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www.see-grid-sci.eu
SEE-GRID-SCI
Hands-On Session:Using Grid
Vladimir SlavnicInstitute of Physics, Belgrade
The SEE-GRID-SCI initiative is co-funded by the European Commission under the FP7 Research Infrastructures contract no. 211338
Regional SEE-GRID-SCI Meteo Training Faculty of Electrical Engineering Banja Luka
July 2-3, 2009
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Setting up the user account
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Setting up the user accountUser Interface (UI)
Access point to Grid
User must have a local account on machine
Basic grid operations: list resources suitable for job submit jobs cancel jobs retrieve job output show job status file operations …
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Setting up the user account Certificates
Grid passportX.509Subject Name (SN)
/C=RS/O=AEGIS/OU=Institute of Physics Belgrade/CN=Vladimir SlavnicCertification Authority (CA)Obtaining a certificate$ grid-cert-request
userkey.pem usercert_request.pem usercert.pemVirtual Organisation (VO)
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Setting up the user accountSetting up
.globusRight permissions:– 444 usercert.pem– 400 userkey.pemChecking a certificate$ grid-cert-info$ grid-cert-info -subject (-enddate) (-issuer)$ openssl verify -CApath \
/etc/grid-security/certificates/ ~/.globus/usercert.pem$ grid-proxy-init -verify
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Setting up the user account Proxies
Standard proxies$ grid-proxy-init$ grid-proxy-info$ grid-proxy-destroyVOMS proxies
– Group – Role
$ voms-proxy-init -voms <vo>$ voms-proxy-init –voms <alias>:<group name>[Role=<role name>]$ voms-proxy-info (-all)
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Setting up the user accountProxy renewal
MyProxy server$ echo $MYPROXY_SERVER$myproxy-init -s <myproxy_server> -d -n$myproxy-info -s <myproxy_server> -d$myproxy-destroy -s <myproxy_server> -d
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Information service
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INFORMATION SERVICElcg-infosites & lcg-info
$lcg-infosites --vo <vo> <option> -v <verbosity> -f <site> --is <bdii>
$ lcg-infosites --vo seegrid ce $ lcg-infosites --vo seegrid se $ lcg-infosites --vo seegrid closeSE
$ lcg-info –list-attrs $ lcg-info --list-se --query 'SE=se.csk.kg.ac.yu' --
attrs CloseCE
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Regional SEE-GRID-SCI Grid MeteoTraining , Faculty of Electrical Engineering Banja Luka, July 2-3, 2009 10 10
INFORMATION SERVICEldap
ldap search examples # RESOURCE ldapsearch -x -H ldap://ce64.phy.bg.ac.yu:2170/ -
b “Mdsvo-name=resource,o=Grid” # sBDII ldapsearch -x -H ldap://ce64.phy.bg.ac.yu:2170 -
b mds-voname=AEGIS01-PHY-SCL,o=grid # top-level BDII
ldapsearch -x -H ldap://bdii.phy.bg.ac.yu:2170/ -b 'Mds-voname=local,o=Grid'
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WatG Browser
Web based Grid Information System browser
Visualization of BDII information
Highly responsive tool because it supportspartial refreshes and desynchronization of a
web page.
Developed with Google Web Toolkit (GWT)open source Java software development framework.
'
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WatG Browser
http://watgbrowser.scl.rs:8080/
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Data management
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DATA MANAGEMENT
Storage element Classic SE LCG Disk pool manager CASTOR
Storage Resource Manager (SRM)
LFC Concept
lfc and lcg commands
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DATA MANAGEMENTGrid file
LFN – Logical File NameGUID - Grid Unique IdentifierSURL – Storage URL
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DATA MANAGEMENTLFC scheme
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DATA MANAGEMENTLFC commands
echo $LFC_HOSTlfc-ls - List file/directory entries in a directorylfc-mkdir - Create directorylfc-ln - Make a symbolic link to a file/directorylfc-ls - List file/directory entries in a directorylfc-chmod- Change access mode of a LFC file/directorylfc-chown - Change owner and group of a LFC file/directorylfc-getacl - Get file/directory access control listslfc-setacl - Set file/directory access control lists
• …
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DATA MANAGEMENTLFC commands examples (1)
Listing the entries of a LFC directory $ lfc-ls /grid/seegrid/vlada
new_file result
Creating directories in the LFC $ lfc-mkdir /grid/seegrid/vlada/new_dir $ lfc-ls -l /grid/seegrid/vlada drwxrwxr-x 0 165 101 0 Feb 19 00:30 new_dir -rw-rw-r-- 1 165 101 27 Feb 18 01:08 new_file -rw-rw-r-- 1 165 101 83 Feb 15 00:30 result
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DATA MANAGEMENTLFC commands examples (2)
Creation of symbolic links $ lfc-ln -s /grid/seegrid/vlada/result \ /grid/seegrid/vlada/result_link $ lfc-ls -l /grid/seegrid/vlada/result_link lrwxrwxrwx 1 165 101 0 Feb 19 00:42 /grid/seegrid/vlada/rezult_link ->
/grid/seegrid/vlada/rezultAdding metadata information to LFC entries$ lfc-setcomment /grid/seegrid/vlada/result "best result"
$ lfc-ls --comment /grid/seegrid/vlada/result /grid/seegrid/vlada/result best result
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DATA MANAGEMENTlcg_utils-Replica Management
echo $LCG_GFAL_INFOSYSlcg-cp Copies a Grid file to a local destination(download)lcg-cr Copies a file to a SE and registers the file in the
catalogue (upload)lcg-del Deletes one file (either one replica or all
replicas)lcg-rep Copies a file from one SE to another SE and
registers it in the catalogue (replicate)lcg-gt Gets the TURL for a given SURL and transfer
protocol
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DATA MANAGEMENTlcg_utils-File Catalogue Interaction
lcg-aa Adds an alias in the catalogue for a given GUIDlcg-ra Removes an alias in the catalogue for a given
GUIDlcg-rf Registers in the catalogue a file residing on an
SElcg-uf Unregisters in the the catalogue a file residing on an SElcg-la Lists the aliases for a given LFN, GUID or SURLlcg-lr Lists the replicas for a given LFN, GUID or SURLlcg-ls Lists file information for given SURLs or LFNs
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DATA MANAGEMENTlcg_utils examples(1)
Upload a file $ lcg-cr file:/home/vlada/banja_luka/mpi.jdl guid:830e7a82-f9fb-4c04-aafd-e24a5f25acdb
specify lfn: $ lcg-cr -l lfn:/grid/seegrid/vlada/mpi \ file:/home/vlada/banja_luka/mpi.jdl guid:25fdcd16-bc76-4458-9c1a-8c597fb33194
Replicate a file (one replica per SE) $ lcg-rep -d grid15.rcub.bg.ac.yu \
lfn:/grid/seegrid/vlada/mpi
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DATA MANAGEMENTlcg_utils examples(2)
List replicas$ lcg-lr lfn:/grid/seegrid/vlada/mpi
srm://grid15.rcub.bg.ac.yu/dpm/rcub.bg.ac.yu/home/ae
gis/generated/2009-02-18/file8f99889c-c00a-4b7b-89d3-d9abf66ba103
srm://se.phy.bg.ac.yu/dpm/phy.bg.ac.yu/home/aegis/generated/2009-02-18/file576fbae0-ba6a-4b21-a205-3d115b2cf7fbList guid
$ lcg-lg lfn:/grid/seegrid/vlada/mpi guid:25fdcd16-bc76-4458-9c1a-8c597fb33194
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DATA MANAGEMENTlcg_utils examples(3)
Listing files and directories $ lcg-ls -l lfn:/grid/seegrid/vlada/mpi -rw-rw-r-- 1 165 101 349
lfn:/grid/seegrid/vlada/mpiCopying files out of the Grid (download)
$ lcg-cp lfn:/grid/seegrid/vlada/mpi \ file:/home/vlada/banja_luka/down/mpiDeleting replicas
lcg-del srm://grid15.rcub.bg.ac.yu/dpm/rcub.bg.ac.yu/home/aegis/generated/2009-02-19/file36d25d0d-ee61-477eb667-40b3791786a4$ lcg-del -a lfn:/grid/aegis/vlada/mpi
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Data Management Web Portal
Developed by Belgrade University Computer CentreUsage Data Management Logical Files Development Environments and Portals
Description Enables easy interaction with grid file catalogue using
simple Web-based user interface. Based on SEE-GRID File Management Java API. Can be integrated with other Web applications.
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Data Management Web Portal
Available features Directory browsing Directory management operations: creating new
subdirectories, renaming/moving and deleting directories, replicating directory content, reading directory attributes and permissions.
Copying and registering of new files to the catalog as well as file deletion.
Reading file attributes and permissions. Replica & alias management operations. Upload and download of files with possible integration
of application-defined upload handlers
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Data Management Web Portal
• http://grid02.rcub.bg.ac.yu:8080/NewDataManagement/login-REFS.jsp
• http://grid02.rcub.bg.ac.yu:8080/NewDataManageme nt/login-WRF-ARW.jsp
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Job operations
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JDL
JDL (Job Description Language) fileattribute = expression
Executable = "test.sh"; Arguments = "fileA fileB";
StdOutput = "std.out";StdError = "std.err";InputSandbox = {"test.sh", "fileA", "fileB"};OutputSandbox = {"std.out", "std.err"};
Environment = {“AEGIS_PATH=$HOME/AEGIS"};Requirements = RegExp("ce64.phy.bg.ac.rs*",other.GlueCEUniqueID);
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SUBMITING JOBS
Generating proxy $ voms-proxy-init -voms <VO_NAME>
Myproxy $ myproxy-init -d –n -s <myproxy_server>
Delegate proxy to WMS $ glite-wms-job-delegate-proxy -d <delegID>
Job matching $ glite-wms-job-list-match -a test.jdl
Job submission $ glite-wms-job-submit -d <delegID> -i
<job_id_file> test.jdl
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MONITORING JOBS
View status of job $ glite-wms-job-status <job_ID> $ glite-wms-job-status -i <job_id_file>
View logging details $ glite-wms-job-logging-info -v
<verbosity_level> <job_ID> $ glite-wms-job-logging-info -v
<verbosity_level> -i <job_id_file>
Verbosity level can be from 0 to 3.
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CANCELING JOBS AND RETRIEVING OUTPUT
Cancel a job $ glite-wms-job-cancel <job_ID> $ glite-wms-job-cancel -i <job_id_file>
Retrieve files from Output Sandbox $ glite-wms-job-output <job_ID> $ glite-wms-job-output -i <job_id_file> $ glite-wms-job-output --dir <directory_path>
<job_ID>
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ADVANCED JOB TYPES
Job Collection - submission of a set of jobs whose description files are placed in one directory Parametric Jobs - submission of a set of jobs having the same descriptions apart from the values of the parametric attributes. Use when your jobs differs only in argument values or input/output files. DAG jobs (Direct Acyclic Graphs) - submission of a set of jobs where the input, output, or execution of one or more jobs depends on one or more other jobs. Interactive JobsMPI Jobs
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JOB COLLECTION
Type = "Collection";InputSandbox = (“fileA”);Requirements = RegExp("ce64.phy.bg.ac.yu*",other.GlueCEUniqueID);nodes = {[JobType = "normal";Executable = "/bin/hostname";Arguments = "-i";StdOutput = "out";InputSandbox = (root.InputSandbox, “fileB”);StdError = "err";OutputSandbox ={"out","err"};],[JobType = "Normal";Executable = "/bin/date";StdOutput = "date";StdError = "err";OutputSandbox= {"date"};]};
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JOB COLLECTIONsubmission
Collection defined in one file $ glite-wms-job-submit -a -o id collection.jdl
Folder contains jdl files $ glite-wms-job-submit -a --collection jdl
• Collection status view• Collection output
$ glite-wms-job-output -i id --dir kolekcija $ ls kolekcija
ids_nodes.map Node_0 Node_1
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PARAMETRIC JOBS
Type = "Job";JobType = "Parametric";Executable = "/bin/echo";Arguments = "_PARAM_";Parameters = {red, green, blue};StdOutput = "colour_PARAM_.txt";StdError = "error_PARAM_.txt";OutputSandbox = {"colour_PARAM_.txt","error_PARAM_.txt"};
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PARAMETRIC JOBS
Type = "Job";JobType = “Parametric";
Executable = "exec"; StdInput = "input_PARAM_.txt";
StdOutput = "output_PARAM_.txt";Parameters = 10;ParameterStart = 1;ParameterStep = 1;InputSandbox = {"<exec>", "<param_file>"};OutputSandbox = {"output_PARAM_.txt"};
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DAG JOBS[
Type = "dag";InputSandbox = {"job.sh"};Nodes = [ nodeA = [
file ="A.jdl" ; ]; nodeB = [
file =“b.jdl" ;]; nodeC = [ file =“C.jdl" ;]; nodeD = [ Description = [ JobType = "Normal"; Executable = "job.sh"; StdOutput = "std.out"; StdError = "std.err"; InputSandbox = {root.InputSandbox[0]}; OutputSandbox = {"std.out","std.err"}; ]; ];];Dependencies = { {nodeA,nodeB},{nodeA,nodeC},{{nodeB,nodeC},nodeD}};]
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Regional SEE-GRID-SCI Grid MeteoTraining , Faculty of Electrical Engineering Banja Luka, July 2-3, 2009 39 39
MPI JOBS
JDL file:Type = "Job";
JobType = "MPICH"; NodeNumber = 5; Executable = "mpi.sh"; Arguments = "mpi"; StdOutput = "mpi.out"; StdError = "mpi.err"; InputSandbox = {"mpi.sh","mpi.c"}; OutputSandbox =\
{"mpi.err","mpi.out","mpiexec.out"};
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Regional SEE-GRID-SCI Grid MeteoTraining , Faculty of Electrical Engineering Banja Luka, July 2-3, 2009 40 40
LINKS
http://aegis-ca.rcub.bg.ac.yu/https://edms.cern.ch/file/722398//gLite-3-UserGuide.pdfhttp://wiki.egee-see.org/index.php/Quick_User_Guide_for_Submitting_Jobshttps://edms.cern.ch/document/590869/1/ http://wiki.egee-see.org/index.php/SEE-GRID_MPI_User_Guidehttp://wiki.egee-see.orghttp://wiki.egee-see.org/index.php/Data_Management_Web_Portal_-_User_Guide