eee Ef oe AAA 100 10 9 Attribute selection Window 100 10 10Customized cluster information display s oaa e 101 pacas al bene od ak be oo be eel eben eh ood bo 101 10 12List of the NorduGrid Users 102 10 LIST OF FIGURES Chapter 1 Preface The NorduGrid s 1 Advanced Resource Connector ARC is a light weight Grid solution designed to sup port a dynamic heterogeneous Grid facility spanning different computing resources and user communities It provides middleware to interface between user applications and distributed resources The NorduGrid ARC middleware is based on the Globus API libraries and services 2 The architecture of the ARC middleware pursues stability and robustness of services which implies complete decentralization and functional independence of the components In order to support this architecture several innovative approaches were used such as the Grid Manager 3 and the User Interface Section 8 Several Globus components were extended and developed fu
33. s Manual The NorduGrid Collaboration NORDUGRID TECH 2 Online Available http www nordugrid org documents GM pdf B K nya The NorduGrid ARC Information System The NorduGrid Collaboration NORDUGRID TECH 4 Online Available http www nordugrid org documents arc_infosys pdf M Ellert ARC User Interface The NorduGrid Collaboration NORDUGRID MANUAL 1 Online Available http www nordugrid org documents ui pdf O Smirnova Extended Resource Specification Language The NorduGrid Collaboration NORDUGRID MANUAL 4 Online Available http www nordugrid org documents xrsl pdf The Grid Monitor The NorduGrid Collaboration NORDUGRID MANUAL 5 Online Available http www nordugrid org documents monitor pdf A Sim A Shoshani et al The Storage Resource Manager Interface SRM Specification v2 2 May 2008 GFD R P 129 Online Available http www ggf org documents GFD 129 pdf RSA Labs RSA Cryptography FAQ Online Available http www nordugrid org documents rsalabs_faq41 pdf Public Key Infrastructure X 509 PKI Proxy Certificate Profile Online Available rfc net rfc3820 html The Open Source toolkit for SSL TLS Web site Online Available http www openssl org M Smith and T A Howes LDAP Programming Directory Enabled Applications with Lightweigt Directory Access Protocol Macmillan 1997 I Foster et al A Security Architecture for Computatio
34. this interface could be a user desiring to view a list of his running but not queued or finished jobs complete with used CPU and wall time memory and job name The Match it yourself tool would be then invoked for the job object and the display request would contain Name Used CPU time Used wall time Used memory KB and Status the latter with a filter Status INLRMS R alo x Search matching resources or objects Resource object job v Nr of attributes def 6 fa Next Figure 10 8 Object class selection window Figure shows the first screen of the Match it yourself interface which welcomes users to select the object class to work with and the amount of attributes to be displayed When not sure about the latter users should specify a top estimate unused fields will be ignored in further searches 101 x Define cluster selection criteria AND of all the expressions will be matched Cluster alias y CPUs total y gt 7 10 Postalcode I select one A Reset Get match START OVER Figure 10 9 Attribute selection window Figure is a snapshot of the screen where the atttributes to display and their selection criteria are specified If a user wishes to display an attribute for all the objects independently of its value the rightmost field may be either kept empty or filled with an asterisk while the middle field should be se
35. treated as a file replication request In this case destination must be an Indexing service or an SRM Following source URL types are supported http https httpg ftp gsiftp rc rls se srm fireman see Section for URL details Example ngtransfer s http www host1 org dati s gsiftp host2 org dir dati se se host org se_service new_file_lfn 9 1 6 ngstage The ngstage command is used to request file staging from tapes to front end disks Since jobs can not read data from tapes directly if an input file is on a tape the job most ikely will fail for a timeout because tape staging process is a rather lengthy one can be few hours To avoid these timeout failures ngstage should be used before submitting jobs that are known to use data archived on tapes ARC 0 6 ARC 0 8 Options In ARC lt 0 5 28 set shoud be used instead of put 9 2 REPLICA LOCATION SERVICE IN EXAMPLES 85 q requestID query the status of a request Use d 1 in addition to show a per file status c requestID cancel a request D do a dry run listing the files that would be staged d debuglevel debug level from 0 to 3 default 0 Setting to 1 when listing a request status will show the status of each file in the request T level if copying fileset directory recurse to the specified level If any given URL is a directory a level of at least 1 must be specified s URL the endpoint of the staging service This must be given
36. xRSL file suggested extension zrsl Such a file contains a plain list of attribute assignment strings relations and boolean operands amp for AND and for OR Attribute names are case insensitive An attribute value pair is a key element of task description It consists of a relation that assigns one or more values to an attribute and is enclosed in round brackets An attribute can have several values blank separated list 41 42 CHAPTER 7 DESCRIBING GRID TASKS or even correspond to pairs of values In the examples above some strings are quoted while some are not When explicitly quoted a string may contain any character However most literals used in job description e g attribute names themselves file names etc don t have to be quoted if they don t contain special characters and blank spaces The special characters are To quote a string containing special characters you can use either single or double quotes If your string however contains both such characters you can define any character as an own delimiter by preceding it with the carat 7 character jobName My good job makes use of a carat escaped asterisk as a delimiter Typically an xRSL job description starts with an ampersand amp to indicate implicit conjunction boolean AND style of all the attribute relations enclosed in parentheses Whenever a disjunct request boolean OR style of two or more attrib
37. 2 gt value2 lt attribute2 gt lt comment line gt lt commented block gt lt attribute2 gt value3 lt attribute2 gt lt client gt lt arc gt If one has an ARC server installation as well one can also use the common block which can have the same contents as the client one and is shared with the server For multi valued attributes several elements or attribute value pairs have to be specified one per each value The following attributes are allowed 22 CHAPTER 3 CLIENT INSTALLATION This attribute is multi valued Specifies which GlISes site indices or individual sites to use to discover computing and storage resources The default is to use the four top level GlISes ldap index1 nordugrid org 2135 0 Grid Mds Vo name NorduGrid ldap index2 nordugrid org 2135 0 Grid Mds Vo name NorduGrid ldap index3 nordugrid org 2135 0 Grid Mds Vo name NorduGrid ldap index4 nordugrid org 2135 0 Grid Mds Vo name NorduGrid Examples e plain text giis l1dap atlasgiis nbi dk 2135 0 Grid Mds Vo name Atlas giis ldap index1 nordugrid org 2135 0 Grid Mds Vo name NorduGrid giis ldap grid tsl uu se 2135 0 Grid Mds Vo name local e XML lt giis gt ldap odin switch ch 2135 0 Grid Mds Vo name Switzerland lt giis gt lt giis gt ldap index1 nordugrid org 2135 0 Grid Mds Vo name NorduGrid lt giis gt lt giis gt ldap grid tsl uu se 2135 0 Grid Mds Vo name local lt giis gt Note that LD
38. 30 60 0 101968 grid nbi dk lon 3 0 28224 grid nbi dk sho 3 60 0 28224 hepax1 nbi dk long 1 4320 0 1724 hepax1 nbi dk short 1 60 0 1724 sleipner byggmek Ith se long 4 2880 0 677995 sleipner byggmek th se short 4 120 0 67755 grendel it uu se nordugrid 5 0 30439 seth hpc2n umu se fque 0 2 251217 grid quark lu se pc 3120 0 33034 grid quark lu se pclong 3 0 33034 1 BeamBeam_sl INLRMS R 1575 c30 hip helsinki fi verylong Figure 10 6 Grid user information 5 Queue since users authorization may be not only cluster based but also queue based the allowed queue information can be accessed by clicking a queue name This brings up the Queue Details window described in Section The simplest way to access the User Information window is via the List of Users Section 10 9 although it can be invoked from any Grid Monitor window where a user name is displayed e g a Job Information or a Queue Details window 10 6 Attributes Overview As it was mentioned above every ARC objectclass attribute appearing in a Grid Monitor window is linked to the Attributes Overview module which queries all the relevant objects on the system and delivers a comparative list of the attributes Similarly to the User Information module querying all the Grid resources takes somewhat long time as the Grid Monitor does not have its own cache This module can also be accessed via the Match it yourself interface Section 10 7 In this case it can list as
39. 6 Certificate Request In order to obtain a valid passport on the Grid you need to create a key pair and submit your public key to your local CA to get an approval This process is called a certificate request The CA will follow its certificate policy and upon successful evaluation of your request your public key will be signed and sent back to you This may involve communication between the CA and your employer or any other adequate procedure As it was mentioned before all the resources i e gatekeepers storage facilities or other services require a CA signed key pair as well in order to be able to operate on the Grid In this case resource owners create host key pairs and send them to be vaidated by the local CA This is similar to registering a car and obtaining a license plate Please always remember that a Grid passport consists of two files the private key file and the public certificate file You need to have both of them the certificate file usercert pem alone is not enough for the Grid If you loose one of your key files you will have to generate a new CA signed key pair To request a personal or a host certificate you must decide to which authority you want to submit such a request Appendix E lists some known authorities and their contact addresses Each CA has its own procedure which you have to follow Typically you must request a certificate from the CA of your country of residence If your country has no
40. AP URLs containing Mds Vo name local refer not to GlSes but to individual sites This feature can be used to add hidden sites that do not register to any GIIS or to list explicitly preferred submission sites Default debug level to use for the ARC clients Corresponds to the d command line switch of the clients Default value is 0 possible range is from 3 to 3 Examples e plain text debug 2 e XML lt debug gt 2 lt debug gt Timeout to use for interaction with LDAP servers gridftp servers etc If a server during e g job submission does not answer in the specified number of seconds the connection is timed out and closed Default value is 20 seconds Examples e plain text timeout 20 e XML lt timeout gt 10 lt timeout gt 3 3 CLIENT CONFIGURATION FILES 23 Default download directory to download files to when retrieving output files from jobs using ngget Default is the current working directory Examples e plain text downloaddir home johndoe arc downloads e XML lt downloaddir gt tmp johndoe lt downloaddir gt This attribute is multi valued Alias substitutions to perform in connection with the c command line switch of the ARC clients Alias definitions are recursive Any alias defined in a block that is read before a given block can be used in alias definitions in that block An alias defined in a block can also be used in alias definitions later in the same block Ex
41. CA you may ask the CNRS catch all CA to provide you with one If you are not a Nordic country resident you may well try upon consulting the NorduGrid personnel at nordugrid support nordugrid org to use the procedures described here to request a certificate from another Certificate Authority However most of them have own established procedures see Appendix E for a reference and you are strongly advised to follow them 4 2 GRID AUTHENTICATION AND CERTIFICATE AUTHORITIES 33 Before requesting the certificate please make sure that your CA public keys and configuration files are installed as described in Section 4 2 4 The certificate request should be prepared by doing the following From the presented list select the appropriate CA for example NorduGrid if you are a Nordic country resident and then enter the requested information at each interactive prompt Typically you should use the suggested default values and your proper data domain name e mail etc Upon request type and confirm your certificate protection password NOTE the certificate protection password is not related to any other password and must be different from e g your system login password Memorize well the password as it can not be reset Although you can change the password any time see Section 4 2 7 if you forget the password you will have to request a new certificate Follow the printed suggestions strictly e g for the Nordic ce
42. Grid Czech Republic CESNET Denmark NorduGrid http www nbi dk HEP CA Estonia Eesti Grid Finland NorduGrid ana CNRS Germany GermanGrid DFN GridGermany Greece Hellas Grid Hungary NIIF KFKIRMKI http pkikfki mu SEE Grid http ww grid auth gr pki seegrid ca Ireland Republic of Grid Ireland http www cs tcd ie grid ireland gi ca rae tucc EEEE Italy INFN Korea Republic Of KISTI Macedonia SEE Grid The Netherlands NIKHEF Norway NorduGrid http www nbi dk HEP CA Pakistan PK Grid net www nop edu pk pk grid ca Poland Polish Grid 117 118 APPENDIX E KNOWN GRID CERTIFICATE AUTHORITIES Portugal LIP Romania SEE Grid Russia RDIG http ihc sinp nsu ru CA Serbia and Montenegro SEE Grid http www grid auth gr pki seegrid ca Slovakia SlovakGrid Slovenia SiGNET Spain Datagrid ES Sweden NorduGrid Switzerland SWITCH Taiwan ASCCG Turkey SEE Grid United Kingdom e Science Grid United States DOE Science Grid FNAL Bibliography 1 2 3 10 11 12 13 14 15 16 17 18 The NorduGrid Collaboration Web site Online Available http www nordugrid org I Foster and C Kesselman Globus A Metacomputing Infrastructure Toolkit International Journal of Supercomputer Applications vol 11 no 2 pp 115 128 1997 available at http www globus org A Konstantinov The NorduGrid Grid Manager And GridFTP Server Description And Administrator
43. ICATION AND CERTIFICATE AUTHORITIES 31 If you reside in any other country please contact your local CA or the CNRS one see Appendix for public keys and configuration files They will have the names similar to those shown in the example above except for the alphanumeric 8 characters hash Install them either in etc grid security certificates or in any other location pointed by the X509_CERT_DIR variable If you are using the standalone client the files must be installed in NORDUGRID_LOCATION share certificates or in any other location pointed by the X509_CERT_DIR variable You can also install all the necessary keys and configuration files in your private HOME globus certificates di rectory in this case however you will not be able to use those einstalled centrally You may have as many keys and configuration files installed as you wish Moreover you must have the public keys of all the CAs that certify the Grid resources you will use and of all the CAs that certify potential users of your own resource Section has some details on such Friendly CAs Please remember that installing a CA key implies that you accept their rules and policies and trust their judgement of users in other words you establish a trust relationship with the authority 4 2 5 Friendly CAs Depending on what is your Grid certificate issuing authority and which Grid resources you intend to use you will have to install public certificates and other at
44. P Online Available http www cs fsu edu engelen soap html 24 R Alfieri et al From gridmap file to VOMS managing authorization in a Grid environment Future Gener Comput Syst vol 21 no 4 pp 549 558 2005 Index A access Control surasan cece eee eee eee eee eens At Dute 4 23 wis as Hea le eae eae ESE authentication cece eee eee eee eee authorization 2i0i66uternds ean ai dened edad B blacklist 434sactes2saundtoredenrteaneraaewiisess C CB E 25 cerificate PASSWOF islandesa certifica a 21 21 CONVE Us gad nae a da peed eae eo ISP si ti ladies ISSUING ora idad ias personal requested TOQUES bio ii 28 29 29 TOVOCA LION trado nan VOL ereere teas iie eee delet aw heeds Certificate Authority 00 cece eee eae 25 Certificate Authority 0 00005 21 certificate change passwOld ooooccoccccccoccncooo CHEN cote donds utes ioodnduedeehdiwbes idawe pervade 11 configuration files 0 0 cece eee eee download vecinita tte as ies install RPM iaa installation ciao ci rebeca as an ca A nds cert genet ett pba oh EE an ERE AAS E O AttPIDULES iisin seis pemee ie geese bpeaee nh Pewes TOG ir a bota commands Sac ds A A O 68 NECA cack lati Pith estes ciate aes NEGD vis sac Gigs A 78 NGVSU to oc EE A A EEEE MOKA AEE EE MS ar aaa A aye ele Mea E ea nee eae HELESUD etarra alain NETESUIMNE taa 175 A 79 O 80 DES ii 167 NpSUDS arde eee aes aes
45. RC Information System servers GIIS is distributed with the middleware and is stored in NORDUGRID_LOCATION etc giislist A user is free to choose any other set of GIIS servers either by listing them in the configuration file or by specifying them via g option ngsub g ldap hostname port basedn myjob xrsl If the port number is omitted the default 2135 is used Two different syntax for the base DN of the LDAP query are accepted e g a NorduGrid top level GIIS can be specified in either of the two following ways ldap index1 nordugrid org 2135 0 Grid Mds Vo name NorduGrid ldap index1 nordugrid org 2135 mds vo name NorduGrid 0 Grid Several GIISes can be specified by repeating the g option ngsub g ldap urli g ldap url2 You may prefer to store the list of GIIS servers in a file other than the default one and use the G option to instruct ngsub to contact those servers instead ngsub G my_GIIS_list myjob xrsl Note that LDAP URLs containing Mds Vo name local refer not to GIISes but to individual sites for example ldap grid tsl uu se 2135 0 Grid Mds Vo name local This feature can be used to add hidden sites that do not register to any GIIS or to list explicitly preferred submission sites 8For ARC lt 0 5 48 use HOME nggiislist file 70 CHAPTER 8 JOB MANAGEMENT If neither the giisurl nor the giislist option is given a list of GIIS URLs is read from the first existing
46. SUD kh Se a we dee Be eh eh ee ag ae Be we A ee ee AS Bek EY 8 24 NECA sci aea a eee RDG LEASES Da Re A de E 68 Oh noo BR oe A A Om OA ik He ee BS ile ee ers 8 2 6 DOI 22sec nvasae dd his close ce Ge waa es 24a a oe Bones A ido a bb DAR RRR ESE OPE bah EES EE Ree os AA AN 52 9 DBTENEWis 22h a o br a di a a ds bee de BR a parda aro ai E aa 8 2 11 Auxilliary files Data Management 9 1 Working with files OL nels 6 beh we ae dake do AA ed b a aa ea eb bee ee a 9 1 4 ngach aca ee ea Aun ewe 9 1 5 ngtransfer lk dad he Rode ade eee de oye 9 2 Replica Location Service in Examples 8 2 DESTA cia aa a a a ea A A ww a 9 2 1 Show all possible attribute names for LFNs o o e o 9 2 2 Show the value of an attribute for an LEN 57 58 58 58 58 59 59 60 60 60 60 61 62 62 65 65 65 66 66 67 71 72 73 79 76 78 78 79 80 9 2 7 9 2 8 Create an LFN PFN pair Wildcard version of the above 9 2 9 Add a PFN to an already existing LEN 9 2 11 Define an LFN attribute in the RLS server 9 2 12 9 2 13 9 2 14 Remove a Storage Element 9 3 Replica Catalog in Examples 9 3 1 9 3 3 Add an attribute with a value to an LFN Add a Storage Element o Define who you ALO o 9 3 2 Create a collection Add a location to a collection 9 3 4 Upload and register a fil
47. a specified by an URL remote directory ARC 0 3 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Options h short help v print version information d debuglevel debug level 0 some 1 more 2 a lot 1l detailed listing L detailed listing including URLs from which file can be downloaded m list all available metadata attributes r level list recursively to given level Arguments URL file or directory URL This tool is very convenient not only because it allows to list files at a Storage Element or records in an indexing service but also because it can give a quick overview of a job s working directory which is explicitly given by job ID Usage examples can be as follows ngls rls rc host 38203 logical_file_name ngls 1 gsiftp lscf nbi dk 2811 jobs 1323842831451666535 ngls L srm grid uio no 58000 srm managerv1 johndoe log2 81 82 CHAPTER 9 DATA MANAGEMENT Examples of URLs accepted by this tool can be found in Section 7 1 1 though ngls won t be able to list a directory at an HTTP server as they normally do not return directory listings 9 1 2 ngcp The ngcp command is a powerful tool to copy files over the Grid It is a part of the Grid Manager but can be used by the User Interface as well ARC 0 3 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Options h short help v print version information d debuglevel debug level from 3 quiet to 3 verbose y cache_path path to local cache use to put file
48. ackage build status For deb based distributions like Debian and Ubuntu Testing Noraueria home wget q http download nordugrid org DEB GPG KEY nordugrid asc 0 Repositories are available for stable releases stable and for packages undergoing testing repository must always be used with the stable one enabled Figure 3 2 Web page with repository set up instructions For RPM based systems package groups are defined such that the client tools installation can be done by simply doing or in a corresponding manner via your favorite package manager Packages provided by NorduGrid belong to the Grid group 18 CHAPTER 3 CLIENT INSTALLATION Packages in the NorduGrid repository are signed with the NorduGrid key you need to install it once before usung the repository e g rpm import http download nordugrid org RPM GPG KEY nordugrid 3 2 2 Globus Toolkit Most modern Grid systems use parts of the Globus Toolkit M Globus packages thus must be installed at your machine prior to any system wide Grid installation You may get it from the Globus project Web site 2 however it is strongly recommended to use the distribution available at the NorduGrid download area as it contains several critical bug fixes With the standalone client and _ repository based installations the necessary Globus Toolkit components are installed automatically Instructions below are only needed if for some reason you can not use tho
49. ameters have the following meaning q perform a query a query all installed packages i print out package information Some older versions can also do multiple relocations but most have one or another bug B 10 UNINSTALLING RPM PACKAGES 109 This command prints out the information stored in your RPM database hence you either have to have the default database location specified in the HOME rpmmacros file or to append dbpath HOME myrpmdb or whatever is your private database location to the directive see Section B 4 for details B 10 Uninstalling RPM Packages Whenever you ll have to uninstall a package issue the instruction Here mypackage is the name of the package as listed by the rpm qai command Command line parameter has the following meaning e uninstall packages This command removes the files associated with the package from your system and erases the correspond ing record from your RPM database You either have to have the default database location specified in the HOME rpmmacros file or to append dbpath HOME myrpmdb or whatever is your private database location to the directive see Section B 4 for details B 11 Building RPM from Source It may happen so that binary RPM packages for your system are unavailable but a source RPM or a tarball is provided You can build a binary RPM yourself from such sources but some extra manipulations should be made first The default RPM top directo
50. amples e plain text alias hosti somehost nbi dk alias host2 otherhost uu se alias myhosts hosti host2 e XML lt alias gt host1 somehost nbi dk lt alias gt lt alias gt host2 otherhost uu se lt alias gt lt alias gt myhosts host1 host2 lt alias gt With the example above ngsub c myhosts will resolve tongsub c somehost nbi dk c otherhost uu se Configures which brokering algorithm to use during job submission The default one is the FastestCpus broker that chooses among the possible targets the target with the fastest CPUs Another possibility is for example the RandomSort broker that chooses the target randomly among the targets surviving the job description matchmaking Examples e plain text broker RandomSort e XML lt broker gt RandomSort lt broker gt 3 3 2 srms conf If any data management commands are used with the Storage Resource Management SRM protocol the file 24 CHAPTER 3 CLIENT INSTALLATION may be created to store cached information on these services For more information see the description inside this file 3 3 3 Deprecated configuration files In ARC lt 0 5 48 configuration was done via files HOME ngrc SH0OME nggiislist and HOME ngalias The main configuration file HOME ngrc could contain user s default settings for the debug level the in formation system query timeout and the download directory used by ngget A sample file could be the following Sample
51. ation starting from the root RPM also relies on a system wide database to register software version numbers dependencies and other relevant data Naturally directory structures are different on different systems and not every user has proper permissions to modify them Also not everybody is allowed to write into the main RPM database Evidently RPM format was created having system administrators in mind Nevertheless even if you are a regular user with no special privileges you can make a fair use of the RPM packages especially so if creators of such packages made them relocatable i e user friendly Luckily most NorduGrid packages are relocatable including the distributed Globus RPMs Below are some quick instructions on how to work with RPM packages without having system administrator privileges B 1 Listing Contents of an RPM Package To list files archived in an RPM package issue an RPM query command Here command line parameters have the following meaning q perform a query 1 list files p use the specified package file myfile rpm in this example B 2 Printing Out an PM Package Information To retrieve general information about a given RPM package issue the following RPM query Here command line parameters have the following meaning q perform a query i print out package information p use the specified package file myfile rpm in this example 105 106 APPENDIX B RPM FOR EVERYBODY This
52. authorization method the NorduGrid Virtual Organization VO following practices of other Grid testbeds This VO maintains a list of people which are authorized to use the Nordic Grid resources The VO tools provide an automatic method for the sites to easily maintain the VO member local Unix user mappings These tools periodically query the VO user database and automatically generate the local grid mapfiles following the local policy formulated in the VO tools configuration file The automatic mapping does not violate the site autonomy because the site administrators retain a full control over their systems thanks to the possibility of denying access to unwished Grid users in the NorduGrid VO tools configuration file The database of the VO is maintained by the VO managers Their responsibility is to add delete or modify user entries The NorduGrid VO is limited to the users affiliated with the Nordic organisations To become a member you must send a request containing your certificate Subject Name see Section 4 2 7 to nordugrid support nordugrid org If you are not a Nordic countries resident you may be added to the Guests VO The NorduGrid VO supports the creation of groups A group is a subset of the a VO and is maintained by an appointed group manager The group manager selects members of the group out of the full VO database With the existence of the user groups the site administrators can implement group based map
53. bs that match either of the criteria logical OR For example ngresub s FAILED c my grid org lt jobid gt will resubmit all failed jobs on the Grid plus all jobs in any state on the cluster my grid org plus the job lt jobid gt 78 8 2 8 ngclean CHAPTER 8 JOB MANAGEMENT If a job fails or you are not willing to retrieve the results for some reasons a good practice for users is not to wait for the Grid Manager to clean up the job leftovers but to use ngclean to release the disk space and to remove the job ID from the list of submitted jobs and from the Information System ARC 0 3 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Options a all all jobs i joblist filename file containing a list of jobIDs c cluster textemname explicitly select or reject a specific site cluster C clustlist textemfilename list of sites clusters to select or reject s status statusstr only select jobs whose status is statusstr f force removes the job ID from the local list even if the job is not found on the Grid t timeout time timeout for queries default 40 sec d debug debuglevel debug level from 3 quiet to 3 verbose default 0 x anonymous use anonymous bind for queries default X gsi use GSI GSSAPI bind for queries v version print version information h help print help page Arguments job list of job IDs and or jobnames Only jobs that have finished can be cleaned Use f option to remove
54. bstitution is defined it should be used in a way similar to shell variables in scripts enclosed in round brackets preceded with a dollar sign without quotes inputfiles myfile ATLAS data somefile Unlike the environment attribute rsl_substitution definition is only used by the client and is valid inside xRSL script It can not be used to define environment or shell variable at the execution site ARC 0 3 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Unique no Operators User input environment lt VAR gt lt string gt lt VAR gt lt string gt GM input Example environment ATLSRC opt atlas src ALISRC opt alice src Defines execution shell environment variables VAR new variable name string any string e g existing combination of variables or a path Use this to define variables at an execution site Unlike the rs1_substitution attribute it can not be used to define variables on the client side 60 CHAPTER 7 DESCRIBING GRID TASKS ARC gt 0 3 12 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Unique yes Operators User input count lt integer gt GM input Example count 4 Specifies amount of sub jobs to be submitted for parallel tasks Ooo ARC gt 0 3 34 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Unique yes Operators User input jobreport lt URL gt GM input Example jobreport https grid uio no 8001 logger Specifies an URL for a logging service to
55. butions are available as well The client package may be installed system wide by a system administrator Section 3 2 or locally by a non privileged user Section 3 1 A multi user computer may have several client installations they do not interfere with each other A full client takes approximately 17 MB of disk space You may install a client at any computer you use e g on your office desktop a notebook your home computer etc You can even load it on a USB memory One thing to remember when using different clients interchangeably is to keep them in sync as described in Section While client installation procedure itself is trivial there is a lot of fine tuning that can be done by an advanced user See Chapter 4 on authorization issues and Section 3 3 on client configuration 3 1 Beginner Installation For a local installation by a user without system administrator privileges it is advised to download and install a stand alone distribution of the NorduGrid ARC client This package is distributed in tgz format and contains all the required third party components Globus components VOMS clients etc Scripts provided with the package do all the necessary initial configuration and setup 3 1 1 Download Download a pre compiled stand alone binary distribution suitable for your operating system from the Nordu Grid Downloads area at http download nordugrid org see Figure 3 1 Normally you should download the stable ver
56. c gridmap utils Utilities for managing gridmap files nordugrid arc ca utils Utilities for maintaining CA files nordugrid arc devel Development files headers static libs nordugrid arc monitor Grid monitor web interface should be installed on a Web server nordugrid arc doc Documentation The strict runtime RPM dependencies are nordugrid arc client gt globus nordugrid arc server gt globus globus config voms nordugrid arc gridmap utils gt perl perl ldap perl libwww perl nordugrid arc ca utils gt wget Dependencies not expressed in the RPM requirements e nordugrid arc server gt standard Perl environment e nordugrid arc ca utils gt openssl native or globus provided ably curl gt 7 9 8 1 9 14 libxml2 e nordugrid arc gridmap utils gt openssl native or provided with Globus and optional prefer Special requirements of the Grid Monitor not expressed in RPM requirements are described in the README file of the nordugrid arc monitor RPM 116 APPENDIX D NORDUGRID ARC BUILD NOTES Appendix E Known Grid Certificate Authorities This list of Certificate Authorities is non authoritative as the authorities and links are subject to change Country CA URL Albania SER Grid Armenia ArmeSFo Austria AustrianGrid Belgium BEGrid EMEETAN Bosnia and Herzegovina SEE Grid Bulgaria SEE Grid Canada GridCanada China IHEP Grid Cyprus Cy
57. cations list of the RPM and yet the package attempt to install in such directory There s little you can do about it except attempting to use the badreloc option As in the case of installation you either have to have the default database location specified in the HOME rpmmacros or to append dbpath HOME myrpmdb private database location to the directive see Section for details B 8 Dealing with Dependencies Even when relocations proceeded smoothly your package may still fail to get installed due to unsatisfied dependencies this is the name for any other software needed by the package which are absent from your private database Section B 4 A bold way to deal with it is to force the installation e g The command line parameters have the following meaning i perform an installation procedure v print extra information h print progress bar with hash marks relocate instruct RPM to install files from oldlocation into newlocation nodeps ignore dependencies This is an admittedly non elegant way A better solution may be to enter the necessary information into the database by installing virtual RPMs which only register a database record without actually installing software however this is clearly package dependent thus you should request such a fake RPM from the package provider B 9 Listing Installed Packages To list all the packages installed via an RPM mecanisms do Here command line par
58. d in the job description respectively Option f is handy for very long output files it prints out only the last lines of the specified output and follows its updates For descriptions of a i and s options see ngstat section For descriptions of the c C g G t and d options refer to the ngsub description in Section When several of the a i c C s and job command line options are specified the comand prints logs for ALL jobs that match either of the criteria logical OR For example ngcat s FINISHED c my grid org lt jobid gt will print logs of all finished jobs on the Grid plus of all jobs in any state on the cluster my grid org plus of the job lt jobid gt 8 2 5 ngget To retrieve the results of a finished job the ngget command should be used It will download the files specified by the outputfiles attribute of job description to the user s computer 74 CHAPTER 8 JOB MANAGEMENT ARC 0 3 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Options a all all jobs i joblist filename file containing a list of jobIDs c cluster textemname explicitly select or reject a specific site cluster C clustlist textemfilename list of sites clusters to select or reject s status statusstr only select jobs whose status is statusstr dir dirname download directory the job directory will be created in this directory j usejobname use the jobname instead of the digital ID as the j
59. ded when a replica is removed from the Grid 88 CHAPTER 9 DATA MANAGEMENT 9 2 11 Define an LFN attribute in the RLS server This action adds new attribute to all the records LFNs Initial value of the attribute is empty NULL Note lt attribute type gt usually is string 9 2 12 Add an attribute with a value to an LEN This action adds an attribute to an LFN and sets it to a given value 9 3 Replica Catalog in Examples The NorduGrid Replica Catalog is nothing but slightly patched Globus Replica Catalog I7 The support for it has been discontinued by Globus a while ago and NorduGrid uses it just as a temporary solution for the distributed data catalogue This Section only presents some usage examples and does not go into details of the Replica Catalog implementation installation and support Only authorised RC managers can perform operations which require write access For details contact nordugrid support nordugrid org The Globus RC is an hierarchical database the catalogue consists of collections each collection consists of logical file names which correspond to one or more physical files at pre defined locations To register an arbitrary file in a RC the following steps should be performed 1 Ensure the collection exists 2 Ensure the physical location of the file is registered as one of the locations for the collection 3 Enter the file record into the RC specifying the location and the file na
60. dryrun option it will capture possible syntax or other errors but will instruct the site not to submit the job for execution If the o option is given the job identifier is also written to a file with the specified filename This file can later be used with the corresponding i option of the other job manipulating ARC client commands ngsub o my_jobid_list myjob xrsl ngkill i my_jobid_list The c option can be used to force a job to be submitted to a particular site cluster or to reject submission to a site The matching is done by string match to the site name i e hostname as defined in the Information System or to an alias as defined in user configuration file see Section 3 3 The c option can be repeated several times for example ngsub c grid nbi dk c grid tsl uu se myjob xrsl This will submit a job to either grid nbi dk or grid tsl uu se To submit a job to any site except badsite abc org use sign in front of the name ngsub c badsite abc org myjob xrsl For convenience you may list the sites in a file and use the C option to refer to the whole list ngsub C preferred_sites myjob xrsl If a cluster name or file name is preceded with a minus sign this site or the list will be avoided during the submission This gives a possibility to blacklist unwanted sites ngsub C blacklist myjob xrsl The ngsub command locates the available sites by querying the Information System By default a list of the A
61. e client from source Make sure that all the necessary external packages are installed see Appendix D for details When all the external packages are in place build the NorduGrid ARC from the source RPM This will create several binary RPMs for the client you will need only nordugrid arc client lt version gt rpm Alternatively to build from the tarball do the following 20 CHAPTER 3 CLIENT INSTALLATION HT E http download nordugrid org stable html 2 aria sotution tor wise area NORDUGRID DOWNLOADS STABLE Computing and Data Handling uuu The latest stable version is 0 8 1 1 2 For other versions pleas NorduGrid Downloads repository tool such as yum apt or up2date to install package recommended Source code repository Browse repository Binary builds Browse all packages Platform selection Install from repositories Vendor Version Architecture debian Package build status me fedora Testing NorduGrid home opensuse ubuntu Figure 3 4 Downloading ARC client RPMs Example shows packages for RHEL5 3 2 5 Install the client Install the client RPM Set up the environment variables Use nordugrid csh for a C shell or for some other environments one will have to do IMPORTANT This client will not be functional untill you install proper public keys necessary to establish contact with Grid services Read Chapter 4 to learn how to do it
62. e e g CPUTime or cputime interchangeably The only attribute which must be specified is executable others can be added by the user depending on the needs in no particular order 7 2 1 Hello World The simplest way to say Hello World is to assume that any cluster on the Grid has the Unix echo executable in the bin directory In most cases it will work so the following xRSL file can be composed amp main executable of the task executable bin echo arguments for the main executable arguments Hello World standard output will be redirected to this file stdout hello txt standard error will be redirected to this file stderr hello err Grid Manager auxilliary logs will be stored in this directory gmlog gridlog give job a distinct name for easy monitoring jobname My Hello Grid instruct cluster that your job should be placed in a queue with the sufficient time limit for the job to get completed cputime 5 chose only those clusters which have a proper ARC installation middleware gt nordugrid arc 0 3 24 In this example strictly speaking only the executable and arguments are needed to describe the task However as the job will be executed in batch like everything on the Grid you will never see the message Hello World on your screen Instead you should instruct the Grid Manager to capture the standard output to a file which you can
63. e file To specify an explicit destination do 90 CHAPTER 9 DATA MANAGEMENT 9 3 5 Register existing at a location file to a collection File registration includes three steps 1 Create a logical file entry in the collection 2 Verify that file location mount point is registered in the collection see Sections and 9 3 9 otherwise it has to be added see Section 9 3 3 3 Register the physical location s If the file size is unknown specify 0 as shown above Logical entries can only be added one by one while physical location s must be added via a filelist one line per file path filel zebra path file2 zebra Note the prepended path relative to the registered location it should be possible to construct a correct URL as LOCATION FILENAME 9 3 6 Remove and unregister a file 9 3 7 Remove a location from a collection 9 3 8 Find locations URL prefixes for a collection 9 3 REPLICA CATALOG IN EXAMPLES 91 or using the Globus interface to LDAP 9 3 9 Find a URL prefix for a location known by name 92 CHAPTER 9 DATA MANAGEMENT Chapter 10 The Grid Monitor The Grid Monitor is perhaps the most convenient utility that allows users and sysadmins alike to check and monitor the status of the ARC Grid facility status of each job display user specific information and otherwise obtain in an intuitive way the information stored in the Information System 4 It is implemented a
64. e found in the Information System The Storage Resources module linked from the main Monitor window displays all the available information for those Storage Elements which publish it Particularly important is the base URL which specifies the Grid mount point that could be used in job descriptions NorduGrid Storage Elements Mozilla Y x NorduGrid Storage Elements 5 8 y Figure 10 11 List of storage elements 10 9 List of Users The List of Users module is different from the rest of the Grid Monitor modules because it does not deal with the NorduGrid MDS Instead it retrieves lists of users from the NorduGrid VO database 20 It serves as a link between the two databases MDS and VO by interfacing each user record to the User Information module Section 10 5 Figure shows a screenshot of a typical VO user list with numbered tags indicating clickable links as follows 1 Name user name as given in the corresponding Grid certificate field linked to the User Information module Section 10 5 102 CHAPTER 10 THE GRID MONITOR 2 E mail E mail address of a user if available It is linked to an e mail URL allowing a message to be sent to a user directly from the browser if such an option is enabled in a browser Chafik Driouichi ry Particle Physics Lund y 3 chafik dric Paula Eerola Particle P Lund paula eern Figure 10 12 List of the NorduGrid users The List of Users is available only from t
65. e setup csh instead of setup sh In some environments you will have to do instead in the nordugrid arc standalone lt version gt directory Upon first execution this will print a lot of informational output Make sure there are no error or failure messages 3 2 System wide installation This Section is oriented primarily towards users with system administrator privileges Local installation by any user is described in Section 3 1 For a system wide installation usage of NorduGrid repositories is strongly recommended for those Linux distributions which support such yum apt Although RPM and DEB packages are available for direct download external software dependencies are far too complex to be described in human readable text and are best managed by the repositories Alternatively the client can be installed from binary tarballs or built from the source When doing this you will have to install build a number of third party packages as well such as Globus gSOAP VOMS LFC client etc 3 2 SYSTEM WIDE INSTALLATION 17 For a fully functioning client the following packages have to be installed in addition to a few standard ones globus and gpt only a subset of Globus packages is actually needed openssl gsoap 1ibxm12 libtool 1tdl openldap nordugrid arc client nordugrid arc libs LFC client voms clients and voms Public keys of your Certificate Authority Optionally certificate request configuration file
66. e to a collection 9 3 5 Register existing at a location file to a collection 9 3 6 Remove and unregister a file 9 3 7 Remove a location from a collection 9 3 8 Find locations URL prefixes for a collection 9 3 9 Find a URL prefix for a location known by name 10 The Grid Monitor 10 1 The Grid Monitor 10 9 List of Users A GACL B RPM For Everybody CONTENTS 103 105 CONTENTS osa eta Ae ene A eee aay bese eay acts beeen esas ere er re ee ree ee rere ee A ee ee ope Raa eae ph eee ds ea oe ees sacs C Globus Toolkit installation notes D NorduGrid ARC build notes D 1 Dependencies D 2 Basic build with autotools D 3 Building with RPM D 4 Binary RPMs runtime requirements E Known Grid Certificate Authorities 107 107 108 108 109 109 113 113 113 114 115 117 CONTENTS List of Figures 1 1 Architectural components of the ARC middleware o e e 11 3 1 Downloading standalone client example for Fedora 10 64bit distribution 16 3 2 Web page with repository set up instructions sooo ee 17 3 3 Downloading external packages from the NorduGrid Web site o 19 3 4 Downloading ARC client RPMs Example shows packages for RHEL5 20 4 1 Downloading NorduGrid Certificate Authority public keys Example shows packages for De 4 2 Downloading NorduGrid Certificate Authority certificate request configuration
67. eee a 6 3 Logging Outh 2 24 24 4446 54854 6s ee G ew he eee de dae as 7 Describing Grid Tasks 7 1 Task Description Language xRSL o GLI URLS 54 be aot io a A Go Ba 7 1 2 Task Description Attributes executable a s sarr ic ro e a o a ae y a e da a a a aia esa executables o outputEilles ua a a RR a AR CPU LIME cali a Re a A ee er aaa Cee oes ee eb ek a ee eee ees see eA has Ghee a 24 Ree eee edn benchmarks he ee ks a we a le a StCOUU se wc ue Sod He ONS 2 es ee G Oe a ae Oe Re ee A foe ak oe oY Ae dee ee hk Eni Ge GAP ew Goto dav ae QUEUE sas Bo ee ee beg eR AE Ee ee Side toe CONTENTS CONTENTS 8 9 red ais Bou oe dedo bee os a Aa eee eye a e A Sota ds Ede he bt Bag kee b eee gods ok Sue es a es Pee Da ee environments sa a aS ee RA ee ERS ee EG hee EO EERE A OY eT ee er ee ee a ere ee eee credentialserver 2 1 2 o evr SA rs Rae Dh eee a eee de dee ae DRS e 6S FSU EE RGR ee RADE AA REO ee oe eee ee ee a a 2 1 Hello World se lt 4928 Ov See EE See a OR ee eee ae ae A ea 2 2 An Own Executable ss 6254 bp ds Ae ee ee ee ee a ee es 2 0 Many Executables uso ey BER Sew eee POG Sew A Boe a Job Management 8 1 First steps the test suite ee Sl MPCs a a a e EE he he or ee es a es eo rs 8 2 Working with JOBS s ece s paoe ai Bb ed a ee ee ee Ra a wane Ea ee GOR de Rear ee RS eke ee ae ae a da 82 2 SOP
68. en if the cached copy is still valid copy forces the cached file to be copied rather than linked to the session dir this is useful if for example the file is to be modified copy option is available in ARC 0 8 1 and above for transfers to file destinations specifies whether the file should be read only unmodifiable or not default is yes indicates whether the GridF TP data channel should be encrypted default is no specifies size of chunks blocks buffers used in GridFTP or HTTP s g transactions default is protocol dependent specifies the algorithm for checksum to be computed for transfer verification or provided to the indexing server This is overridden by any metadata options specified see below If this option is not provided the default for the protocol is used checksum no dis ables checksum calculation adler32 and no options are available in ARC 0 8 1 and above means the file should be treated as executable specify if file must be uploaded to this destination even if job processing failed default is no defines file matching pattern currently works for file listing re quests sent to an se endpoint make software use GUIDs instead of LFNs while communicating to indexing services meaningful for rls only make software try to overwrite existing file s i e before writing to destination tools will try to remove any information content associated with specified URL to distinguish between two kind
69. endly interface to the openss1 toolkit For further information please read the man pages for openssl verify and x509 commands or use the Globus commands with the help option Section 4 2 7 describes some most often used commands 4 2 7 Working with certificates examples Certificate request the following command creates a key pair for a user or a gatekeeper and prepares a formal certificate request tKeys and certificates as well as their locations can have different names In the instructions above the default naming scheme was used If you would like to use different names feel free to contact nordugrid support nordugrid org for further directions 34 CHAPTER 4 GRID CERTIFICATES Change pass phrase of the certificate use this command to change the pass phrase password of the private key file userkey pem Please note that once you forget the pass phrase the certificate has to be requested anew as there is no way to re generate a password Inspect a certificate to print all the information from the public certificate file usercert pem do the following In particular the line starting Subject contains your certificate Subject Name SN that has to be communicated to a VO manager or a site administrator in order to get access to the Grid see Section 5 Duplicate a certificate with a new pass phrase using this tool your private key is encoded with a new pass phrase and stored in the new_userkey pem file fi
70. er is your private database location to the directive see Section B 4 for details B 7 Relocating RPM Packages As it was mentioned in Section an RPM package may contain information on relocatable directories Such directories are listed as relocations meaning that their contents can be relocated during the installation in another directory To perform such an installation do the following Here oldlocation is one of the relocatable directories of the original package as listed by the rpm qip myfile rpm command and newlocation is your preferred destination specified as an absolute path starting with The command line parameters have the following meaning i perform an installation procedure v print extra information h print progress bar with hash marks relocate instruct RPM to install files from oldlocation into newlocation 108 APPENDIX B RPM FOR EVERYBODY As of RPM version 4 2 1 multiple relocations are possible To use this option specify several relocation pairs on the command line i e The order of such pairs in the line is important as RPM will attempt to create new directories and quite naturally can not skip a level If the package information as listed by rpm qip contains several relocations you must specify a relocate pair for all of them It may turn out that the package creator forgot to describe some pathes as relocateable so that they do not appear in the relo
71. ere are few exceptions though for example NorduGrid CA serves all the Nordic countries while in bigger countries like USA France or Germany there are ceveral CAs For a non authoritative list of CA s refer to Appendix E The role of CAs is not only to confirm users identities and certify resources but also to keep track of abuse of the issued certificates CA s regularly publish Certificate Revocation Lists CRL with which all the Grid services comply If your private key happened to be in possession of another person or your identity was used for illegal exploits your certificate is revoked and you will be unable to work on Grid The same is true for resource certificates if a computer is used for repetitive offences its certificate will be revoked 4 2 3 Globus Grid certificates In the Globus framework the key pair of public key cryptography consists of the key file default name userkey pem and the public certificate file default name usercert pem This means every Grid user must have these two files every time she has to communicate with Grid resources The userkey pem file or resourcekey pem when a Grid resource is concerned contains the private key encrypted with a password called pass phrase by Globus 30 CHAPTER 4 GRID CERTIFICATES The pass phrase is a password to protect a certificate Any certificate be it a user a host or a service one must be protected by a separate password DO NOT confuse it w
72. es 91 middleware 00 0 ccc cece eee eee cece e eens Mod le civic ad N O OT NECA iii a A a e 68 MSc err Sedan rra aE o E deta E keen Sa Gees at 78 Dil eae ed HK arrasar hens Sede aE NGS ei ssa d Gruen Pee E E dale ae ately STONE a eii a a 74 O aee nie abstr dh Saeed A O E A dee Peake ewes eke oe glade es HESTA EE decade eis e eae 80 HESTA sn panies oo tae ado ais 67 A sno vat oe God pate ae aes DESC al cod doi dae Netes O 34 NSANSLET sii a eins nordugrid authuser 0 200s cece eee eee 89 nordugrid cluster 0 00 c cece cece eee eens 89 NOPduPrid jODi rih cides tit eee eta 89 nordugrid queue 0 0 cece eee eee eee 89 NORDUGRID_LOCATION 04 O Objects iii dea ews ood P PASS WO G5 25th sra di 25 CHANGE ira is DIORY iii 124 33 Initialization catador 33 Q QUCUG s irc add a e i 92 attributes cerdas ac A 4ss eect Ene ia etg SiE ths A Seeded QUCUC NAME 6 EE eee eee ences 192 R R plica CataloB viciosos ta ca A A O ea EES A A oie deguw ed eao a enes TOSQUICES ooo 194 A ert E E va giagadesing sd runtime environment 0 cece cece ee eee S signature digitals ics dseniuateeoegee ewesedyeierenw ey 25 Nr da is AA A 26 STOLA A gail sca th Ga a Ge dare tie ee aine Sia pane Storage Element 0 ce cece tinii eee coo Storage resources 6 eee cece eee eee eee eee Subject aie arias pedepass Submit JOD eis arrieros idad SUPDO iaa id w E 8
73. ey or asymmetric cryptography for authentification of users resources and ser vices 9 According to the basics of the public key cryptography each actor on the Grid a user or a service must have a key pair a public and a private key The public key is quite naturally made public while the private key must be kept secret AVOID STORING YOUR PRIVATE KEY ON A PUBLIC FACILITY SUCH AS A SHARED ACCESS COMPUTER KEEP IT ON YOUR PRIVATE COMPUTER INSTEAD COMPROMISED KEYS ARE REVOKED BY THE AUTHORITY Encryption and authorization is performed using the public key while decryption and digital signature is performed with the private key Since Grid services act on behalf of users such services and all the resources which provide them must have a key pair as well 4 2 2 Certificate Authorities Keys are generated by users or service administrators with the help of standard tools see e g Section 4 2 7 In order to become accepted by other parties public keys must be signed by trusted authorities of the Grid called Certificate Authorities CA It is important to note that generating a key pair does not automatically provide you access to the Grid resources A CA needs to sign your key pair thus confirming your identity This signing procedure of the CA is often referred to as issuing a certificate Issuing a certificate is similar to issuing a national passport to a person and typically there is one CA per country Th
74. ge resources User base NorduGrid Guests ATLAS Figure 10 1 The Grid Monitor In Figure 10 1 the numbered tags indicate clickable objects as explained below 1 Cluster a cluster alias linked to the cluster description module Section 10 2 which provides complete information about the current status of a cluster 2 Load a graphical and numeric representation of the cluster load showing both Grid and non Grid submitted locally running processes Red bar shows percentage of Grid processes while the grey bar shows total relative occupancy of a cluster Numbers indicate the absolute amount of running processes with first figure corresponding to the Grid and second to the non Grid ones It should 10 2 CLUSTER DESCRIPTION 95 be noted that number of processes does not necessarily correspond to the number of running jobs a parallel job can occupy several processors By clicking on a bar a user accesses the list of all Grid jobs ruming on a cluster Section 10 4 Queueing number of queueing jobs which includes jobs queued in an LRMS as well as those being pre processed by the Grid Manager 3 Only jobs which can be potentially executed in a Grid queue are counted The number is linked to the same module as the Load item with the only difference that it displays the list of the Grid queued jobs Note that although non Grid jobs are counted in the total number of queued jobs they can not be listed by the Grid Monitor as t
75. gly based on the Resource Specification Language RSL developed by the Globus project 14 RSL allows job options and definitions to be parsed to resource management systems The ARC architecture requires certain extensions to the RSL This concerns not only introduction of new attributes but also differentiation between two levels of the job options specifications User side RSL i e the set of attributes specified by a user in a job specific file This file is interpreted by the User Interface UI 5l and after the necessary modifications is passed to the Grid Manager GM B GM side RSL i e the set of attributes pre processed by the UI and ready to be interpreted by the GM As a user you have to know only the user side part and utilize it to describe your Grid tasks In what follows the description of the NorduGrid extended RSL further denoted as xRSL is given using the following notations lt XXXX gt parameter to be substituted with a corresponding string or a number xxxx optional parameter xxxlyyylzzz list of possible values of a parameter als same as above 7 1 Task Description Language xRSL For a complete description of Globus RSL see reference 14 xRSL uses the same syntax conventions but changes the meaning and interpretation of some attributes A Grid task is described by the mean of xRSL attributes which can be either passed via a command line or more conveniently be collected in a so called
76. he job status are b begin PREPARING q queued INLRMS f finalizing FINISHING e end FINISHED c cancellation CANCELLED d deleted DELETED When no notification flags are specified default value of eb will be used i e notifications will be sent at the job s beginning and at its end No more than 3 e mail addresses per status change accepted ARC 0 3 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 58 CHAPTER 7 DESCRIBING GRID TASKS Unique no Operators User input replicaCollection lt URL gt GM input Example replicaCollection ldap grid uio no 389 lc TestCollection rc NorduGrid nordugrid dc org Location of a logical collection in the Replica Catalog URL LDAP directory specified as an URL 1dap host port dn reran ARC 0 3 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Unique yes Operators User input rerun lt integer gt GM input Example rerun 2 Number of reruns if a system failure occurs integer an integer number If not specified the default is 0 Default maximal allowed value is 5 The job may be rerun after failure in any state for which reruning has sense To initiate rerun user has to use the ngresume command architecture ARC 0 3 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Unique no Operators l User input architecture lt string gt GM input Example architecture i686 Request a specific architecture string architecture
77. he top Grid Monitor window Appendix A GACL Many parts of ARC middleware use the Grid ACL manipulation library GACL to allow user control access to various objects The GACL is a part of GridSite project 19 To get more information about GACL please refer to the project s Web site at http www gridsite org The GACL is an XML document In ARC there can be no more that one document assigned to object if supported Each GACL document consist of multiple lt entry gt tags Each such tag contains multiple and various identification tags followed by permission tags lt allow gt and lt deny gt Each permission tag lists applied permissions Available values are lt write gt lt read gt lt list gt lt admin gt Their exact meaning varies a bit depending on kind of object applied and permissions specified in lt deny gt overwrite those in lt allow gt Identification tags supported in ARC are as follows lt any user gt Matches anyone lt auth user gt User with subject name in certificate same as lt any user gt in ARC lt person gt Matches certificate with specified subject name lt dn gt subject lt dn gt lt person gt lt dns gt Matches if user connects from a computer with specified hostname lt hostname gt hostname lt hostname gt lt dns gt lt voms gt Matches if user presents credentials with matching VOMS information lt voms gt All items inside lt voms gt tag are optional VOMS
78. hey do not provide any information to the Grid Information System Match it yourself link to the Match it yourself interface Section 10 7 which allows users to compose non standard monitor requests Storage resources link to the list of available storage resources Section 10 8 User base several auxiliary links providing an access to the VO listing module Section 10 9 The main purpose of this link is to provide an easy access to the user specific information such as the list of submitted jobs and available resources 10 2 Cluster Description N NorduGrid Cluster Details Attribute Distinguished name objectClass Front end domain name Cluster alias Contact string E mail contact LRMS type LRMS version LRMS details Architecture Operating sy Homogeneous cluster CPU type slowest Memory MB smallest Total CPUs CPU machines Occupied CPUs Queued jobs Total amount of jobs Local Storage Element Session directories area Unallocated disk space MB Grid middleware Runtime environment Mds validfrom Mds validto CPU min 0 to 120 120 to inf active Net nordugrid cluster name grid quark lu se Mds Wo name local o grid Mds nordugrid cluster grid quark lu se Lund Grid Cluster gsiftp grid quark lu se 2811 jobs grid siteadmin quark lu se grid support quark lu se OpenPBS 2 3 12 FIFO scheduler single job per processors i686 Linux 2 4 3 20mdk True Pentium III Copperm
79. iic Linux 3 2 SYSTEM WIDE INSTALLATION 19 A E GIA http Ildownload nordugrid org external v NORDUGRID anid solution tor Wide area EXTERNAL SOFTWARE Computing and Data Handing uuu Here you can find information about the following external s NorduGrid Downloads component Source code repository e Globus Toolkit y e gsOAP Browse repository VOMS Browse all packages BDIlv4 e BDIlv5 Install from repositories ii The following components provide various CA certificates Package build status y e IGTF Lu e Other CAs NorduGrid home e Cert request configuration Figure 3 3 Downloading external packages from the NorduGrid Web site nordugrid arc client nordugrid arc libs LFC client voms clients and voms In case you already have Globus Toolkit VOMS and LFC installed you will have to download full source ARC client RPMs nordugrid arc lt version gt src rpm or a tarball nordugrid arc lt version gt tgz and then re build the ARC client 3rd party clients VOMS LFC are available as External software see Fig 3 3 ARC client RPMs are available by selecting Slow start all packages after chosing your operating system see Fig 3 4 Make sure to select stable release for a system wide installation of ARC 3 2 4 Build If you have installed Globus as described in Section skip to Section If you are installing on top of an older Globus version you have to rebuild th
80. ile or directory name if it is meant to be identical to the source Since the job ID is in fact a gsiftp URL of the job top directory you can use ngcp to copy files from the job directory at any time 9 1 WORKING WITH FILES 83 Usage examples of ngcp are ngcp gsiftp 1scf nbi dk 2811 j0bs 1323842831451666535 jo0b o0ut file home myname job2 out ngcp gsiftp aftpexp bnl gov threads 10 rep my file rc threads 40grid uio no 1c Collection rc Catalog zebra f ngcp http www nordugrid org data somefile gsiftp hathi hep lu se data 9 1 3 ngrm The ngrm command allows users to erase files at any location specified by a valid URL ARC 0 3 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Options h short help y print version information d debuglevel debug level 0 some 1 more 2 a lot c continue with meta data even if it failed to delete real file C cache_data_path store cached data Arguments source source URL A convenient use for ngrm is to erase the files in a data indexing catalog RC RLS or such as it will not only remove the physical instance but also will clean up the database record Here is an ngrm example ngrm rc grid uio no lc Collection rc Catalog badfile 9 1 4 ngacl This command retrieves or modifies access control information associated with a stored object if service supports GridSite GACL language 19 for access control ARC 0 3 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8
81. ile s containing the output file information can be defined in the xRSL script as the path to the file relative to the session directory preceeded by The format of these files is lines of 2 values separated by a space The first value contains name of the output file relative to the session directory and the second value is a URL to which the file will be uploaded Example outputFiles output files output files is generated by the user and contains filel gsiftp grid domain org filel file2 gsiftp grid domain org file2 After the job completes the file output files in the session directory will be read and any files described within will be uploaded to the given URLs Please note that the outputFiles attribute is not meant to operate with directories you must specify a pair lt local_to_job gt destination for each file One exception is when you want to preserve an entire directory at the remote computer for later manual download via ngget In that case simply add the trailing backslash at the end of the remote directory name You can not upload a directory to a URL location only to your local disk ARC gt 0 3 17 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Unique yes Operators User input cpuTime lt time gt GM input cpuTime lt tttt gt Example cpuTime 240 Maximal CPU time request for the job For a multi processor job this is a sum over all requested processors time time in m
82. ine 1001 MHz 256 4 2cpu 2 3 2 5 nordugrid se name grid quark lu se Mds Wo name Sweden o grid obs 27834 globus 2 0 9ng nordugrid HEAD ATLAS 3 0 1 ATLAS 3 2 1 DC1 ATLAS 3 2 1 05 08 2002 19 23 44 05 08 2002 19 24 14 CPUs Running O Grid 0 Queueing O Grid 0 Figure 10 2 ARC enabled cluster details 96 CHAPTER 10 THE GRID MONITOR The cluster description module displays all the cluster attributes stored in the MDS as well as most relevant information about the queues accessible by the Grid users The window thus contains two lists as shown in Figure 1 Attributes this is a dump of all the attributes of the nordugrid cluster objectclass dynamic and static ones Such attributes as cluster alias or domain name are static others are dynamic with the values obtained by the MDS from the information providers e g total CPU number amount of jobs or available disk space More details about these attributes can be found in the Grid Information System description 4 Each attribute apart of the MDS time stamps is linked to the Attributes Overview module Section 10 6 such that clicking on an attribute name brings the list of the values of this particular attribute on all the ARC enabled clusters For instance this is the most convenient way to browse available disk space or runtime environment values over the system 2 Queues the list of queues at a given cluster accessible by the Grid users While the
83. int out a string like i386 or i586 or i686 and such which is the hardware architecture name of your machine Appendix C Globus Toolkit installation notes ARC requires Globus Toolkit 4 or 5 You can get Globus Toolkit 5 from NorduGrid repositories for the supported Linux distributions If you need special installation instructions please refer to the Globus installation guide 111 112 APPENDIX C GLOBUS TOOLKIT INSTALLATION NOTES Appendix D NorduGrid ARC build notes This section describes the build procedure of the NorduGrid middleware ARC from tarball or from source RPM D 1 Dependencies Before trying to compile the ARC tools make sure you have installed the following software packages e GNU make GNU autotools e C compiler and library e Grid Packaging Tools GPT 22 e Globus Toolkit 4 or 5 2 which contains GridFTP client libraries Globus RLS RSL libraries gSOAP e GACL 19 e VOMS e MySQL client libraries e 1ibxm12 Note that NorduGrid provides packaged versions of GPT Globus gSOAP and VOMS while GACL is distributed within the NorduGrid source The rest of the dependencies are available in any standard Linux distributions D 2 Basic build with autotools The build is using the GNU autotools This means that a standard installation can be made with 113 114 APPENDIX D NORDUGRID ARC BUILD NOTES The configure script accepts the usual options with the addi
84. inutes if no unit is specified tttt time converted by the ARC Client from time to seconds The client converts time specified in the user side XRSL file to seconds If no time unit is specified the client assumes the time given in minutes Otherwise a text format is accepted i e any of the following will be interpreted properly make sure to enclose such strings in quotes 1 week 3 days 2 days 12 hours 1 hour 30 minutes 36 hours 9 days 240 minutes If both cpuTime and wallTime are specified the ARC Client converts them both cpuTime can not be specified together with gridTime or benchmarks 50 CHAPTER 7 DESCRIBING GRID TASKS This attribute should be used to direct the job to a system with sufficient CPU resources typically a batch queue with the sufficient upper time limit Jobs exceeding this maximum most likely will be terminated by remote systems If time limits are not specified the limit is not set and jobs can run as long as the system settings allow note that in this case you can not avoid queues with too short time limits ARC gt 0 5 27 ARC 0 6 ARC 0 8 Unique yes Operators User input wallTime lt time gt GM input wallTime lt tttt gt Example wallTime 240 Maximal wall clock time request for the job time time in minutes if no unit is specified tttt time converted by the ARC Client to seconds The client converts time specified in the user side XRSL file second
85. is MESJ diaria aera Mogae MOS cir oni nthe owes Cad naan E aA NGULANSLED eis oie ees Te aA See ia Computing Element 0 00008 configuration A deka Gade dyed bee Lads adds broker sca ds aii eee a ATA IN A A dae bom deprecated fileS oooooococccococococc o downloaddir 0 00 cece eee eee eee ee GUIS oe O SPS CON aiii dai A Patent terete tat aa D data management 0 02sec eee eee disk Space wisi dds Wiad de had hanks oped kaa iS dry T fe ictieadsateusda thes outs ore a te E ESM ill 8 eiein cheek dts bbe hoon wae EAE oeneo executable 00 cece cece eee een en enees executables 0 00 cece cece eee eee e eee enes G Susi ocn enei aniue A eE E ies Globus Toolkit i e soe ceont eersiees shane sion installation RPM ereenn teua EREE tarballVia a di GLOBUS_LOCATION 0 eee eee GLOBUS_REPLICA_CATALOG MANAGER 85 Plat leo ia bee ewer Grid Manager sci 4d cdeciderawcdeg dae eienn aai Strid MONO vita a edi nianie e a 90 J job DU id beg a A IM A QUCUEs oia reia rios e information 0 cece cece eee eee Maelo E a tied 193 Ol Cluster ena hoesess A see brdoew aes EE AS 193 Parallel oi ta tee eee ed O tartrate E CUCUEING 0 eee eee ee eee eee nes A eaters eae Eeey 91 122 IN 168 JOD ID ura ria oa K key O oie whey nite decades de eveaus A l TETTETETT 25 PUDliC iii da iet heredad tiio e aa 25 M Match it yourself cci arinevessnieveeian
86. is important to distinguish c and k options as well as C and K The former stands for cluster and is used to instruct ngresub to look for jobIDs and descriptions only at a given site cluster or exclude a cluster This is convenient to use together with the a option in case you would like to re submit all the jobs which were originally sent to a specific site cluster The latter option k stands for kluster and should be used to specify preferred re submission target Important examples ngresub c fire ii uib no myjobi will resubmit all jobs on fire ii uib no and the job myjob1 to any cluster except the cluster at which the job is currently while ngresub k fire ii uib no myjobi will resubmit the job myjob1 from wherever it was to fire ii uib no note the usage of c and k options ngresub c gridi ua org k grid2 ub org will resubmit all your jobs from cluster grid1 ua org to grid2 ub org If the re submission was successful the original job will be removed from the remote cluster unless you specify the keep option Old Grid Manager log gmlog records are not preserved and are not transferred to the new site For descriptions of a i and s options see ngstat section For descriptions of the c C g G description in Section o dryrun dumpxrsl t and d options refer to the ngsub When several of the a i c C s and job command line options are specified the comand resubmits ALL jo
87. ith a user or a system administrator log in password The certificate file usercert pem contains your public key together with additional important information such as the Subject Name SN of the certificate holder the name of the signing CA and a digital signature of this CA The important role of the CA is to establish a trustful connection between the identity of the user and the public key in the certificate file The digital signature of the CA in the user s certificate file officially declares that the public key in the file indeed belongs to the specific user Subject Name This is similar to the police department stamp in your passport it confirms that the document indeed contains correct information The certificate files are encoded with the x 509 TO format and need special tools to get decrypted See Section for some examples 4 2 4 Associating yourself with a proper CA To generate a certificate request you must know to which CA this request will be submitted The process is similar to a passport application you must chose to which country authority to apply and that authority will decide whether to grant your request or not Many countries have a CA or even several depending on the area of activities these authorities cover Some countries have one CA for all like the Nordic countries Yet most countries have no CA and citizens of such have to establish a CA and make sure it complies with intrenational rules a
88. job to the default queue if such is specified in the GM configuration ARC 0 3 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Unique yes Operators User input startTime lt time gt GM input startTime lt tttt gt Example startTime 2002 05 25 21 30 Time to start job processing by the Grid Manager such as e g start downloading input files time time string YYYY MM DD hh mm ss tttt time string YYYYMMDDhhmmss Z converted by the ARC Client from time 7 1 TASK DESCRIPTION LANGUAGE XRSL 97 Actual job processing on a worker node starts depending on local scheduling mechanisms but not sooner than startTime ARC 0 3 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Unique yes Operators User input lifeTime lt time gt GM input lifeTime lt tttt gt Example lifeTime 2 weeks Maximal time to keep job files the session directory on the gatekeeper upon job completion time time in minutes if no unit is specified tttt time seconds converted by the ARC Client from time Typical life time is 1 day 24 hours Specified life time can not exceed local settings ARC 0 3 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Unique yes Operators User input notify lt string gt string GM input Example notify be your name your domain com Request e mail notifications on job status change string string of the format b q f e c d user1 domaini user2 domain2 here flags indicating t
89. k to any available site as there are no specific requirements specified The job will be executed in a batch mode and the standard output will be written to a file hello txt at the execution site You will have to retrieve this file manually using the ngget command If a job is successfully submitted a job identifier job ID is printed to standard output The job ID uniquely identifies the job while it is being executed A typical job ID looks like follows gsiftp site it uni org 2812 jobs 10308913211503407485 You should use this as a handle to refer to the job when doing other job manipulations such as querying job status ngstat killing it ngkill re submitting ngresub or retrieving the result ngget Every job ID is a valid URL for the job session directory You can always use it to access the files related to the job by using data management tools see Chapter 9 The job description in xRSL or JSDL format can be given either as an argument on the command line as in the example above or can be read from a file Several jobs can be requested at the same time by giving more than one filename argument or by repeating the f or e options It is possible to mix e and f options in the same ngsub command tWhen using ARC lt 0 5 48 client omit e tWhen using ARC lt 0 5 48 one must prepend file name with f 8 2 WORKING WITH JOBS 69 To validate your job description without actually submitting a job use the
90. later retrieve This is how stdout attribute appears in the xRSL It may happen that something goes wrong e g echo is located in usr bin and an error will be produced To be able to analyze the errors users are advised to use stderr and gmlog attributes which instruct the Grid Manager where to store possible error messages The job name is a convenient way to identify the task Although every job is assigned a unique Grid ID this ID is far from intuitive As soon as you plan to submit more than one job you should think of a set of good names for them this will save you a lot of time The attribute _jobname should be used to associate every job with a user defined name l Since the Grid will parse the task to a batch system it is always a good idea to specify the needed CPU time Some clusters are known to have the default execution time set to 0 which effectively kills any job The cputime attribute takes the time value in minutes and passes it to the Grid Manager Do not overestimate the time as your job may end up in a long queue and wait an unnecessarily long time before being executed The last attribute in this example is middleware This may be quite helpful in an environment where some clusters run untested versions of the middleware When you are not sure what to specify do ngsub v and use the printed version number 62 CHAPTER 7 DESCRIBING GRID TASKS 7 2 2 An Own Executable In the previous Section the
91. list of GIIS URLs q queues show information about clusters and queues 1 long long format extended information t timeout time timeout for queries default 40 sec d debug debuglevel debug level from 3 quiet to 3 verbose default 0 x anonymous use anonymous bind for queries default X gsi use GSI GSSAPI bind for queries v version print version information h help print help page Arguments job list of job IDs and or jobnames The ngstat command returns the status of jobs submitted to the Grid When several of the a i c C s and job command line options are specified the comand returns information for ALL jobs that match either of the criteria logical OR For example ngstat s FINISHED c my grid org lt jobid gt will return information about all finished jobs on the Grid plus about all jobs in any state on the cluster my grid org plus about the job lt jobid gt A job can be referred to either by the jobID that was returned by ngsub at submission time or by its name if the job description specified a job name More than one jobID and or job name can be given If several jobs were submitted with the same job name the status of all those jobs will be shown If the i option is used the list of jobIDs is read from a file with the specified name By specifying the a option the status of all jobs of this user in the system will be shown ngstat uses local list of jobs see
92. maxDisk for ARC lt 0 3 16 52 CHAPTER 7 DESCRIBING GRID TASKS Unique no Operators l gt lt gt lt User input disk lt integer gt GM input none Example disk 500 Disk space required for the job integer disk space Mbytes This attribute is used at the job submission time to find a system with sufficient disk space However it does not guarantee that this space will be available at the end of the job as most known systems do not allow for disk space allocation Eventually a remote system can terminate a job that exceeds the requested disk space ARC 0 3 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Unique no Operators l gt lt gt lt User input runTimeEnvironment lt string gt runTimeEnvironment lt string gt GM input For ARC lt 0 5 39 runTimeEnvironment lt string gt lt string gt Example runTimeEnvironment gt APPS HEP ATLAS 10 0 1 Required runtime environment string environment name The site to submit the job to will be chosen by the ARC Client among those advertising specified runtime environments Before starting the job the GM will set up environment variables and paths according to those requested Runtime environment names are defined by Virtual Organizations and tend to be organized in name spaces To request several environments repeat the attribute string runTimeEnvironment ENV1 runTimeEnvironment ENV2 etc To make a disjunct request use a boolean
93. me RELATIVE TO THE LOCATION 9 3 REPLICA CATALOG IN EXAMPLES 89 The limitation of the Globus RC is that it is impossible to assign arbitrary logical file names a logical file name must be the actual file name eventually prepend with the path relative to the registered location 9 3 1 Define who you are This is the strongly recommended first step simplifying authentication at the NorduGrid Replica Catalog Or for C shells The quoted string O Grid 0 NorduGrid OU nordugrid org CN Jane Doe is your identity as specified in the Subject of your Grid certificate Use grid cert info command Section 4 2 7 to find it 9 3 2 Create a collection Here grid uio no is the server address for the NorduGrid catalogue and A_Collection is your new collection name Since the RC is an LDAP database collection URL must contain the LDAP complying Distinguished Name which includes the full NorduGrid RC name space dc nordugrid dc org Default port number is 389 but if it is different it should be specified in a standard IP manner after the server address separated by a column 9 3 3 Add a location to a collection The location name CASTOR should later be used as a mount point instead of the physical URL gsiftp 9 3 4 Upload and register a file to a collection You must have a valid Grid proxy see Section 6 1 to perform this operation In the example above the first available registered location will be used to store th
94. mitted as a main task to a Local Resource Management System LRMS string file name including path local to the computing element CE Executable is a file that has to be executed as the main process of the task It could be either a pre compiled binary or a script Users may transfer their own executables or use the ones known to be already installed on the remote system CE If an executable has to be transferred to the destination site CE from some source it has to be specified in the inputFiles list If it is not specified in inputFiles the source is expected to be local to the user client and will be added as such to the inputFiles list by the ARC Client If the file name starts with a leading slash it is considered to be the full path to the executable at the destination site CE otherwise the location of the file is relative to the session directory where job input and files are stored If the xRSL string is entered from the command line and is enclosed in double quotes standard shell expan sion of variables takes place That is if the file name contains an environment variable the value of this variable is resolved locally but if the name itself is also enclosed in double quotes it will be resolved at the remote computing element executable ROOT_DIR myprog exe ROOT_DIR is resolved locally will cause errors if the path does not exist at the execution machine executable ROOT_DIR my
95. modules 1 Job name this field is linked to the Job Information window Section 10 4 providing access to the detailed information on a given job Unlike the Job Information or Queue Information modules which list jobs local to a cluster the User Information module collects all the jobs submitted by a given user to the whole system 2 Cluster since the User Information window displays all the jobs associated with a given user the description of each respective cluster is available by clicking the cluster name This brings up a cluster description window described in Section 3 Queue this field is linked to the Queue Details module Section 10 3 thus giving access to the information about the status of the relevant queue 4 Cluster the upper part of the User Information window lists the Grid resources available for a user Each cluster to which a user is authorized to submit jobs is indicated by its name Cluster names are linked to the Cluster Description window Section 10 2 giving detailed information on available resources 10 6 ATTRIBUTES OVERVIEW 99 0 x Information for J Kiem Cluster queue Free CPUs E pc30 hip helsinki fi gridlong 0 0 21983 pc30 hip helsinki fi gridshort 0 0 21983 pc30 hip helsinki fi verylong 0 0 21983 grid gio no default 3 0 5004 grid Wo no veryshort 3 0 5004 grid fi uib no default 3 0 6905 fire ii uib no dque 50 0 509832 Iscf nbi dk gridlong 30 4320 0 101968 Iscf nbi dk gridshort
96. n name is specified for different source locations Make sure all filename values are different If the list does not contain the standard input file as specified by stdin and or the executable file as specified by executable if the given name the ARC Client appends these files to the list If the lt source gt is a URL it is passed by the ARC Client to the GM without changes if it is a local path or void the ARC Client converts it to lt size gt and lt checksum gt and uploads those files to the execution cluster Please note that the inputFiles attribute is not meant to operate with directories for reasons of access control and checksum verifications You must specify a pair lt local_to_job gt lt source gt for each file ARC 0 3 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Unique yes Operators User input executables lt string gt string GM input Example executables myscript sh myjob exe List of files from the inputFiles set which will be given executable permissions string file name local to the computing element and relative to the ses sion directory If the executable file as specified in executable and is relative to the session directory is not listed it will be added to the list by the ARC Client 48 CHAPTER 7 DESCRIBING GRID TASKS ARC gt 0 3 34 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Unique yes Operators User input cache yes no GM input
97. n not be a local file URL Using a Replica Catalog pseudo URL see Section 7 1 1 you should make sure that the location is already defined in the Replica Catalog If more than one such location is specified only those found in the Replica Catalog for this collection will be used Grid Manager will store output files in one location only the first randomly picked location that exists If no locations are specified all those found in the Replica Catalog for this collection will be tried If in a rc pseudo URL the server component host port DN is not specified server specified in the replicaCollection attribute will be used Tf the list does not contain standard output standard error file names and GM log files directory name as specified by stdout stderr and gmlog the ARC Client appends these items to the outputFiles list If the lt URL gt is not specified void use the quotes files will be kept on SE and should be downloaded by the user via the ARC Client If specified name of file ends with the entire directory is kept 7 1 TASK DESCRIPTION LANGUAGE XRSL 49 A convenient way to keep the entire job directory at the remote site for a manual retrieval is to specify outputfiles In some cases the list of output files may only be known after the job has completed ARC allows a user to specify a list of output files dynamically in a file or files in the session directory as part of their job The f
98. nal Grids in CCS 98 Proceedings of the 5th ACM conference on Computer and communications security ACM Press November 1998 pp 83 92 The Globus Resource Specification Language RSL v1 0 Online Available http www globus org toolkit docs 2 4 gram rsl_specl html A Konstantinov The NorduGrid Smart Storage Element The NorduGrid Collaboration NORDUGRID TECH 10 Online Available http www nordugrid org documents SE pdf gLite Lightweight Middleware for Grid Computing Web site Online Available http glite web cern ch glite H Stockinger et al File and Object Replication in Data Grids Cluster Computing vol 5 no 3 pp 305 314 July 2002 A L Chervenak et al Performance and Scalability of a Replica Location Service in Proceedings of the 13th IEEE International Symposium on High Performance Distributed Computing HPDC 04 IEEE Computer Society Press 2004 pp 182 191 119 120 BIBLIOGRAPHY 19 A McNab The GridSite Web Grid security system Research Articles Softw Pract Exper vol 35 no 9 pp 827 834 2005 20 Description of the NorduGrid Virtual Organisation Online Available http www nordugrid org NorduGridVO vo description html 21 RedHat Package Manager Web site Online Available http www rpm org 22 Grid Packaging Tools Web site Online Available http www gridpackagingtools org 23 R A van Engelen gSOA
99. nd for queries default X gsi use GSI GSSAPI bind for queries v version print version information h help print help page The ARC ARC client keeps a local list of jobs in the user s home directory see section 8 2 11 If this file is lost corrupt or the user wants to recreate the file on a different workstation the ngsync command will recreate this file from the information available in the Information System Since the information about a job in the system can be slightly out of date in case the user submitted or removed a job very recently a warning is issued when this command is run The f option disables this warning As the Information System has a certain latency do not use ngsync immediately after submitting or killing a job first wait a few minutes For descriptions of the c C g G t and d options refer to the ngsub description in Section 8 2 2 ngsub The ngsub command is the most essential one as it is used for submitting jobs to the Grid resources ngsub matches user s job description to the information collected from the Grid and the optimal site is being selected for job submission The job description is then being forwarded to that site in order to be submitted to the Local Resource Management System LRMS which can be e g PBS or Condor or SGE etc ARC 0 3 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Options c cluster textemname explicitly select or reject a specific site cluste
100. nd is consequently accepted by others Meanwhile the French Committee for Scientific Research CNRS issues certificates for most academic and edcational users but this is a provisional arrangement The list of some known CAs can be found in Appendix E Unfortunately there is no commonly accepted world wide body that keeps track of and validates various CAs In case you are a Nordic country resident and have no certificate you should request it from the NorduGrid Certificate Authority To do this you should download at http download nordugrid org section CA certificates see Figure 4 2 two packages 1 Public keys of the NorduGrid Certificate Authority 2 The corresponding certrequest config configuration package The standalone ARC client installation keeps keys and configuration files in the directory NORDUGRID_LOCATION share certificates which by default contains all the files necessary for the Nordic users If you use a centralized ARC installation install the RPM packages using or use the provided tarballs The following files will be installed in etc grid security certificates 1 0e8352 0 1 0e8352 crl_url 1 0e8352 signing policy globus host ssl conf 1 0e8352 globus user ss1 conf 1f0e8352 grid security conf 1f0e8352 You may well prefer installing the files in any location other than etc grid security certificates and point the X509_CERT_DIR variable to such alternative location 4 2 GRID AUTHENT
101. ning or waiting to this queue Figure shows the Grid queue description window with clickable fields marked by numbered tags as follows List of queues available for a given user can be obtained through the User Information module 10 4 JOB INFORMATION 97 1 Attributes the dump of the queue attributes Just like the cluster attributes Section 10 2 they can be both static and dynamic Every attribute is linked to the Attributes Overview module Section 10 6 which allows the values of each attribute across the entire ARC system to be browsed N ae Cluster name each queue is associated with the cluster whose name is shown at the top of the window Clicking the cluster name brings up the Cluster Description window Section 110 2 Job name from the Queue Details window users can get access to detailed information about every job in the queue by clicking the job name Each job name is linked to the Job Information module described in Section 10 4 Owner The Grid authentication mechanism allows every job to be associated to a corresponding user even though an actual Unix account owner may be a generic griduser The Grid Monitor uses this feature to display explicitly each job owner In the Queue Details window as in all other modules the user s name is linked to the User Information module Section 10 5 which displays all the resources available for a given user as well as the list of the user s jobs w we A lt
102. nted to issue Grid certificates in Nordic countries This section describes basics of Grid security and explains what are Certificate Authorities what are their functions and what you should do in a generic case in order to obtain proper certificates 4 2 1 Grid Login Proxies One of the main purposes of the Grid is to provide a transparent access to computing and storage resources For a user it means that a single login procedure must give access to all the available Grid resources Technically this is implemented via a system of proxies A user issues a temporary public proxy which contains encrypted information about the issuer and allows Grid services to act on her behalf while the proxy is valid Thus when a user wants to contact a resource her client upon request presents the proxy to the remote server which saves user from typing in login name and password 4 2 GRID AUTHENTICATION AND CERTIFICATE AUTHORITIES 29 Any Grid operation requires a valid proxy issued by the user Validity of proxies is time limited typically they expire in 12 hours although users can issue proxies of any lifetime To make such handshake between the user s client and a Grid service happening the following conditions must be satisfied the remote server must be able to check the proxy authenticity the user her client in turn must be able to check the remote server authenticity through its credentials The Grid utilizes public k
103. ob directory name keep keep files on gatekeeper do not clean t timeout time timeout for queries default 40 sec d debug debuglevel debug level from 3 quiet to 3 verbose default 0 x anonymous use anonymous bind for queries default X gsi use GSI GSSAPI bind for queries v version print version information h help print help page Arguments job list of job IDs and or jobnames Only the results of jobs that have finished can be downloaded The job can be referred to either by the jobID that was returned by ngsub at submission time or by its name if the job description contained a job name attribute The files to be retrieved by ngget should be described by the xRSL as follows outputfiles filel file2 That is while the filenames must be listed no output destination should be requested This will tell the Grid Manager not to erase the files after job s end and allow the ARC client to download them Files specified as stdout sterr and the gmlog directory are always treated as outputfiles by the system which means you don t have to add them to the output files list By default ngget will create in your current directory a new folder by the same name as the remote session directory typically a numerical string This new directory will contain all the files listed for download in your job description If you would like to store the files in another location use the dir option The option
104. ob submission will print out the job handle or job ID which may look like gsiftp site it uni org 2812 jobs 10308913211503407485 This will mean that your test job is sent for execution to the site site it uni org and the output is available via this gsiftp URL gsiftp is the Grid analogue of FTP and uses your proxy instead of login password authentication To see what is the status of the job do A typical output will look like Job gsiftp site it uni org 2812 jobs 10308913211503407485 Jobname ngtest job 1 Status ACCEPTED You can check what the job sent to the standard output by doing If ngcat displays the words hello grid the first test has completed successfully You can now clean up by deleting all the job traces You can check what the job sent to the standard output by doing For more test options check All the job manipulation commands ngstat ngcat ngclean etc can with a bulk of jobs with a specific cluster and otherwise have many other options Check Section 8 for the complete description To learn how to describe and submit your own job proceed to Section 7 6 3 LOGGING OUT 39 6 3 Logging Out Logging out is performed by destruction of the proxy You can either physically erase the corresponding file or issue 40 CHAPTER 6 GRID SESSION Chapter 7 Describing Grid Tasks To describe a task to be submitted to the NorduGrid ARC resources a special scripting language is used It is stron
105. ons should be addressed to Chapter 2 Roadmap On your way to start enjoying the power of Grid computing you will have to pass the following milestones 1 Client install the client on your computer or get access to a computer where the client is installed See Chapter 3 on client installation 2 Certificate obtain your Grid passport a personal certificate See Chapter 4on certificates for details 3 Access become a member of a user group authorized to use a set of resources also known as Virtual Organisation See Chapter 5 on Virtual Organisations 4 Hands on start a Grid session and try simple tests See Chapter 6 for guidance 5 xRSL learn how to describe your task and corresponding requirements in Grid parlance See Chapter 7 for guidelines 6 User interface get acquainted with the task and data management on Grid job submission status monitoring cancellation result retreival etc See Chapters 8 and 9 for complete description 7 User support whenever encountering a Grid problem write to nordugrid support nordugrid org 13 14 CHAPTER 2 ROADMAP Chapter 3 Client Installation The very first step to get acquainted with ARC enabled facilities is to download and install the client package There are several ways to do it you just have to chose which suits you best Binary distributions are available for several GNU Linux flavors such as RedHat and its derivatives Debian SuSE Fedora Source distri
106. or not For descriptions of a i and s options see ngstat section For descriptions of the c C g G t and d options refer to the ngsub description in Section When several of the a i c C s and job command line options are specified the comand retrieves ALL jobs that match either of the criteria logical OR For example ngget s FINISHED c my grid org lt jobid gt will retrieve all finished jobs on the Grid plus all jobs in any state on the cluster my grid org plus the job lt jobid gt 8 2 6 ngkill It happens that a user may wish to cancel a job This is done by using the ngkill command A job can be killed amost on any stage of processing through the Grid ngkill options job ARC 0 3 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Options a all all jobs i joblist filename file containing a list of jobIDs c clusters show information about clusters C clustlist textemfilename list of sites clusters to select or reject s status statusstr only select jobs whose status is statusstr keep keep files on gatekeeper do not clean t timeout time timeout for queries default 40 sec d debug debuglevel debug level from 3 quiet to 3 verbose default 0 76 CHAPTER 8 JOB MANAGEMENT x anonymous use anonymous bind for queries default X gsi use GSI GSSAPI bind for queries v version print version information h help print help page Arguments job
107. ordugrid Please note that as of the 0 4 Release the standard install is not fully supported yet we recommend to use the with nordugrid location switch Furthermore make builds the full middleware containing server client monitor and documentation modular builds such as make client or make server are not supported yet D 3 Building with RPM NorduGrid can be built using RPM From a tar gz file do Source RPMs are configured with the with nordugrid location switch and binary builds are fully relocatable In terms of RPMs the build requirements can be satisfied with the following packages D 4 BINARY RPMS RUNTIME REQUIREMENTS gpt gt 3 globus gt 2 4 3 9ng gsoap gt 2 5 2 voms 1 9 14 voms devel 1 9 14 1ibxm12 devel MySQL devel 115 Note that the naming convention above might not correspond exactly to the naming used on your system Also be aware that on some systems the RPM dependencies are broken This means for example that libxm12 may not be explicitly required by lixm12 devel while it should be D 4 Binary RPMs runtime requirements The RPMs created by rpmbuild as in Section D 23 are nordugrid arc client Client programs nordugrid arc server Server side meta package depending on all necessary packages nordugrid arc gridftpd GridF TP package nordugrid arc grid manager Grid manager package nordugrid arc infosys ldap Infosys and infoindex package nordugrid ar
108. ow down the submission To speed it up you may want to specify a shorter timeout default is 40 seconds with the t option ngsub t 5 myjob xrsl A default value for the timeout can be set by the first existing of Eh O AON E timeout option in client section in HOME arc client conf timeout option in common section in HOME arc client conf NGTIMEOUT option in HOME ngrc ARC lt 0 5 48 timeout option in client section in ARC_LOCATION etc arc conf timeout option in common section in ARC_LOCATION etc arc conf timeout option in client section in etc arc conf timeout option in common section in etc arc conf The user interface transforms input xRSL job description into a format that can be understood by the Grid Manager to which it is being submitted By specifying the dumpxrsl option the transformed xRSL is written to stdout instead of being submitted to the remote site 8 2 WORKING WITH JOBS 71 8 2 3 ngstat The ngstat command is used for obtaining the status of jobs that have been submitted with ARC ARC 0 3 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Options a all all jobs i joblist filename file containing a list of jobIDs c clusters show information about sites clusters C clustlist textemfilename list of sites clusters to select or reject s status statusstr only select jobs whose status is statusstr g giisurl url URL of a central Information System server G giislist filename
109. pings such that all the members of a certain group are mapped to the same local Unix user in addition to the default user based mappings Technically the VO database is stored in an LDAP database For this purpose a GSI 13 enabled OpenLDAP server is used providing an entry and attribute level access control based on the Grid certificates The database managers being authenticated and authorized through their certificates make use of the OpenLDAP command line tools in order to add delete or modify entries in the VO database The Nordic Grid sites periodically 4 times a day run the nordugridmap utility in order to query the VO LDAP 35 36 CHAPTER 5 GETTING ACCESS TO GRID RESOURCES VIRTUAL ORGANISATIONS server and automatically create update local user mappings according to a site policy as defined in a nordugridmap conf configuration file 5 2 Other Virtual Organisations Except of the core Nordic VO NorduGrid maintains a Guests VO similar in organisation and implementation to the NorduGrid one Every user willing to try NorduGrid ARC facilities can be added to the Guests VO upon contacting nordugrid support nordugrid org Many other VOs are operating on the Grid typically consisting of people involved in the same research project Each such VO has a manager who maintains the database and negotiates resources available for the members It is recommended for every user to join a VO in order to get access to the Grid In case
110. prog exe ROOT_DIR will be resolved remotely ARC 0 3 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Unique yes Operators User input arguments lt string gt string GM input arguments lt executable gt lt string gt string Example arguments 10000 ATLAS input dat List of the arguments for the executable string an argument executable the executable to be run by LRMS taken by the ARC Client from the user specified executable attribute 7 1 TASK DESCRIPTION LANGUAGE XRSL 47 ARC 0 3 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Unique yes Operators User input inputFiles lt filename gt lt source gt GM input inputFiles lt filename gt lt URL gt lt filename gt size checksum Example inputFiles local_to_job gsiftp sel 1lu se p1 remote_one local_to_job dat scratch local_to_me dat same_name_as_in_my_current_dir List of files to be copied to the computing element before the execution filename destination file name local to the computing element and always relative to the session directory source source of the file gsiftp https ftp http URLs or a path local to the submission node If void use the quotes the input file is taken from the submission directory URL URL of the file see Section 7 1 1 size file size in bytes checksum file checksum as returned by cksum ARC Client does not check whether the same destinatio
111. query will print out all the essential information stored by the creator of the RPM package in question This may contain such fields as package name and version creator s name build date and what s most important for users relocations Section B 7 explains how to make use of this information B 3 Simple Unpacking of an RPM Archive In many cases you would only need to extract files from an RPM archive without performing complex operations with an RPM database There is a simple way to do it This method makes use of the generic GNU CPIO utility which deals with copying files to and from archives The rpm2cpio command converts from RPM to CPIO format and the output of this conversion is redirected to the cpio command Command line parameters for the latter have the following meaning i extract contents make directories create directories when necessary As a result all the contents of the RPM package will be extracted into the current directory creating relative paths B 4 Creating a Private RPM Database To achieve higher flexibility and to get access to more RPM functionality you may want to make a step for ward and create your own RPM database You only have to do it once by issuing the following instructions Mentioned in this example directory HOME myrpmdb can of course be substituted with any other location which suits you best The only requirement is that you must have write permissions in this location
112. r C clustlist textemfilename list of sites clusters to select or reject g giisurl url URL of a central Information System server GIIS G giislist filename list of GIIS URLs e xrsl filename string describing the job to be submitted f file filename file describing the job to be submitted 68 CHAPTER 8 JOB MANAGEMENT o joblist filename file where the job IDs will be stored dryrun add dryrun option to the job description dumpxrsl do not submit dump transformed job description to stdout U unknownattr allow unknown attributes in job description pass them through t timeout time timeout for queries default 40 sec d debug debuglevel debug level from 3 quiet to 3 verbose default 0 x anonymous use anonymous bind for queries default X gsi use GSI GSSAPI bind for queries v version print version information h help print help page Arguments task strings or files describing the jobs to be submitted Option e was introduced in ARC gt 0 5 49 in ARC lt 0 5 48 strings describing the job should not be pre pended with option e in ARC gt 0 5 49 files describing the job don t have to be pre pended with option f A simple Hello World job would look like ngsub e amp executable bin echo arguments Hello World stdout hello txt Use single quotes for the xRSL string and double quotes for attribute values Such a request would submit the tas
113. re not advised to create or remove these records Certain ARC services e g the Smart Storage Element insert these records automatically as a part of the registration process There are two ways of working with RLS interactively which means you only authenticate yourself once per session or issuing a separate command for every operation Examples below show both interactive marked I and command line C variants of every instruction server rls rls nordugrid org 39281 is used as an example replace it with your favorite server name port combination Below strings 1fn or pfn have to be typed just like this 1fn or pfn while lt lfn gt and lt pfn gt have to be replaced with actual LFNs and PFNs 9 2 1 Show all possible attribute names for LFNs 9 2 2 Show the value of an attribute for an LFN Suppose LFNs have an associated attribute dq_guid To find its value for a given LFN do 9 2 3 Show the values of all attributes for a LEN 9 2 REPLICA LOCATION SERVICE IN EXAMPLES 87 9 2 4 Show all the storage services 9 2 5 Show PFNs for LFN 9 2 6 Show LFN for a PFN 9 2 7 Wildcard version of the above 9 2 8 Create an LFN PFN pair This example shows how to create a new record LFN PFN pair it implies that LFN did not exist before 9 2 9 Add a PFN to an already existing LEN This is an action needed when a new replica of a file is created 9 2 10 Delete a PFN from an LFN This action is nee
114. rst it asks for your old pass phrase then twice for the new Verify the certificate to verify the usercert pem certificate using the public key of the issuing CA which is supposed to be in located in the specified CApath do this Dump contents of the certificate with this command you can display the contents of the usercert pem certificate Convert your Grid certificate into a Web one you can use your Grid certificate to to authenticate yourself on the Web via Internet browsers Before importing your certificate into a browser you must convert it from the original pem format to pkcs12 one Here cert p12 can be any name you like preferably with the p12 extension This file can be imported into any modern browser and serve as a Web cerificate Use your Grid passphrase to manage it Chapter 5 Getting Access to Grid Resources Virtual Organisations NB possession of a Grid certificate even signed by a legal CA does not automatically allow you to use any Grid resources As it was mentioned above in order to be able to do such things as copy files over the Grid or submit Grid jobs your identity should be mapped to a local account on each resource be it a computing cluster or a storage facility As long as this mapping is done you are authorized to use a resource as any local user 5 1 NorduGrid Virtual Organisation To facilitate and automate such mapping for the Nordic Grid users NorduGrid has set up a collective
115. rther such as the Information Model 4 and XRSL Extended Resource Specification Language Section 7 ARC main components are see Figure 1 1 e Grid services running on the resources the Grid Manager the gridftpd and the information services e Indexing services for the resources and data e Clients making intelligent use of the distributed information and data available on the Grid NorduGrid ARC Middleware Components Mandatory elements Optional elements Figure 1 1 Architectural components of the ARC middleware This User Guide puts together descriptions of user end parts of the ARC middleware serving as a user manual and a reference It also includes basic examples and the ARC client installation instructions The User Guide does not provide detailed description of third party tools such as the Globus giving only minimal necessary information The definitive description of the components and services can be found in separate manuals 11 12 CHAPTER 1 PREFACE User Interface The NorduGrid toolkit user interface user manual 5 xRSL Extended Resource Specification Language 6 Grid Manager The NorduGrid Grid Manager description and administrator s manual 3 Grid Monitor The Grid Monitor usage manual 7 Detailed installation and configuration instructions are included into the ARC software distribution available for download at Any further questi
116. rtificate do the following Alternatively simply send the file HOME globus usercert_request pem to the contact e mail address of your CA ca nbi dk in case of a Nordic certificate For detailed step by step instructions check Section 4 1 3 The certificate request procedure creates the new directory globus in your HOME area and places there three filest usercert_request pem the official certificate request to be mailed to your CA userkey pem your private key usercert pem your public certificate placeholder initiated with zero size The userkey pem holds your private key encoded with your pass phrase you are prompted to supply this pass phrase during the key pair generation This file must only be readable by its owner that is you The usercert_request pen file contains your unsigned public key together with your Subject Name and the name of your CA The grid cert request creates also an empty usercert pen file just as a placeholder which later must be overwritten with your CA signed certificate that you will receive by e mail When and if the CA fulfils your request they will send you the actual public certificate which you must store as HOME globus usercert pem overwriting the placeholder You can use the openss1 11 cryptography toolkit and the Globus provided commands to create check and convert between different formats and to manipulate your certificate files actually the Globus commands are just a fri
117. ry is usr src redhat for a RedHat system Naturally as a user you have no write permission there To solve the problem start by creating a new directory structure in any place which has enough disk space and write permission Now you should instruct RPM to use this directory instead of the system wide one assuming you created the rpmtop structure above in home yourname Next thing you should take care of is the temporary directory for RPM builds which by default is var tmp also unavailable for mere mortals The solution is similar to the above to create your own directory in any place which has enough disk space and write permission This directory should also be specified in your rpmmacros file That s it from now on you should be able to build binary RPMs from source by using the command 110 APPENDIX B RPM FOR EVERYBODY depending whether the sources are provided as source RPM mypackage src rpm or as a tarball mypackage tar gz The command line options are correspondingly ba build binary and source packages from a source RPM ta build binary and source packages from gzipped tarball Your RPMs will be placed in home yourname rpmtop RPMS i386 directory of the example above In case your architecture is different from i386 please take care of creating a corresponding subdirectory in rpmtop RPMS e g rpmtop RPMS alpha Tf you do not know what is the architecture use This command will typically pr
118. s While some of these packages are available from standard repositories nordigrid and few other non common ones have to be taken from the NorduGrid repositores see Section 3 2 1 Installation of the certification related packages is related to security issues and is discussed in Chapter 4 3 2 1 Installation via repositories NorduGrid provides a number of repositories for various operating systems These are primarily YUM and APT repositories containing RPM packages though work is on going on providing also DEB packages Repositories can be defined either by manually adding the necessary information to your system repository configuration or by installing a corresponding package For latest details always visit http download nordugrid org and check the Install from repositories section see Figure 3 2 CIAO http download nordugrid org repos html NORDUGRID Computing and Data Handling 27 Grid solution ror wide rea NORDUGRID DOWNLOADS REPOSITORY INFORMATION ARC middleware NorauGrid Downloads Repository information Source code repository Yum and apt repositories are available for several systems NorduGrid RPM packages an Browse repository signed and in order to verify them you must install the NorduGrid GPG key Browse all packages For rpm based distributions like Red Hat and Fedora Install from repositories rpm import http download nordugrid org RPM GPG KEY nordugrid P
119. s If no time unit is specified the client assumes the time given in minutes Otherwise a text format is accepted i e any of the following will be interpreted properly make sure to enclose such strings in quotes 1 week 3 days 2 days 12 hours 1 hour 30 minutes 36 hours 9 days 240 minutes If both cpuTime and wallTime are specified the ARC Client converts them both wallTime can not be specified together with gridTime or benchmarks If only wallTime is specified but not cpuTime the corresponding cpuTime value is evaluated by the ARC Client and added to the job description This attribute should be used to direct the job to a system with sufficient CPU resources typically a batch queue with the sufficient upper time limit Jobs exceeding this maximum most likely will be terminated by remote systems If time limits are not specified the limit is not set and jobs can run as long as the system settings allow note that in this case you can not avoid queues with too short time limits ARC gt 0 3 31 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Unique yes Operators User input gridTime lt time gt GM input none Example gridTime 2 h 7 1 TASK DESCRIPTION LANGUAGE XRSL ol Maximal CPU time request for the job scaled to the 2 8 GHz Intel Pentium 4 processor time time in minutes if no unit is specified The attribute is completely analogous to cpuTime except that it will be recalculated to
120. s a set of pop up Web pages connected by hyperlinks making it easy to browse and navigate Some limited searching capacity is also available through the Match it yourself module The structure of the Grid Monitor to great extent follows that of the Information System 4 The basic objects are defined by the following schema s objectclasses nordugrid cluster a cluster nordugrid queue a queue at the cluster accessible by the ARC users nordugrid job a Grid job associated with a queue nordugrid authuser a user authorized to submit jobs to a given queue The Grid Monitor also uses the NorduGrid Virtual Organisation VO organisationalPerson and Storage Element nordugrid se objectclasses and their attributes For each objectclass either an essential subset of attributes or the whole list of them is presented in an easily accessible inter linked manner This is realized as a set of windows each being associated with a corresponding module There are nine major modules 1 An overall Grid Monitor 2 Cluster Description 3 Queue Details 4 Job Information 5 User Information 6 Attributes Overview 7 Customizeable Display Tool Match it yourself 8 List of Storage Facilities 9 List of Users Each module displays both dynamic and static information for example a queue name is static while the amount of running jobs in this queue is dynamic Most of the displayed objects are linked to appropria
121. s of httpg gssapi stands for implemention using only GSSAPI functions to wrap data and gsi uses additional headers as implmented in Globus IO specify the space token to be used for uploads to SRM storage elements supporting SRM version 2 2 or higher specify if before writing to specified location software should try to create all directories mentioned in specified URL Currently this applies to FTP and GridFTP only Default for those protocols is yes Local files are referred to by specifying either a location relative to the job submission working directory or by an absolute path the one that starts with preceded with a file prefix URLs also support metadata options which can be used for registering additional metadata attributes or querying the service using metadata attributes These options are specified at the end of the LFN and consist of name and value pairs separated by colons The following attributes are supported guid GUID of the file in the metadata service checksumtype Type of checksum Supported values are cksum default md5 and adler32 checksumvalue The checksum of the file The checksum attributes may also be used to validate files that were uploaded to remote storage 7 1 TASK DESCRIPTION LANGUAGE XRSL 45 Examples of URLs are http grid domain org dir script sh egsiftp grid domain org 2811 threads 10 secure yes dir input_12378 dat ldap grid domain org 389 1c collection1 rc Nordugrid dc nord
122. se Case A If you already have a Globus installed on your system check that the following variables are defined and point to the proper locations If the variables are not defined set them according to your installation Typically GLOBUS_LOCATION is opt globus and GPT_LOCATION is opt gpt Case B If there is no Globus installation or you want to profit from the Globus Toolkit distribu tion with the most recent bug fixes and patches download from http download nordugrid org see Figure 3 3 and install the necessary packages in the following order You may well want to install the Globus Toolkit from pre compiled tarballs provided at the NorduGrid download site In such a case take care to execute post installation procedures Here lt globus location gt is the directory to which you unpacked Globus by default opt globus NB on some systems and distributions certain additional external packages need to be installed in order to make the Globus Toolkit operational Some of those are available from the NorduGrid downloads area External software section See Appendix C for additional information 3 2 3 Download the client In case you can not use repositories you will have to install the following client packages by downloading them from the NorduGrid epea Such packages as VOMS or LFC client can be downloaded from the original gLite repository as well however it only has binaries for Scient
123. send reports about job to The default is set up in the cluster configuration URL URL It is up to a user to make sure the requested logging service accepts reports from the set of clusters she intends to use eredentialserver ARC gt 0 5 45 ARC 0 6 ARC 0 8 Unique yes Operators User input credentialserver lt URL gt GM input Example credentialserver myproxy myproxy nordugrid org username user Specifies an URL which Grid Manager may contact to renew extend delegated proxy of job Only MyProxy servers are supported URL URL of MyProxy server It is up to a user to make sure the specified MyProxy server will accept requests from Grid Manager to renew expired credentials URL may contain options username and credname to specify user name and credentials name which Grid Manager should pass to MyProxy server If username is not specified DN of user credentials is used instead 7 2 Examples In this section you can find some examples of xRSL job description While the xRSL specifications can be passed to ngsub see Section 8 2 2 as a single string on the command line it is much more convenient to create a file with an arbitrary name containing the xRSL string and 7 2 EXAMPLES 61 pass this file to ngsub e g ngsub filename The format of the file is not important see Section 7 1 as long as it does not contain Microsoft DOS linefeeds Attribute names are case insensitive that is you can us
124. server subject lt voms gt lt vo gt name of VO lt vo gt lt group gt VOMS group lt group gt lt role gt 103 104 APPENDIX A GACL VOMS group lt role gt lt capability gt VOMS group lt capability gt lt voms gt lt vo gt Matches if server recognises that user belongs to specified VO lt name gt This tag is specific to server setup name of VO lt name gt lt vo gt Here is an example of valid VOMS GACL document lt xml version 1 0 gt lt gacl version 0 0 1 gt lt entry gt lt voms gt lt vo gt NorduGrid lt vo gt lt group gt developers lt group gt lt role gt coordinator lt role gt lt voms gt lt allow gt lt admin gt lt write gt lt allow gt lt entry gt lt entry gt lt voms gt lt vo gt NorduGrid lt vo gt lt group gt developers lt group gt lt voms gt lt allow gt lt read gt lt list gt lt allow gt lt entry gt lt gacl gt Appendix B RPM For Everybody You ve been told that working with RPMs needs system administrator privileges You ve been misled RPM stands for RedHat Package Manager and is a sophisticated archiving format allowing not only to pack a set of files and directories in a single archive but also to install them in an easy to manage manner While a Tape Archive tar or a ZIP archive with which you may be familiar with simply packs files with their relative paths RPM stores entire directory inform
125. sion as this is the one less likely to have problems However bear in mind that stable releases are not very frequent and may lack newest features or recent bugfixes Latest successful nightly builds are available for early testers 3 1 2 Unpack Put the downloaded package in a directory of your choice and execute This will create a new directory nordugrid arc standalone lt version gt and the downloaded tgz package can be safely removed 15 16 CHAPTER 3 CLIENT INSTALLATION E E EE D http download nordugrid org stable html NORDUGRID aria sotution tor wise area NORDUGRID DOWNLOADS STABLE Computing and Data Handling uu The latest stable version is 0 8 1 1 2 For other versions pleas NorduGrid Downloads repository tool such as yum apt or up2date to install package recommended Source code repository Browse repository Binary builds Browse all packages Platform selection Install from repositories Vendo Verdon Architecture debian Package build stat ackage build status fedora Testing NorduGrid home opensuse ubuntu Quick art Standalone client package Slow start aSo need othe Figure 3 1 Downloading standalone client example for Fedora 10 64bit distribution 3 1 3 Configure Configure and set up environment variables most notably NORDUGRID_LOCATION and GLOBUS_LOCATION by doing the following If you are working in a C shell us
126. source in the following list Eh TOA LR E AN giis options in client section in HOME arc client conf giis options in common section in HOME arc client conf SHOME nggiislist one GIIS per line ARC lt 0 5 48 giis options in client section in ARC_LOCATION etc arc conf giis options in common section in ARC_LOCATION etc arc conf ARC_LOCATION etc giislist one GIIS per line giis options in client section in etc arc conf giis options in common section in etc arc conf etc giislist one GIIS per line If you would like to get diagnostics of the process of resource discovery and requirements matching a very useful option is d The following command ngsub d 2 myjob xrsl will print out the steps taken by the ARC client to find the best cluster satisfying your job requirements A default value for the debug level can be set by the first existing of 1 debug option in client section in HOME arc client conf 2 debug option in common section in HOME arc client conf 3 NGDEBUG option in SHOME ngrc ARC lt 0 5 48 4 debug option in client section in ARC_LOCATION etc arc conf 5 6 7 debug option in common section in ARC_LOCATION etc arc conf debug option in client section in etc arc conf debug option in common section in etc arc conf It often happens that some sites that ngsub has to contact are slow to answer or are down altogether This will not prevent you from submitting a job but will sl
127. t hello txt The inputfiles attribute instructs the User Interface to copy the file from home john bin say_hello on your local computer to say_hello in the session directory at the execution machine If the file resides at an GridFTP or HTTP server use gsiftp or http respectively instead of file to specify the protocol 7 2 3 Many Executables The Grid Manager is capable of managing more than one executable file and xRSL provides means for users to specify such files A typical example is when a user script prepares and starts a pre compiled binary In this case both files must be given executable permissions but only the main script should be submitted for execution by the local system To make this working users must list all the files which need executable permissions in the executables attribute as shown below amp executable run sh arguments 1664900 100000 executables ffungen inputFiles ffungen outputFiles ffun hbook gsiftp hathi hep lu se test flong flong1 hbook jobName flong1 stdout flong1 out join yes 7 2 EXAMPLES 63 notify e john doe mail org ftpThreads 6 middleware NorduGrid 0 8 1 64 CHAPTER 7 DESCRIBING GRID TASKS Chapter 8 Job Management Job submission on the NorduGrid ARC is made via the User Interface UI part of the ARC 5 The UI provides a set of command line tools that submit jobs trace their status kill jobs retrieve job ou
128. t longer than the proxy validity it will not be able to finish correctly because of the proxy expiration Either for this reason or on the contrary if you d like to have your proxy short lived it is possible to create a proxy with a user defined lifetime In this example a proxy will live 27 hours and 45 minutes The grid proxy init command has several options e g you can select a location of the newly generated proxy or specify another location for your Grid certificate and or key For detailed information on these options use grid proxy init help If you are using different computers to log in to the Grid it is strongly advised NOT TO COPY your private key across the systems Instead use a dedicated machine to generate a proxy and then copy the proxy file to another computer preferably into your HOME directory and describe the new proxy location in the X509_USER_PROXY environment variable 37 38 CHAPTER 6 GRID SESSION 6 1 1 Proxy Handling Tips To avoid troubles please always try to make sure that your proxy has a validity period sufficient for your task to come to completion However it is not advised to generate proxies with lifetimes of several days 6 2 First Grid test ARC comes with a test suite that allows users to quickly test their installation and most of the Grid functionality The very first test can be performed by issuing This will produce some informative output and upon a successfull test j
129. t or error The command ngcat assists here extracting the corresponding information from the execution cluster and pasting it on the user s screen It works both for running tasks and for the finished ones This allows a user to check the output of the finished task without actually retreiving it 8 2 WORKING WITH JOBS 73 ARC 0 3 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Options a all all jobs i joblist filename file containing a list of job IDs c clusters show information about clusters C clustlist textemfilename list of sites clusters to select or reject s status statusstr only select jobs whose status is statusstr o stdout show the stdout of the job default e stderr show the stderr of the job f follow show tail of the requested file and follow its changes 1 gmlog show the grid error log of the job t timeout time timeout for queries default 40 sec d debug debuglevel debug level from 3 quiet to 3 verbose default 0 x anonymous use anonymous bind for queries default X gsi use GSI GSSAPI bind for queries v version print version information h help print help page Arguments job list of job IDs and or jobnames The ngcat command can return the standard output of a job o option the standard error e option and the errors reported by the Grid Manager 1 option ngcat can only operate on jobs where either stdout stderr and or gmlog files were specifie
130. t to Whenever a filter has to be applied an operator should be selected in the middle column and a match string 10 8 STORAGE RESOURCES 101 Attribute values Mozilla sur st Name Cluster alias Operating system CPUs total Postal code 1 Cluster Iscf nbi dk LSCF NBI RedHat 7 2 28 DK 2100 Linux 2 4 20 13 7smp 2 Cluster toornaarsuk distiab diku dk DistLab DIKU RedHat 9 17 DK 2100 Linux 2 4 20 20 9 START OVER Figure 10 10 Customized cluster information display specified in the rightmost field For example if only clusters containing NBI in their domain names have to be shown the attribute filter would be Front end domain name nbi Matches are case insensitive Figure 10 10 is the result of the search according to the criteria defined in the exampel in Figure 10 9 Three filters were applied on operating system attribute total number of CPUs and postal code in this case we were selecting any cluster which is not in Sweden Since we wanted to display each cluster s alias as well this attribute was added to the selection but with a match everything scope The attribute matching method is exactly the same as used by the Attributes Overview module Section 10 6 and it re uses the screen layout shown in Figure 10 7 10 8 Storage Resources Although there is no well defined Storage Element concept in the NorduGrid some information about the storage resources can b
131. task For example a simple Hello World task description would specify bin echo as the executable and Hello World as the argument In xRSL language it will look as follows You can actually use this description from the command line i e your first Grid job should be submitted as In a more complex case a binary executable may have to be downloaded from a remote location process an input data and create an output file This task specification will have to include locations of all three files executable input and output and perhaps few other requirements e g the necessary disk space and an e mail address to which the notification of the task completion should be sent Such an xRSL file may be written like the following When using ARC lt 0 5 48 client omit e 46 CHAPTER 7 DESCRIBING GRID TASKS As you can see the xRSL attribute names are largely self explanatory xRSL handles most possible task description attributes and next Sections contain the comprehensive list of them complete with usage ex amples The following attributes can be specified in a user s xRSL script Some are to be modified by the UI before being passed to the GM If this is the case corresponding GM input is described ARC 0 6 ARC 0 8 Unique yes Operators User input executable lt string gt GM input for ARC lt 0 5 25 executable bin echo Example executable local_to_job exe The executable to be sub
132. te modules such that with a simple mouse click a user can launch another module expanding the information about the corresponding object or attribute Each such module opens in an own window and gives access to other modules in turn providing thus rather intuitive browsing In what follows these modules are described in detail an overview of their functionality is given and usage hints are provided 93 CHAPTER 10 THE GRID MONITOR 10 1 The Grid Monitor The basic module providing access to the most required information is the Grid Monitor showing the overall status of the system It serves as a starting point for browsing the system information The purpose of this module is to give a quick overview of the current status of the ARC Grid by showing the list of the available clusters and the most essential information about them an alias number of working processors number of occupied processors and number of queueing jobs In the current implementation the main Grid Monitor window contains also the link to the user base of the ARC Grid Figure shows a screenshot of the running monitor All the information shown is dynamic including organizational names countries in Grid Monitor Mozilla Ioj xj Grid Monitor 2003 08 14 CEST 17 44 46 Processes mm Grid mm Local CPUs Load processes Grid local Queueing Finland Japan HS Norway wo nes Sweden TOTAL 19 clusters 936 41 664 O Match it yourself Stora
133. the prime number program the Makefile and the executable is downloaded to the cluster chosen from various servers and the program is compiled before the run In this way the test job constitute a fairly comprehensive test of the basic setup of a grid cluster This test job does nothing but print hello grid to stdout This test job tests download capabilities of the chosen cluster by downloading 8 inputfiles over different protocols HTTP FTP gsiFTP and RLS Working with jobs 8 2 1 ngsync It is advised to start every grid session by running ngsync especially when changing workstations The reason is that your job submission history is cached on your machine and if you are using ARC client installations on different machines your local lists of submitted jobs will be different To synchronise these lists with the information in the Information System use the ngsync command 8 2 WORKING WITH JOBS 67 ARC 0 3 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Options c cluster textemname explicitly select or reject a specific site cluster C clustlist textemfilename list of sites clusters to select or reject g giisurl url URL of a central Information System server G giislist filename list of GIIS URLs f force don t ask for confirmation t timeout time timeout for queries default 40 sec d debug debuglevel debug level from 3 quiet to 3 verbose default 0 x anonymous use anonymous bi
134. the actual CPU time request for each queue depending on the published processor clock speed gridTime can not be specified together with cpuTime or wallTime If only gridTime is specified but not cpuTime the corresponding cpuTime value is evaluated by the ARC Client and added to the job description ARC gt 0 5 14 ARC 0 6 ARC 0 8 Unique yes Operators User input benchmarks lt string gt lt value gt lt time gt GM input Example benchmarks mybenchmark 10 1 hour 30 minutes Evaluate a job s cpuTime based on benchmark values string benchmark name value benchmark value of reference machine time the cpuTime the job requires on the reference machine benchmarks can not be specified together with cpuTime or wallTime If only benchmarks is specified but not cpuTime the corresponding cpuTime value is evaluated by the ARC Client and added to the job description ARC gt 0 3 17 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Unique yes Operators User input memory lt integer gt GM input Example memory gt 500 Memory required for the job per rank integer size Mbytes Similarly to cpuTime this attribute should be used to direct a job to a resource with a sufficient capacity Jobs exceeding this memory limit will most likely be terminated by the remote system ARC gt 0 3 17 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 tWas called maxMemory for ARC lt 0 3 16 tWas called
135. time 2000 PBS comment Job started on Mon Aug 05 at 14 21 Standard output file dc1 002000 simul 01217 hlt pythia_jet_17 lo0g Standard error file dc1 002000 simul 01217 hlt pythia_jet_17 log Submission machine 130 225 212 51 47832 Iscf nbi dk Mds validfrom 05 08 2002 19 25 41 Mds validto 05 08 2002 19 26 11 Figure 10 5 Grid job statistics The job information window is invoked by clicking on a job name in any Grid Monitor window which lists jobs It is handled by the same module which produces running queued job list and contains simple dump of all the available job attributes see Figure 10 5 Just like in the Cluster Description and Queue Description windows each attribute is clickable as indicated by a tag numbered 1 in Figure 10 5 and is linked to the Attributes Overview module Section 10 6 This is a convenient way to compare jobs that reside on the system 10 5 User Information The User Information module of the Grid Monitor gives access to all the available information related to a given user This includes the list of available resources queues processors and disk space and the list of user jobs residing on the system at the time of query To collect this information the whole system has to be queried therefore invocation of this module typically takes quite a bit of time at least compared to most other modules Figure 10 6 shows a typical User Information window where the numbered fields are linked to other Grid Monitor
136. ting system name and version The site to submit the job to will be chosen by the ARC Client among those advertising specified operating system Usage is identical to that of runTimeEnvironment and middleware Use the gt operator to request a version equal or higher stdin ARC 0 3 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Unique yes Operators User input stdin lt string gt GM input Example stdin myinput dat The standard input file string file name local to the computing element The standard input file should be listed in the inputFiles attribute otherwise it will be forced to that list by the ARC Client stdout ARC 0 3 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Unique yes Operators User input stdout lt string gt GM input Example stdout myoutput txt The standard output file string file name local to the computing element and relative to the ses sion directory 54 CHAPTER 7 DESCRIBING GRID TASKS The standard output file should be listed in the outputFiles attribute otherwise it will be forced to that list by the ARC Client If the standard output is not defined ARC Client assigns a name stderr ARC 0 3 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Unique yes Operators User input stderr lt string gt GM input Example stderr myjob err The standard error file string file name local to the computing element and relative to the ses sion direc
137. tion of enable experimental Enable experimental code enable rpath hack Do not rpath Globus libraries in binaries enable docs Build the documentation with sysv scripts location lt PATH gt Location of the SYSV init scripts e g etc init d with monitor prefix lt PATH gt Specify the location of the Grid Monitor PHP scripts with monitor local prefix lt PATH gt Specify the relative location of the Grid Monitor PHP scripts with gsoap location lt PATH gt Specify the gSOAP installation path with mysql location lt PATH gt Specify the MySQL installation path with libxml location lt PATH gt Specify the libxm1 installation path with nordugrid location lt PATH gt Specify the ARC installation path with globus location lt PATH gt Specify the Globus installation path with gpt location lt PATH gt Specify the GPT installation path with globus makefile header Use globus makefile header to generate makefile stubs with flavor lt flavor gt Specify the Globus build flavor or without flavor for a flavor independent build Note that using with nordugrid location opt nordugrid switch will install the software using the opt nordugrid prefix and place the software in subdirectories opt nordugrid bin opt nordugrid lib opt nordugrid libexec For a standard install the prefix usr local will place the software in nordugrid subdirectories usr local bin usr local lib nordugrid usr local libexec n
138. tly globus request config releases globus config tags gpt gsoap SHIFT or CTRL click to select multiple packages Reset Get latest certificate_authorities certrequest config 0 1 2004 04 07 CEST 15 53 12 Figure 4 2 Downloading NorduGrid Certificate Authority certificate request configuration package Example shows packages for Debian Linux 4 1 QUICK START WITH CERTIFICATES 27 4 1 2 Certificates for system wide client installation System wide client installation from RPMs or tarballs as described in Section 3 2 does not include files public keys and configuration templates necessary for certificate request and usage operations Therefore you have to obtain them from the relevant Authority see Section for information on different Certificate Authorities Examples in this Section refer to the NorduGrid one You will have to download and install two packages ca_NorduGrid ca_NorduGrid certrequest config The packages are available as RPM or tarball files from the NorduGrid download area at http download nordugrid org inthe CA certificates section You will need nordugrid certificates and certrequest config package see Figures 4 1 and 4 2 for illustration Install the downloaded packages e g for RPMs You have now all the necessary requisits to request a NorduGrid certificate and to use it for your authenti cation Continue to Section to learn how to request a personal certificate 4 1 3
139. tory The standard error file should be listed as an outputFiles attribute otherwise it will be forced to that list by the ARC Client If the standard error is not defined ARC Client assigns a name If join is specified with value yes ARC Client adds stderr to the pre processed xRSL script with the same value as stdout ARC 0 3 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Unique yes Operators User input join yes no GM input none Example join yes If yes joins stderr and stdout files into the stdout one Default is no mlog ARC 0 3 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Unique yes Operators User input gmlog lt string gt GM input Example gmlog myjob log A name of the directory containing grid specific diagnostics per job string a directory local to the computing element and relative to the session directory This directory is kept in the session directory to be available for retrieval ARC Client forces it to the list if outputFiles 7 1 TASK DESCRIPTION LANGUAGE XRSL 55 ARC 0 3 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8 Unique yes Operators User input jobName lt string gt GM input Example jobName My Job nr 1 User specified job name string job name This name is meant for convenience of the user It can be used to select the job while using the ARC Client It is also available through the Information System ARC 0 3 ARC 0 4 ARC 0 5 ARC 0 6 ARC 0 8
140. tput and perform some other related functions For a complete description and configuration details please refer to the UI manual 5 The following sections will concentrate on job and data management tools and utilities in the ARC client 8 1 First steps the test suite ARC comes with a fairly complete test suite that tests different functionalities of the middleware The test suite consists of one utility called ngtest that contains a variety of test examples which can be executed This utility can be used either for testing a newly installed cluster or by a new user that wants to try out a few simple things on the Grid for the first time The utility can print helpful output about installed user credentials user authorization on computing resources and storage elements VO membership information and it can also be used to submit various test jobs testing either the software installation on the client or some server The utility comes with the nordugrid arc client and the nordugrid arc standalone packages 8 1 1 ngtest ARC gt 0 5 49 Options E certificate prints information about installed user and CA certificates j job number submit test job given by the number 1 2 3 possible R resources print user authorization information for clusters and storage elements 0 configuration print user configuration V vo print VO membership information for the user r runtime time run testjob 1 for the specified n
141. tributes of the necessary authorities Table 4 1 presents a short check list summarizing which certificates you would need Will use NorduGrid resources Will use other Grid resources NorduGrid CA certificate and signing policy Your certificate NorduGrid certificate Other Grid certificate Your issuing CA certificate and signing policy file if any and the NorduGrid CA certificate and Certificates signing policies and other attributes if any of all the CAs that certified the resources signing policy NorduGrid CA certificate and signing policy and certificate re quest configuration files No Grid certificate Table 4 1 Check list of needed certificates The recommended procedure to obtain other CA certificates and attributes is to fetch them directly from the CAs in question They are typically available from their respective Web sites for a non authoritative list see Appendix E If for some reason it is impossible to fetch your CA attributes e g Web site unavailable holiday season etc you may download the necessary files from the NorduGrid downloads area at http download nordugrid The attributes are platform and system independent Install the CA attributes either from RPMs rpm Uvh lt your CA name gt or from the provided tarballs IMPORTANT The rule of thumb when installing the NorduGrid ARC middleware is always to check the contents of the etc grid securit
142. uent queries it is not possible to obtain the per file status 9 2 Replica Location Service in Examples This section lists basic examples showing how to access and manipulate the records in the Globus Replica Location Server RLS I8 Only authorised RLS managers can perform operations that require write access ARC is interfaced to the Globus RLS RLS relies on a simple relational database that does not support data sets or collections An RLS record consists of a logical file names LFN which corresponds to one or Globus RLS is substantially different from EDG LCG RLS the latter is not described here and is not interfaced to ARC 86 CHAPTER 9 DATA MANAGEMENT more physical files PFN Each logical file has also an associated set of attributes such as size checksum GUID etc LFNs are usually just file names e g because the Grid can not guess what logical name one would assign to a file PFNs are transport normal URLs of the files e g Each LFN can have several PFNs replicas NorduGrid RLS has additional special storage service records that represent storage facilities Such special records allow to index storage facilities and help the Grid to locate destinations for output files These storage service records have a special format they have fixed LFN __storage_service__ Storage service PFNs include complete path to the expected file destination thus resembling a collection e g Regular users a
143. ugrid dc 0rg rc grid domain org 1c collection1 rc Nordugrid dc nordugrid dc org zebra f1 zebra rls gsiftp se domain org datapath file25 datOgrid domain org 61238 myfile02 dat fireman fireman_host 8443 glite data catalog interface FiremanCatalog data root file home auser griddir steer cra lfc srm srm domain org griddir lfc domain org user filel1 guid bc68cdd0 bf94 41ce ab5a 06a1512764dc checksumt ype adler32 checksumvalue 123456787 lfc lfc domain org cache no guid bc68cdd0 bf94 41ce ab5a 06a1512764d This is a destination URL The file will be copied to the GridFTP server at se domain org with the path datapath file25 dat and registered in the RLS indexing service at grid domain org with the LFN myfile02 dat 2This is a destination URL The file will be copied to srm domain org at the path griddir file1 and registered to the LFC service at 1fc domain org with the LFN user file1 The checksum will be compared to what is reported by the SRM service after the transfer The given GUID and checksum attributes will also be registered in the LFC 3This is a source URL The file is registered in the LFC service at 1fc domain org with the given GUID and can be copied or queried by this URL 7 1 2 Task Description Attributes A task is typically described by a binary executable to be processed by a computer parameters passed to that executable and requirements which must be met by a system to be able to execute the
144. umber of minutes default 5 c cluster textemname explicitly select or reject a specific cluster ngtest was available in ARC 0 4 and earlier 0 5 x versions but had a substantially different functionality 65 66 CHAPTER 8 JOB MANAGEMENT C clustlist textemfilename list of clusters to select or reject g giisurl url URL of a central Information System server G giislist filename list of GIIS URLs o joblist filename file where the job IDs will be stored dryrun add dryrun option to the xRSL dumpxrsl1 do not submit dump transformed xRSL to stdout t timeout time timeout for queries default 40 sec d debug debuglevel debug level from 3 quiet to 3 verbose default 0 x anonymous use anonymous bind for queries default X gsi use GSI GSSAPI bind for queries v version print version information h help print help page Default values of some options e g timeout or giislist are shared with other client commands and can be specified in the user configuration file Section 3 3 Usage examples discover resources available for the user ngtest R print out certificate information ngtest E submit a test job ngtest J 1 submit a test job to a selected site ngtest J 1 c grid place org submit a test job with dianostics printout ngtest J 1 d 2 Test job descriptions 8 2 1 This test job calculates prime numbers for 2 minutes and saves the list The source code for
145. utes is needed the following construc tion can be used In expressions the following operands are allowed Commented lines should start with and be closed with Comments can not be nested Multiple job descriptions in one file are realized via a standard Globus RSL multi request operand which should precede the multiple job descriptions The xRSL attributes can be written in a single string or split in lines arbitrary blank spaces between attribute value pairs and inside relations are ignored 7 1 1 URLs File locations in ARC can be specified both as local file names and as Internet standard Uniform Resource Locators URL There are also some additional URL options that can be used The following transfer protocols and metadata servers are supported 7 1 TASK DESCRIPTION LANGUAGE XRSL 43 ftp ordinary File Transfer Protocol FTP gsiftp GridFTP the Globus enhanced FTP protocol with security encryption etc developed by The Globus Alliance http ordinary Hyper Text Transfer Protocol HTTP with PUT and GET methods using multiple streams https HTTP with SSL v3 httpg HTTP with Globus GSI ldap ordinary Lightweight Data Access Protocol LDAP srm Storage Resource Manager SRM service 8 se ARC Smart Storage Element service 15 lfc LFC catalog and indexing service of EGEE gLite rc Globus Replica Catalog RC rls Globus Replica Location Service RLS 18 file local to the
146. while the Queue Details module lists the jobs in a given queue the Job Information window gives an overview of all the Grid jobs on a cluster 2 Owner this field is also identical to the one in the Queue Details window the user s name is linked to the User Information module Section 10 5 which displays all the resources available for a given user and the list of the user s jobs 3 Queue the name of the queue is liked to the Queue Details window Section 10 3 which gives a snapshot of the queue status including all the Grid jobs submitted to a particular queue running or waiting 4 Cluster name clicking on the cluster name brings up the Cluster Description window Section 10 2 which gives a general overview of a given cluster and the status of its queues those available for the Grid users 98 CHAPTER 10 THE GRID MONITOR N NorduGrid Jobs Netscape Job ID gsiftp Ascf nbi dk 2811 jobs 1 7462021 731217695386 Attribute Value Distinguished name nordugrid pbsjob globalid qsiftp lscf nbi dk 2811 jobs 1746202 objectClass Mds nordugrid pbsjob ID gsiftp lscf nbi dk 2811 jobs 17462021731217695386 Owner 0 Grid O NorduGrid OU nbi dk CN Jakob Langgaard Nielsen Job name dc1 002000 simul 01217 hlt pythia_jet_17 Job submi time GMT 05 08 2002 12 21 11 Execution queue gridlong Execution cluster Iscf nbi dk Job status INLRMS R Used CPU time 421 Used wall time 422 Used memory KB 94764 Requested CPU
147. with q c and 1 options t seconds timeout in seconds This is not a timeout for staging the file s but a timeout for calls to the service per forming the staging A timeout of this kind does not necessarily mean that the staging request has failed v print version information h short help Arguments URL file URL currently only srm meta protocol is sup ported The command will return a request ID that should be used to monitor the status with q option or cancel the request c option A list of currently active requests can be found using the 1 option If either of these three options are used URL of the file server performing the staging must also be specified through the s option this usually consists of the protocol srm and hostname of the URL s passed in the inital request Every URL in the request must have the same host name as the command sends request to one file server at a time Wildcards are allowed at the end of a URL and URLs can be directories but r must be used if the contents of a directory are to be staged If a given URL is a directory r 1 will stage all files in that directory Example ngstage srm srm ndgf org pnts ndgf org data atlas tape file 1MM ngstage q 2139909111 s srm srm ndgf org This requests a file to be staged and queries request status After the first time a successful request is queried it is internally marked as aborted by the system For any subseq
148. y certificates and or X509_CERT_DIR folder and to make sure that it does contain certificates and signing policy files of your certificate issuer CA and the friendly CAs A typical listing of the folder should look as follows gt ls 1 X509_CERT_DIR 1f0e8352 0 1f0e8352 signing_policy bc870044 0 bc870044 signing policy 32 CHAPTER 4 GRID CERTIFICATES d64ccb53 0 Here 8 symbol file names with extension 0 are the certificates containing public keys of different CAs Different users may trust different CAs not necessarily those centrally accepted In such a case they should collect the keys of CAs they trust either in the HOME globus certificates directory or in any other place they define as X509_CERT_DIR In such a case Grid utilities will look for the keys only in the user specified directory If you have a HOME globus certificates directory make sure it contains your own CA key as well as other friendly CA keys If your central system installation is missing a key you always can install it in your HOME globus certificates directory but then you must copy all the other needed keys to this directory In general the certificates and configuration files can be located in any of the following directories etc grid security certificates NORDUGRID_LOCATION share certificates X509_CERT_DIR HOME globus certificates The latter has the precedence as each user is free to chose whom to trust 4 2
149. you do not belong to or do not qualify for any existing VO you always can establish your own VO and be your own manager You will have to contact the Grid resource owners one by one and negotiate resource allocation with them Feel free to contact nordugrid support nordugrid org for initial instructions or possible assistance Chapter 6 Grid Session Before starting your first Grid session check whether the following have been accomplished 1 You have the ARC client installed see Chapter 3 2 You have a valid Grid certificate see Section 4 3 You are authorised at at least one Grid site see Section 5 6 1 Logging Into The Grid Access to the Grid resources in the Globus world is made via a so called prory a kind of a temporary token which you pass to the Grid services allowing them to act on your behalf Initialization of the proxy is done via the standard Globus command This command searches for your public certificate and private key in the default directory HOME globus and upon a pass phrase confirmation creates a file containing your Grid proxy in the tmp directory of your computer The proxy file name typically starts with x509up_u which is followed by your UNIX Linux UID Your Globus proxy is public hence anybody having access to it can impersonate you To minimize this risk proxies have limited lifetime By default a proxy is valid for 24 hours This however means that if your Grid task will las

The Advanced Resource Connector User Guide

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