SEE-GRID-SCI Hands-On Session: Using Grid Vladimir Slavnic Institute of Physics, Belgrade Serbia The...

www.see-grid-sci.eu

SEE-GRID-SCI

Hands-On Session:Using Grid

Vladimir SlavnicInstitute of Physics, Belgrade

[email protected]

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

Regional SEE-GRID-SCI Grid MeteoTraining , Faculty of Electrical Engineering Banja Luka, July 2-3, 2009 2 2

Setting up the user account


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 …


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)


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


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)


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


Information service


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


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'


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.

'


WatG Browser

http://watgbrowser.scl.rs:8080/

http://watgbrowser.scl.rs:8080/


Data management


DATA MANAGEMENT

Storage element Classic SE LCG Disk pool manager CASTOR

Storage Resource Manager (SRM)

LFC Concept

lfc and lcg commands


DATA MANAGEMENTGrid file

LFN – Logical File NameGUID - Grid Unique IdentifierSURL – Storage URL


DATA MANAGEMENTLFC scheme


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

• …


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


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


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


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


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



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



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


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.



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



• http://grid02.rcub.bg.ac.yu:8080/NewDataManagement/login-REFS.jsp

• http://grid02.rcub.bg.ac.yu:8080/NewDataManageme nt/login-WRF-ARW.jsp

http://grid02.rcub.bg.ac.yu:8080/NewDataManagement/login-REFS.jsp

http://grid02.rcub.bg.ac.yu:8080/NewDataManagement/login-REFS.jsp

http://grid02.rcub.bg.ac.yu:8080/NewDataManageme%20nt/login-WRF-ARW.jsp

http://grid02.rcub.bg.ac.yu:8080/NewDataManageme%20nt/login-WRF-ARW.jsp


Job operations


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);


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


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.


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>


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


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"};]};


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


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"};


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"};


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}};]


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"};


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

http://aegis-ca.rcub.bg.ac.yu/

https://edms.cern.ch/file/722398/gLite-3-UserGuide.pdf

https://edms.cern.ch/file/722398/gLite-3-UserGuide.pdf

http://wiki.egee-see.org/index.php/Quick_User_Guide_for_Submitting_Jobs

http://wiki.egee-see.org/index.php/Quick_User_Guide_for_Submitting_Jobs

https://edms.cern.ch/document/590869/1/

http://wiki.egee-see.org/index.php/SEE-GRID_MPI_User_Guide

http://wiki.egee-see.org/index.php/SEE-GRID_MPI_User_Guide

http://wiki.egee-see.org/

SEE-GRID-SCI Hands-On Session: Using Grid Vladimir Slavnic Institute of Physics, Belgrade Serbia The...

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