GRID commands lines

1. GRID commands lines Original presentation from David Bouvet CC/IN2P3/CNRS

2. Plan of this presentation • Job submission • proxy • JDL • submit command lines • Data management • basic command lines • Data management in the job • LFC data logical file catalog

3. Proxy creation and job submission • voms-proxy-init -voms egeode • Cannot find file or dir: /afs/in2p3.fr/home/d/dbouvet/.glite/vomsesYour identity: /O=GRID-FR/C=FR/O=CNRS/OU=CC-LYON/CN=David BouvetEnter GRID pass phrase:Creating temporary proxy ........................................... DoneContacting cclcgvomsli01.in2p3.fr:15001 [/O=GRID-FR/C=FR/O=CNRS/OU=CC-LYON/CN=cclcgvomsli01.in2p3.fr] "egeode" DoneCreating proxy .................................... DoneYour proxy is valid until Sat Nov 4 02:56:14 2006 • voms-proxy-info • subject : /O=GRID-FR/C=FR/O=CNRS/OU=CC-LYON/CN=David Bouvet/CN=proxyissuer : /O=GRID-FR/C=FR/O=CNRS/OU=CC-LYON/CN=David Bouvetidentity : /O=GRID-FR/C=FR/O=CNRS/OU=CC-LYON/CN=David Bouvettype : proxystrength : 512 bitspath : /tmp/x509up_u2028timeleft : 11:58:53 • voms-proxy-info -all • subject : /O=GRID-FR/C=FR/O=CNRS/OU=CC-LYON/CN=David Bouvet/CN=proxyissuer : /O=GRID-FR/C=FR/O=CNRS/OU=CC-LYON/CN=David Bouvetidentity : /O=GRID-FR/C=FR/O=CNRS/OU=CC-LYON/CN=David Bouvettype : proxystrength : 512 bitspath : /tmp/x509up_u2028timeleft : 11:58:25=== VO egeode extension information ===VO : egeodesubject : /O=GRID-FR/C=FR/O=CNRS/OU=CC-LYON/CN=David Bouvetissuer : /O=GRID-FR/C=FR/O=CNRS/OU=CC-LYON/CN=cclcgvomsli01.in2p3.frattribute : /egeode/Role=NULL/Capability=NULLtimeleft : 11:58:25

4. JDL job creation • JDL : Job Distinguish Language • A minimum of files commands and attributs are specified : • The program to be executed by the job and input arguments • Save output and error messages in files • Save the output result (OutputSandbox) • JDL simple example : • Executable = "/bin/echo ";Arguments = "Hello World ";StdOutput = "message.txt ";StdError = "stderror ";OutputSandbox = {" message.txt", "stderror "}; • Ex: • Executable = “gridTest”;StdError = “stderr.log”;StdOutput = “stdout.log”;InputSandbox = {“/home/joda/test/gridTest”};OutputSandbox = {“stderr.log”, “stdout.log”};InputData = “lfn:testbed0-00019”;DataAccessProtocol = “gridftp”;Requirements = other.Architecture==“INTEL” && \ other.OpSys==“LINUX” && other.FreeCpus\ >=4;Rank = “other.GlueHostBenchmarkSF00”; Job attributs Data attributs Grid resources attributs

5. Job submission commands on the UI • edg-job-submit • Submit the job • Return the job ID • edg-job-list-match • Query the RB and list all execution places that are matching job requirements without executing the job. • edg-job-cancel • Just cancel the job • edg-job-status • Query the RB and return job status • edg-job-get-output • Retrieve and return the job output to the user • edg-job-get-logging-info • Return all logging information about the submitted job, all this information from the WMS is usefull for debug

6. Example: edg-job-list-match ui2$ edg-job-list-match myjobJDL.jdlSelected Virtual Organisation name (from JDL): egeodeConnecting to host rb1.egee.fr.cgg.com, port 7772*************************************************************************** COMPUTING ELEMENT IDs LIST The following CE(s) matching your job requirements have been found: *CEId* ce1.egee.fr.cgg.com:2119/jobmanager-lcgpbs-egeode grid10.lal.in2p3.fr:2119/jobmanager-pbs-egeode gridgate.cs.tcd.ie:2119/jobmanager-pbs-egee hudson.datagrid.jussieu.fr:2119/jobmanager-lcgpbs-egeode marseillece01.mrs.grid.cnrs.fr:2119/jobmanager-pbs-egeode polgrid1.in2p3.fr:2119/jobmanager-pbs-egeode scaicl0.scai.fraunhofer.de:2119/jobmanager-lcgpbs-egeode cclcgceli02.in2p3.fr:2119/jobmanager-bqs-short cclcgceli02.in2p3.fr:2119/jobmanager-bqs-long cclcgceli02.in2p3.fr:2119/jobmanager-bqs-medium***************************************************************************

7. RB/WMS match making • The RB Resource Broker is the main component of the WMS Workload Management System. • It should find the best computing (CE) and resource site for the current job • It query the mains information system of the grid the evaluate this information. • The chosen CE must match to all job requirements if more than one CE is matching theses requirements then the CE with the best rank will be chosen.

8. LCG commands to query resources • lcg-infosites --vo egeode ce#CPU Free Total Jobs Running Waiting ComputingElement---------------------------------------------------------- 58 15 0 0 0 ce1.egee.fr.cgg.com:2119/jobmanager-pbs-egeode 132 107 0 0 0 grid10.lal.in2p3.fr:2119/jobmanager-pbs-egeode 88 44 0 0 0 polgrid1.in2p3.fr:2119/jobmanager-pbs-egeode 167 62 105 85 20 cclcgceli02.in2p3.fr:2119/jobmanager-bqs-long 484 483 1 0 1 cclcgceli02.in2p3.fr:2119/jobmanager-bqs-short 484 436 48 25 23 cclcgceli02.in2p3.fr:2119/jobmanager-bqs-medium 62 0 0 0 0 marseillece01.mrs.grid.cnrs.fr:2119/jobmanager-pbs-egeode 5 5 0 0 0 hudson.datagrid.jussieu.fr:2119/jobmanager-lcgpbs-egeode 30 1 2 0 2 scaicl0.scai.fraunhofer.de:2119/jobmanager-lcgpbs-egeode 42 33 13 13 0 gridgate.cs.tcd.ie:2119/jobmanager-lcgpbs-egee

9. DATA management tools • Replica-Manager tool RM • LCG File Catalog (LFC) is storing all files location • Data transfers on the grid are mainly using: gsiftp It’s a FTP transfer protocol over the grid authentication and security layer. It is using certificates and proxy instead of password. • The replica-manager tool includes all facilities and interactions between gsiftp and LFC for file creation and file replication • Resource Broker RB • the RB can handle small data transfers from/to jobs • the RB can use the LFC to find data and to send it to the job

10. Data management commands (1) • How to copy a data file on to the GRID ? • In this exemple I want to copy the file : /home/myhome/myfile01 on the SE (storage element) se1.private.gridprototype and the register it in the LFC by the name: myfile01.testthe command to use is: lcg-cr -d se1.private.gridprototype -l lfn:/grid/egeode/myfile01.test --vo egeode file:/home/myhome/myfile01 • Storage Element – data server on the GRID • Logical File Name – symbolic (or logical) file name to call and manipulate the file on the grid without precising the real file location. • The lcg-cr command returns a grid unique ident: “GUID” : guid:76373236-b4c7-11d8-bb5e-eba42b5000d0 • GUID (Global Grid Unique ID) are permanents LFN names are temporary

11. Data management commands (2) • How to find data with listReplicas (lr) • lcg-lr --vo egeode lfn:/grid/egeode/myfile01.test # via LFN sfn://se1.private.gridprototype/grid/egeode/tutorial/data/generated/2004-11-10/file7115df45-b4c7-11d8-bb5e-eba42b5000d0 • lcg-lr --vo egeode \ # via GUID guid:76373236-b4c7-11d8-bb5e-eba42b5000d0 sfn:// se1.private.gridprototype/grid/egeode/tutorial/data/generated/2004-11-10/file7115df45-b4c7-11d8-bb5e-eba42b5000d0 • “replicas” means that you can create many copies of the same file on differents SE on the GRID • LFN and GUID are referencing all file copies on the GRID

12. Data management commands (3) • How to find information on LFC/DMS/SE (Data Management System) • lcg-infosites –-vo egeode se Avail Space(Kb) Used Space(Kb) Type SEs----------------------------------------------------------181360000 73300000 n.a se1.egee.fr.cgg.com122076 58659616 n.a grid11.lal.in2p3.fr60240000 715760000 n.a grid05.lal.in2p3.frn.a n.a n.a polgrid2.in2p3.fr381870000 2838130000 n.a polgrid4.in2p3.fr1870977288 1594260 n.a cclcgseli01.in2p3.fr103160000 171880000 n.a sedpm.mrs.grid.cnrs.fr34253292 753684 n.a barentz.datagrid.jussieu.fr4112779628 567932436 n.a scaise-2.scai.fraunhofer.de80648588 143813576 n.a gridstore.cs.tcd.ie

13. Data management commands (4) • How to query the LFC catalog to get the symbolic (logical) view of my datas ? lfc-ls -l /grid/egeode/DATA/myProject/ -rw------- 1 103 101 7136386 Oct 19 11:17 I1133511009100.DAT-rwx------ 1 103 101 213408898 Oct 03 2006 I1133611009100.DAT-rwx------ 1 103 101 213408898 Oct 03 2006 I1133621009100.DAT-rwx------ 1 103 101 213408898 Oct 03 2006 I1133631009100.DAT-rwx------ 1 103 101 181619794 Oct 03 2006 I1133641009100.DAT-rw------- 1 103 101 3226762 Nov 29 15:20 I2222221009100.DAT-rw------- 1 103 101 3226762 Nov 29 15:36 I3333331009100.DAT-rw------- 1 103 101 10476082 Oct 19 16:41 I6666661009100.DAT-rw------- 1 103 101 108305128 Mar 30 10:24 I8888881009100.DAT-rw------- 1 103 101 993490 Feb 23 16:19 I9999991009100.DAT-rw------- 1 103 101 1574758400 Nov 28 12:33 KI.DAT-rw------- 1 103 101 6109200 Oct 19 16:39 P7777771009100.DAT

14. Local and jobs, data management (1) • JDL syntaxis to retrieve jobs output data (for small data files only!) • Output data are generated in the working directory of the worker node • At the end of the job, output data are located in the temporary directory of the RB machine. • Just use edg-job-get-output to retrieve data manually • To do it automatically in the job, you must know files names to be retrieved for example: • OutputSandbox = {“higgs.root", “graviton.HDF"}; • This method can not be applied to big data files, output data size must be less than 100 Mb

15. Local and jobs, data management (2) • Job output data will be stored in a local file • The job program should know the local file name • lcg-*-* commands are used to: • transfer and copy output data on a storage element SE • Register output data as available data on the GRID ? • Where do the job ouput data will be stored ? On which SE ? In which directory ? • The 2 possible options are : •  by default it will be the SE “local” • or you have to specify a symbolic (logical) name and directory noLFN name is generated by default

16. JDL syntaxis for data output • the JDL OutputData attribut specify the place to store data, if no LFN is precise, the WMS will choose the closest storage element SE to the current worker node WN. • At the end of the job output data files are erased from the WN • In the JDL a file for this operation is added to the sandbox : DSUpload_<unique jobstring>.out • OutputData = { [ OutputFile = “myfile01.out”; StorageElement = “se1.private.gridprototype”; LogicalFileName = “lfn:/grid/egeode/logicalmyfile01”;], [ OutputFile = “myfile02.out”; StorageElement = “se1.private.gridprototype”; LogicalFileName = “lfn:/grid/egeode/logicalmyfile02”;] };

17. JDL syntaxis for data input • Just use the field: InputSandbox InputSandbox = {“input-ntuple.root“, “job.sh”}; • Again this method can not be used for big data submission to the input of the job • InputData = “lfn:/grid/cms/myfile01.dat” • For big files you have to query data files from the LFC, it means that theses data files must have been previouly loaded to the GRID. • The RB is using the file:.BrokerInfo on the worker node WN to store information about jobs data files. • In the job execution script you can use edg-brokerinfo and lcg-*-*commands to create a local copy of the file on the WN working directory

18. Replication commands • How to duplicate data from one SE to another SE • lcg-rep --vo egeode lfn:/grid/egeode/myfile01.test\ –d se5.private.gridprototype • then if you use the list of replicas command : lcg-lr • lcg-lr --vo egeode lfn:/grid/egeode/myfile01.test • sfn://se1.private.gridprototype/grid/egeode/tutorial/data/generated/2004-11-10/file7115df45-b4c7-11d8-bb5e-eba42b5000d0sfn://se5.private.gridprototype/grid/egeode/tutorial/data/generated/2004-11-10/file3498dg93-h3b6-38s2-kf7d-ksr38h8379q7

19. LFC commands (1) • For the end user the LFC catalog (LCG File Catalog) is presented like a local file sytem. It is possible to create new directory structures in this catalog, and it is also possible to create logical links on files. • The default LFC catalog is the central main catalog of the VO. • lcg-infosites –vo egeode lfcreturn the name of the central main catalog • lcg-infosites –vo egeode lfcLocalreturn the list of local file catalog of the VO • To use a local file catalog, just change LFC_HOST variable : • export LFC_HOST=<LFC new hostname>

20. LFC commands (2) • LFC root directory stucture: • /grid/<VO_name> ( the variable LFC_HOME can be defined to point on this root ) • Commands to list the content of the catalog: • lfc-ls /grid/egeode/... • New directory creation : • lfc-mkdir /grid/egeode/.../<my_directory> • Others commands : • lfc-ln, lfc-rm, lfc-getacl, lfc-setacl...

21. Questions ?