EGEE-II INFSO-RI-031688 Enabling Grids for E-sciencE gLite Demo Yaodong Cheng CC-IHEP, Chinese...

EGEE-II INFSO-RI-031688

Enabling Grids for E-sciencE

www.eu-egee.org

gLite Demo

Yaodong ChengCC-IHEP, Chinese Academy of Sciences [email protected]

The 6th Joint Training of OMII-Europe&CNGrid, Hong Kong, 10-11 January, 2008


EGEE-II INFSO-RI-031688 The 6th Joint Training of OMII-Europe&CNGrid, Hong kong, 10-11 January, 2008 2/39

Start…

• Follow the link

http://training.omii-europe.org/Tutorials/glite3.0/Tutorials.html

• Login into UI– ssh UI_Machine -l chyd– wget

http://training.omii-europe.org/Tutorials/glite3.0/tutorial.tar.gz – tar -xvzf tutorial.tar.gz



outline

• Security– globus– VOMS

• Information Systems

• Workload Management System (WMS)

• Data Management



Security

• If you want to use grid resource, you need to:– get your certificate from trusted CA– Join a VO (dteam, gilda, atlas, cms, bes, …)

Send request to given VOMS server (web)

– Log into a UI (local or ssh remote machine)– Create your proxy

Sign a new short lived certificate using your certificate in order to vulnerability

• Proxy operations– Create– Query– Destroy



Security Demo

• List your certificate– [chyd@glitedemo2 chyd]$ ls -l ~/.globus-rw-r--r-- 1 chyd u07 2360 Jan 7 17:36 usercert.pem-rw------- 1 chyd u07 1916 Jan 7 17:36 userkey.pem

• Inspect what your public key contains– [chyd@glitedemo2 chyd]$ grid-cert-infoCertificate: Data: Version: 3 (0x2) Serial Number: 306 (0x132) Signature Algorithm: sha1WithRSAEncryption Issuer: C=CN, O=HEP, CN=gridca-cn/[email protected] Validity Not Before: May 13 13:44:22 2007 GMT Not After : May 12 13:44:22 2008 GMT Subject: C=CN, O=HEP, O=IHEP, OU=CC, CN=yaodong cheng Subject Public Key Info: Public Key Algorithm: rsaEncryption RSA Public Key: (2048 bit) Modulus (2048 bit): 00:dc:42:64:bf:1b:61:f1:75:8f:ce:9e:8f:75:a1: 3a:7d:2b:e5:41:1b:de:c1:2d:be:f0:8a:75:73:ef: …



Proxy

• Create proxy– [chyd@glitedemo2 chyd]$ grid-proxy-init Your identity: /C=CN/O=HEP/O=IHEP/OU=CC/CN=yaodong chengEnter GRID pass phrase for this identity:Creating proxy ................................................. DoneYour proxy is valid until: Tue Jan 8 21:39:29 2008

• Query proxy info– [chyd@glitedemo2 chyd]$ grid-proxy-infosubject : /C=CN/O=HEP/O=IHEP/OU=CC/CN=yaodong cheng/CN=proxyissuer : /C=CN/O=HEP/O=IHEP/OU=CC/CN=yaodong chengidentity : /C=CN/O=HEP/O=IHEP/OU=CC/CN=yaodong chengtype : full legacy globus proxystrength : 512 bitspath : /tmp/x509up_u60003timeleft : 11:59:19

• VOMS proxy – Extends the proxy with info on VO membership, group, roles– Voms-proxy-init –voms VO_NAME– VOMS-proxy-info –all– VOMS-proxy-destroy



Testing proxy

cd /home/chyd/omii/tutorial

[chyd@glitedemo2 tutorial]$ edg-job-list-match --vo dteam hostname.jdl

Selected Virtual Organisation name (from --vo option): dteam

Connecting to host lcg005.ihep.ac.cn, port 7772

***************************************************************************

COMPUTING ELEMENT IDs LIST

The following CE(s) matching your job requirements have been found:

a01-004-128.gridka.de:2119/jobmanager-pbspro-gLite3

…

apcpc79.in2p3.fr:2119/jobmanager-pbs-dteam

[chyd@glitedemo2 tutorial]$ grid-proxy-destroy

[chyd@glitedemo2 tutorial]$ edg-job-list-match --vo dteam hostname.jdl

Selected Virtual Organisation name (from --vo option): dteam

**** Error: UI_PROXY_NOT_FOUND ****

Proxy certificate not found.



Information Demo



Information system

• The Information System (IS) provides information about grid´s resources and their actual status

• Resource level: Grid Resource Information Server (GRIS)– One GRIS on top of each CE, SE, RB, MyProxy (no WNs).– Sensors and scripts get status of concrete resources statically (e.g.

GlueCEUniqueID) or dynamically (e.g. GlueCEStateWaitingJobs) • Site level: Grid Index Information Server (GIIS)

– Compiles all the information of the different GRISs in a site.– LCG-2 recommends using a BDII instead of a GIIS

Improves robustness and stability. Called the site BDII.

• Top level: Berkeley DB Information Index (BDII) – Keeps all Grid information about the VOs (generally only one). – Stores information from local BDIIs or GIISs in its database. – Only queries sites that are included in a configuration file.



BDII

RB Local GRIS

SELocal GRIS

CE Local GRIS

BDII-A BDII-B

SELocal GRIS

SELocal GRIS

CE Local GRIS

SELocal GRIS

BDII-C

Site 1 Site 2 Site 3

Site BDII Site BDII Site BDII



lcg-infosites

• Actually just a perl script wrapping a series of LDAP commands – allow the user to retrieve information on Grid resources for the

most common cases

• Query CE– [chyd@glitedemo2 tutorial]$ lcg-infosites --vo dteam ce|more#CPU Free Total Jobs Running Waiting ComputingElement

----------------------------------------------------------

121 0 0 0 0 ce.phy.bg.ac.yu:2119/jobmanager-pbs-dteam

457 1 0 0 0 ce64.phy.bg.ac.yu:2119/jobmanager-pbs-dteam

126 2 0 0 0 fangorn.man.poznan.pl:2119/jobmanager-pbs-dteam

32 2 0 0 0 agh2.atlas.unimelb.edu.au:2119/jobmanager-lcgpbs-dteam – lcg-infosites –v 1 or 2

-v 1: Only the names of the queues are given -v 2: more information, RAMMemory, Operation system and its

version, the processors



lcg-infosites (cont.)

• Query SE– [chyd@glitedemo2 tutorial]$ lcg-infosites --vo dteam se

Avail Space(Kb) Used Space(Kb) Type SEs----------------------------------------------------------16070000000 34 n.a se.phy.bg.ac.yu4378660000 301320000 n.a se1.egee.man.poznan.pl21530000000 2108852 n.a agh3.atlas.unimelb.edu.au

– Obtain which SE is closest to which CE. The term "close" in grids can have several interpretations including

physical distance apart and speed of data access (available bandwidth)

The closest SE to a CE is defined by the manager of the CE. To see the closet SE to each CE use the command: [chyd@glitedemo2 tutorial]$ lcg-infosites --vo dteam closeSE Name of the CE: grid-ce.lns.infn.it:2119/jobmanager-lcgpbs-infinite

grid-se.lns.infn.it Name of the CE: t2-ce-01.mi.infn.it:2119/jobmanager-lcgpbs-cert t2-se-01.mi.infn.it



Workload Management System



Simple job

• cd /home/chyd/omii/tutorial• more hostname.jdl

# Type = "Job";

JobType = "Normal";

Executable = "/bin/hostname";

StdOutput = "hostname.out";

StdError = "hostname.err";

OutputSandbox = {"hostname.err","hostname.out"};

Arguments = "-f";

ShallowRetryCount = 3;

RetryCount = 0;

• edg-job-submit --vo dteam -o jobid hostname.jdl• more jobid ###Submitted Job Ids###

https://lcg005.ihep.ac.cn:9000/YJ9ZXtspVpiaFHwxUGr36g

• edg-job-status -i jobid



hostname.jdl

• JobType = "Normal"; – The type of job to run. One of: Normal (simple, sequential job), interactive,

MPICH • Executable = "/bin/hostname";

– The executable that is eventually run on the worker node.• StdOutput = "hostname.out";

– All the standard output of the job will be stored in the named file • StdError = "hostname.err";

– All the standard output of the job will be stored in the named file• OutputSandbox = {"hostname.err","hostname.out"};

– List of files created by the job which have to be retrieved. • Arguments = "-f";

– The arguments passed to the executable as a string• ShallowRetryCount = 3;

– If the job fails before arriving at the worker node the number of times to attempt resubmitting the job.

• RetryCount = 0; – If the job fails after arriving at the worker node the number of times to

attempt resubmitting the job



Get output

• edg-job-status -i jobidStatus info for the Job : https://lcg005.ihep.ac.cn:9000/YJ9ZXtspVpiaFHwxUGr36g

Current Status: Done (Success)Exit code: 0Status Reason: Job terminated successfullyDestination: dgc-grid-35.brunel.ac.uk:2119/jobmanager-lcgpbs-rampdownreached on: Tue Jan 8 03:02:36 2008

• edg-job-get-output -i jobidOutput sandbox files for the job: - https://lcg005.ihep.ac.cn:9000/YJ9ZXtspVpiaFHwxUGr36g have been successfully retrieved and stored in the directory: /tmp/jobOutput/chyd_YJ9ZXtspVpiaFHwxUGr36g

• cd /tmp/jobOutput/chyd_YJ9ZXtspVpiaFHwxUGr36g• [lcg003] /tmp/jobOutput/chyd_YJ9ZXtspVpiaFHwxUGr36g

> lshostname.err hostname.out

• more hostname.out dgc-grid-37.brunel.ac.uk



env.jdl

• edg-job-submit --vo dteam -o jobid env.jdl• More env.jdl

JobType = "Normal";

Executable = "/bin/bash";

StdOutput = "env.out";

StdError = "env.err";

InputSandbox = {"getenv.sh"};

OutputSandbox = {"env.err","env.out","Env.txt"};

Arguments = "getenv.sh";


RetryCount = 0;

• InputSandbox = {"getenv.sh"}; – Not available on any of the worker nodes

• Executable = "/bin/bash";Arguments = "getenv.sh"; – File permissions may change when “getenv.sh” is transferred



env.jdl

• OutputSandbox = {"env.err","env.out","Env.txt"}; – Env.tex is produced by getenv.sh, which looks like #!/bin/bash

host=`hostname -f`echo Getting Env On $hostenv > Env.txt

• edg-job-status -i jobidCurrent Status: Done (Success)Exit code: 0Status Reason: Job terminated successfullyDestination: lcg2ce.ific.uv.es:2119/jobmanager-pbs-dteamLreached on: Tue Jan 8 03:42:08 2008

• edg-job-get-output -i jobid• ls –l /tmp/jobOutput/chyd_m23nUzTmKg9ftHzyGtd6yQ

-rw-r--r-- 1 chyd zh 0 Jan 8 11:51 env.err-rw-r--r-- 1 chyd zh 32 Jan 8 11:51 env.out-rw-r--r-- 1 chyd zh 4450 Jan 8 11:51 Env.txt



Specify requirements

• more req1.jdl # Type = "Job";

JobType = "Normal";

Executable = "/bin/bash";

StdOutput = "env.out";

StdError = "env.err";

InputSandbox = {"getenv.sh"};

OutputSandbox = {"env.err","env.out","Env.txt"};

Arguments = "getenv.sh";


RetryCount = 0;

Requirements = (other.GlueCEUniqueID == "moss-g4.man.poznan.pl:2119/blah-pbs-omiieurope");

• You can get these requirements from information system– lcg-infosites– lcg-info



Data Management DEMO



Environment variables

• $ echo $LCG_GFAL_INFOSYS– lcg007.ihep.ac.cn:2170

• echo $LCG_CATALOG_TYPE

– lfc• echo $LFC_HOST

– gilda02.ihep.ac.cn

• If one or more of them has different or empty value, please set it (them) in this way: for example– export LCG_GFAL_INFOSYS=lcg007.ihep.ac.cn:2170– export LCG_CATALOG_TYPE=lfc– export LFC_HOST=gilda02.ihep.ac.cn



Command sets

• Two sets of commands– lfc-*

Interact with the LFC catalogue server that manages logical filenames (lfns), including mapping logical filenames to filenames to "site URLs".

– lcg-* Used to copy files to and from an SE, and to replicate files Interact with both the storage elements and the catalogue server

LFC

SE SE

lfc-*

lcg-*

UI



LFC Catalog commands

lfc-chmod Change access mode of the LFC file/directory

lfc-chown Change owner and group of the LFC file-directory

lfc-delcomment Delete the comment associated with the file/directory

lfc-getacl Get file/directory access control lists

lfc-ln Make a symbolic link to a file/directory

lfc-ls List file/directory entries in a directory

lfc-mkdir Create a directory

lfc-rename Rename a file/directory

lfc-rm Remove a file/directory

lfc-setacl Set file/directory access control lists

lfc-setcomment Add/replace a comment



Listing file and directory

• For each of the supported VO a separate "top level" directory exists under the "/grid" directory. You can see all the files that are stored for the gilda VO. First ensure you have a running VOMS proxy and then type: – $ lfc-ls -l /grid/dteam

• You will see a listing of the contents of the /grid/dteam, directory.

• Rather than having to type an absolute path for every file and directory you use, it is instead possible to define a HOME directory from which you may use relative file/directory paths. Set this now by setting the environment variable LFC_HOME as follows: – $ export LFC_HOME=/grid/dteam/tutorial



Create directory

• Before creating and uploading any of your own files create a personal directory for storage by typing: – $ lfc-mkdir $USER

• To check that you have created your directory type: – $ lfc-ls -l

and you should see your directory (plus possibly those of other attendees).



Add metadata information

• lfc-setcomment path comment

lfc-setcomment adds/replaces a comment associated with a file/directory in the LFC Catalog

• Example:lfc-setcomment /grid/dteam/tutorial/<your user> ‘Hello World’

• Check your job with lfc-ls --comment –l /grid/dteam/tutorial

drwxr-xr-x 0 119 104 0 Jan 08 16:04 john hello world



Delete metadata information

• Delete metadata informationlfc-delcomment path

lfc-delcomment deletes a comment previously added

• Example: lfc-delcomment /grid/dteam/tutorial/<your user>

• Check if it was successful with lfc-ls --comment -l

drwxr-xr-x 0 119 104 0 Jan 08 16:04 john



lcg-utils

• The LCG Data Management tools (usually called lcg-utils) allow users to copy files between UI, CE, WN and a SE, to register entries in the File Catalogs and replicate files between SEs.

• Check if LCG_GFAL_INFOSYS environment variable is correctly set to the local GILDA Information Index (BDII)– Eg:export LCG_GFAL_INFOSYS=lcg007.ihep.ac.cn:2170



lcg-utils commands

lcg-cp Copies a Grid file to a local destination

lcg-cr Copies a file to a SE and registers the file in the LRC

lcg-del Deletes one file (either one replica or all replicas)

lcg-lg Gets the guid for a given lfn or surl

lcg-rep Copies a file from SE to SE and registers it in the LRC

lcg-aa Adds an alias in RMC for a given guid

lcg-la Lists the aliases for a given LFN, GUID or SURL

lcg-gt Gets the turl for a given surl and transfer protocol

lcg-lr Lists the replicas for a given lfn, guid or surl

lcg-ra Removes an alias in RMC for a given guid

lcg-rf Registers a SE file in the LRC (optionally in the RMC)

lcg-uf Un-registers a file residing on an SE from the LRC



Upload file into SE

• use lcg-infosites in order to find which the available SE– $[lcg003] /home/chyd > lcg-infosites --vo dteam se|grep

ihep.ac.cn– 307078859 867594697 n.a cmsse01.ihep.ac.cn– 3912097491 86517061 n.a srm.ihep.ac.cn– 266947853 854038611 n.a atlasse01.ihep.ac.cn– 531101511 216222799 n.a lcg004.ihep.ac.cn

• The command is lcg-cr (LCG copy and register). Type the following to store this file on the lcg004.ihep.ac.cn storage element

$ lcg-cr --vo dteam -v -d lcg004.ihep.ac.cn -l lfn:/grid/dteam/chyd/hosts file:///etc/hosts

guid:41a0c124-7f2f-44fd-bb10-b3a820d1f72c



Get the file SURL

• For several purpose, FTS for instance, is useful to know the file SURL (they can be many if the file has replicas somewhere). The appropriate command is lcg-lr (list-replicas) [lfn | guid] – [lcg003] /home/chyd > lcg-lr --vo dteam

lfn:/grid/dteam/chyd/hosts

srm://lcg004.ihep.ac.cn/pnfs/ihep.ac.cn/data/dteam/generated/2008-01-08/file56ecb1c7-62dc-40e7-95aa-37b5a4635455



Replicate file

• A file can be stored on multiple SE's and then a running job can access the closest SE with the file on it, thus giving faster access times to the data. This also helps protect against failures/access difficulties with a particular SE. To find the list of SE'S available to you see the tutorial on lcg-infosites which can be found here. We will replicate the file just created to the SE lcg004.ihep.ac.cn with the command – $ lcg-rep -v --vo dteam -d srm-dteam.cern.ch lfn:/grid/dteam/chyd/hosts

• There is no output from this command on success, but you can check that the replica was created by listing all the replicas of your file, that is done by using the LCG list replicas command: – $lcg-lr --vo dteam lfn:/grid/dteam/chyd/hostsYou should get two replicas listed, as here: srm://lcg004.ihep.ac.cn/pnfs/ihep.ac.cn/data/dteam/generated/2008-01-

08/file56ecb1c7-62dc-40e7-95aa-37b5a4635455srm://srm-dteam.cern.ch/castor/cern.ch/grid/dteam/generated/2008-01-

08/file75d0c933-64e1-4078-8a2d-237e5bf2e6d8



Create symbolic link

• As an example of some of some of the other functionality available a second lfn for the file you uploaded is created. This is very similar to the Unix symbolic link. A second lfn is created with the command: – $ lfc-ln -s /grid/dteam/chyd/hosts /grid/dteam/chyd/hosts_ln

• Note the file path for the source file was used so as to avoid problems with relative links being used from the wrong directory. If you now list the contents of your directory you should see both names, but the symbolic link has 0 size and also the link target is shown: – $ lfc-ls -l /grid/dteam/chyd-rw-r--r-- 1 119 104 187 Jan 08 16:22 hostslrwxrwxrwx 1 119 104 0 Jan 08 16:37 hosts_ln -> /grid/dteam/chyd/hosts



Download a file from SE to UI

• Having already uploaded a file the next step is to show downloading a file. To download the file you already uploaded using the new lfn you have just created use the command: – $ lcg-cp --vo dteam lfn:/grid/dteam/chyd/hosts file:///$PWD/hosts

• You can check that the file you just downloaded is the same as the file you uploaded with cat command– $ cat hosts



lcg-aa

• Adding an alias for a given GUID

lcg-aa --vo vo guid lfnwhere

vo specifies the Virtual Organization the user belongs to guid specifies the Grid Unique Identifier of the file you want to add the

alias to lfn specifies the new alias

• Example:– $ lcg-lg lfn:/grid/dteam/chyd/hosts guid:41a0c124-7f2f-44fd-bb10-b3a820d1f72c

– $ lcg-aa --vo dteam guid:41a0c124-7f2f-44fd-bb10-b3a820d1f72c lfn:/grid/dteam/chyd/hosts_alias



lcg-la

• To check if the previous command was successful, you can use lcg-la command to list the aliases for a given LFN, GUID or SURL

• lcg-la lfn:/grid/dteam/chyd/hostslfn:/grid/dteam/chyd/hosts

lfn:/grid/dteam/chyd/hosts_ln

lfn:/grid/dteam/chyd/hosts_alias



lcg-gt

• get the TURL for a given SURL and transfer protocol• $ lcg-gt surl protocol

– surl: specifies the Site URL. An SURL scheme can be sfn: for a classical SE or srm:

– Protocol: specifies the protocol which will be used to access the file.• $ lcg-lr lfn:/grid/dteam/chyd/hosts srm://lcg004.ihep.ac.cn/pnfs/ihep.ac.cn/data/dteam/generated/2008-01-08/file56ecb1c7-62dc-40e7-95aa-

37b5a4635455 srm://srm-dteam.cern.ch/castor/cern.ch/grid/dteam/generated/2008-01-08/file75d0c933-64e1-4078-8a2d-

237e5bf2e6d8

• $ lcg-gt srm://lcg004.ihep.ac.cn/pnfs/ihep.ac.cn/data/dteam/generated/2008-01-08/file56ecb1c7-62dc-40e7-95aa-37b5a4635455 dcap dcap://lcg004.ihep.ac.cn:22125//pnfs/ihep.ac.cn/data/dteam/generated/2008-01-08/file56ecb1c7-62dc-40e7-95aa-37b5a4635455

• $ lcg-gt srm://srm-dteam.cern.ch/castor/cern.ch/grid/dteam/generated/2008-01-08/file75d0c933-64e1-4078-8a2d-237e5bf2e6d8 rfio rfio://castorpublic.cern.ch:9002?svcClass=dteam&castorVersion=2&path=/castor/cern.ch/grid/dteam/generated/2008-01-08/file75d0c933-64e1-4078-8a2d-237e5bf2e6d8



References

WMS User's Guide https://edms.cern.ch/file/572489/1/EGEE-JRA1-TEC-572489-WMS-guide-v0-2.pdf

JDL Attributes Specification Fabrizio Pacini

https://edms.cern.ch/file/555796/1/EGEE-JRA1-TEC-555796-JDL-Attributes-v0-8.pdf

Omii-Europe traininghttp://training.omii-europe.org/Tutorials/glite3.0/Tutorials.html



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EGEE-II INFSO-RI-031688 Enabling Grids for E-sciencE gLite Demo Yaodong Cheng CC-IHEP, Chinese...

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