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/dbou
  vet/.glite/vomsesYour identity
  /OGRID-FR/CFR/OCNRS/OUCC-LYON/CNDavid
  BouvetEnter GRID pass phraseCreating temporary
  proxy ...........................................
  DoneContacting cclcgvomsli01.in2p3.fr15001
  /OGRID-FR/CFR/OCNRS/OUCC-LYON/CNcclcgvomsli0
  1.in2p3.fr "egeode" DoneCreating proxy
  .................................... DoneYour
  proxy is valid until Sat Nov 4 025614 2006
• voms-proxy-info
• subject /OGRID-FR/CFR/OCNRS/OUCC-LYON/CND
  avid Bouvet/CNproxyissuer
  /OGRID-FR/CFR/OCNRS/OUCC-LYON/CNDavid
  Bouvetidentity /OGRID-FR/CFR/OCNRS/OUCC-LY
  ON/CNDavid Bouvettype proxystrength
  512 bitspath /tmp/x509up_u2028timeleft
  115853
• voms-proxy-info -all
• subject /OGRID-FR/CFR/OCNRS/OUCC-LYON/CND
  avid Bouvet/CNproxyissuer
  /OGRID-FR/CFR/OCNRS/OUCC-LYON/CNDavid
  Bouvetidentity /OGRID-FR/CFR/OCNRS/OUCC-LY
  ON/CNDavid Bouvettype proxystrength
  512 bitspath /tmp/x509up_u2028timeleft
  115825 VO egeode extension information
  VO egeodesubject
  /OGRID-FR/CFR/OCNRS/OUCC-LYON/CNDavid
  Bouvetissuer /OGRID-FR/CFR/OCNRS/OUCC-LY
  ON/CNcclcgvomsli01.in2p3.frattribute
  /egeode/RoleNULL/CapabilityNULLtimeleft
  115825

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 gridTestStdError
  stderr.logStdOutput stdout.logInputSandb
  ox /home/joda/test/gridTestOutputSandbox
  stderr.log, stdout.logInputData
  lfntestbed0-00019DataAccessProtocol
  gridftpRequirements other.ArchitectureINT
  EL \ other.OpSysLINUX
  other.FreeCpus\ gt4Rank
  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.com2119/jobmanager-lcgpbs-egeode
grid10.lal.in2p3.fr2119/jobmanager-pbs-egeode
gridgate.cs.tcd.ie2119/jobmanager-pbs-egee
hudson.datagrid.jussieu.fr2119/jobmanager-lcgpbs-
egeode marseillece01.mrs.grid.cnrs.fr2119/jobman
ager-pbs-egeode polgrid1.in2p3.fr2119/jobmanager
-pbs-egeode scaicl0.scai.fraunhofer.de2119/jobma
nager-lcgpbs-egeode cclcgceli02.in2p3.fr2119/job
manager-bqs-short cclcgceli02.in2p3.fr2119/jobma
nager-bqs-long cclcgceli02.in2p3.fr2119/jobmanag
er-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.com2119/j
  obmanager-pbs-egeode 132 107 0
  0 0 grid10.lal.in2p3.fr2119/jobman
  ager-pbs-egeode 88 44 0
  0 0 polgrid1.in2p3.fr2119/jobmanager-pb
  s-egeode 167 62 105 85
  20 cclcgceli02.in2p3.fr2119/jobmanager-bqs-lo
  ng 484 483 1 0 1
  cclcgceli02.in2p3.fr2119/jobmanager-bqs-short
  484 436 48 25 23
  cclcgceli02.in2p3.fr2119/jobmanager-bqs-medium
  62 0 0 0 0
  marseillece01.mrs.grid.cnrs.fr2119/jobmanager-pbs
  -egeode 5 5 0 0
  0 hudson.datagrid.jussieu.fr2119/jobmanager-l
  cgpbs-egeode 30 1 2 0
  2 scaicl0.scai.fraunhofer.de2119/jobmana
  ger-lcgpbs-egeode 42 33 13
  13 0 gridgate.cs.tcd.ie2119/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 Its 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.egee.fr.cgg.com and the register it in the
  LFC by the name myfile01.test the command to
  use is
• lcg-cr -d se1.egee.fr.cgg.com -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
• guid76373236-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.egee.fr.cgg.com/grid/egeode/tutorial/dat
  a/generated/2004-11-10/file7115df45-b4c7-11d8-bb5e
  -eba42b5000d0
• lcg-lr --vo egeode \ via GUID
• guid76373236-b4c7-11d8-bb5e-eba42b5000d0
• sfn// se1.egee.fr.cgg.com/grid/egeode/tutorial/da
  ta/generated/2004-11-10/file7115df45-b4c7-11d8-bb5
  e-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.fr
34253292 753684 n.a
barentz.datagrid.jussieu.fr4112779628
567932436 n.a scaise-2.scai.fraunhofer.d
e80648588 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
1117 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 1520
I2222221009100.DAT-rw------- 1 103 101
3226762 Nov 29 1536
I3333331009100.DAT-rw------- 1 103 101
10476082 Oct 19 1641
I6666661009100.DAT-rw------- 1 103 101
108305128 Mar 30 1024
I8888881009100.DAT-rw------- 1 103 101
993490 Feb 23 1619
I9999991009100.DAT-rw------- 1 103 101
1574758400 Nov 28 1233
KI.DAT-rw------- 1 103 101
6109200 Oct 19 1639 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? no LFN 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_ltunique jobstringgt.out
• OutputData OutputFile
  myfile01.out StorageElement
  se1.egee.fr.cgg.com LogicalFileName
  lfn/grid/egeode/logicalmyfile01,
  OutputFile myfile02.out StorageElement
  se1.egee.fr.cgg.com 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.egee.fr.cgg.com
• then if you use the list of replicas command
  lcg-lr
• lcg-lr --vo egeode lfn/grid/egeode/myfile01.test
• sfn//se1.egee.fr.cgg.com/grid/egeode/tutorial/dat
  a/generated/2004-11-10/file7115df45-b4c7-11d8-bb5e
  -eba42b5000d0sfn//se5.egee.fr.cgg.com/grid/egeod
  e/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_HOSTltLFC new hostnamegt

20
LFC commands (2)

• LFC root directory stucture
• /grid/ltVO_namegt
• ( 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/.../ltmy_directorygt
• Others commands
• lfc-ln, lfc-rm, lfc-getacl, lfc-setacl...

21
Questions ?