INFSO-RI-508833 Enabling Grids for E-sciencE GILDA WMS Praticals Ruediger Berlich /...

INFSO-RI-508833

Enabling Grids for E-sciencE

www.eu-egee.org

GILDA WMS Praticals

Ruediger Berlich / Forschungszentrum KarlsruheMike Mineter / National e-Science Centre

slides contributed by INFN Catania

Melbourne, 30.01.2006

EGEE Tutorial, Melbourne, 30.01..2006 2


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User Interface Access

Host: glite-tutor.ct.infn.it

Username: melbourneXX (XX=01…30)

Password: GridMELXX (XX=01…30)

PassPhrase: MELBOURNE

GENIUS: https://glite-tutor.ct.infn.it



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VOMS/Proxy/MyProxy Management



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acknowledgements

• With acknowledgements to:Emidio GiorgioINFNCatania



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Outline

• VOMS proxy creation– Create VOMS proxy certificate using voms-proxy-init

• MyProxy – Store a proxy certificate– Retrieve a new proxy from MyProxy server



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Please logon to the GILDA

User Interface

Login : [email protected] where

XX=01,..30Passwd : GridMELXX XX=01,..,30



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Preliminary : .globus directory

• .globus directory contains your personal public / private keys

Pay attention to permissions !In future when you use the EGEE grid, you must obtain

and download these to this directory ... Details according to your Certificate Authority. On the GILDA testbed this is done for you.

[glite-tutor] /home/giorgio > ls -l .globustotal 8-rw-r----- 1 giorgio users 1613 Oct 4 19:30 usercert.pem-r-------- 1 giorgio users 1914 Oct 4 19:30 userkey.pem



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voms-proxy-init : options

• Main options -voms <vo-name:[command]>

command syntax is :/<voname>/group for group specify (default none) command syntax is :/<voname>/Role=<role name> for Role choice

(default none)

-valid x:y, create a proxy valid for x hours and y minutes-vomslife x, create a proxy with AC valid for x hours (max 24 h)

voms-proxy-init –-voms gildav:/gildav/Role=VO-Adminvoms-proxy-init --voms gildav:/gildav/tutors

PEM PASSPHRASE : MELBOURNE



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VOMS proxy creation

voms-proxy-init --voms gildavYour identity: /C=IT/O=GILDA/OU=Personal

Certificate/L=INFN/CN=Emidio Giorgio/[email protected]

Enter GRID pass phrase for this identity:[insert your certificate passphrase]Creating temporary

proxy ............................................. Done

/C=IT/O=INFN/OU=Host/L=CNAF/CN=cert-voms-01.cnaf.infn.it

/C=IT/O=INFN/CN=INFN Certification AuthorityCreating proxy ............................................. DoneYour proxy is valid until Mon Jun 13 09:06:00 2005



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Verify your credentials

• voms-proxy-info

• Principal options : --all prints all proxy options --file specifies a different location of proxy file



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Verify obtained credentials

[giorgio@glite-tutor:~]$ voms-proxy-info --all subject : /C=IT/O=GILDA/OU=Personal

Certificate/L=INFN/CN=Emidio Giorgio/[email protected]/CN=proxy

issuer : /C=IT/O=GILDA/OU=Personal Certificate/L=INFN/CN=Emidio Giorgio/[email protected]

identity : /C=IT/O=GILDA/OU=Personal Certificate/L=INFN/CN=Emidio Giorgio/[email protected]

type : proxystrength : 512 bitspath : /tmp/x509up_u513timeleft : 20:59:53VO : gildavsubject : /C=IT/O=GILDA/OU=Personal


issuer : /C=IT/O=INFN/OU=Host/L=CNAF/CN=cert-voms-01.cnaf.infn.it

attribute : /gildav/Role=NULL/Capability=NULLtimeleft : 20:58:28



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Long term proxy : MyProxy

• myproxy server:– myproxy-init

Allows to create and store a long term proxy certificate:

– myproxy-info Get information about stored long living proxy

– myproxy-get-delegation Get a new proxy from the MyProxy server

– myproxy-destroy– Check out them with myproxy-xxx --help option



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myproxy-init[giorgio@glite-tutor:~]$ myproxy-init -s grid001.ct.infn.it Your identity: /C=IT/O=GILDA/OU=Personal


Enter GRID pass phrase for this identity:Creating proxy .....................................................

DoneProxy Verify OKYour proxy is valid until: Sun Jun 19 21:18:27 2005Enter MyProxy pass phrase:Verifying password - Enter MyProxy pass phrase:A proxy valid for 168 hours (7.0 days) for user giorgio now exists

on grid001.ct.infn.it.

•Principal options • -c hours specifies lifetime of stored credentials • -t hours specifies the maximum lifetime of credentials when retrieved• -s <hostname> specifies the myproxy server where to store credentials• -d stores credential with the distinguished name in proxy, instead of user name (mandatory for some data management services and proxy renewal)• For proxy renewal it’s also mandatory –n (no passphrase). You’ve to specify also subject of principals that can renew a delegation (-R subject, or -A for any principal)



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myproxy-info

• Useful to retrieve info on stored credentials• Need local credentials to be performed• If credentials have been initialized with –d switch, you have

also to specify it there

[giorgio@glite-tutor:~]$ myproxy-info -s grid001.ct.infn.it username: giorgioowner: /C=IT/O=GILDA/OU=Personal Certificate/L=INFN/CN=Emidio Giorgio/[email protected] timeleft: 167:55:34 (7.0 days)



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myproxy-get-delegation

• This command is used to retrieve a delegation from a long lived proxy stored on myproxy server

• It is independent by the machine ! You don’t need to have your certificate on board

• If credentials have been initialized with –d switch, you have to specify it also in myproxy-get-delegation request

[giorgio@glite-tutor:~]$ myproxy-get-delegation \-s grid001.ct.infn.itEnter MyProxy pass phrase:A proxy has been received for user giorgio in /tmp/x509up_u513



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myproxy-destroy

• Delete, if existing, the long lived credentials on the specified myproxy server

[glite-tutor] /home/giorgio > myproxy-destroy \ -s grid001.ct.infn.it Default MyProxy credential for user giorgio was successfully removed.



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Workload Management System

Giuseppe La RoccaValeria Ardizzone



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• In the glite middleware a user can submit and cancel jobs, query their status, and retrieve their output. These tasks go under the name of Workload Management.

• There are two different User Interfaces to accomplish these tasks. One is the Command Line Interface and the other is the Graphical User Interface.

Workload Management System



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It is possible to see which CEs are eligible to run a job specified by a given JDL file using the command

glite-job-list-match hello.jdl

where <jdl file> is the file containing the job description

Connecting to host lxshare0380.cern.ch, port 7772

Selected Virtual Organisation name (from UI conf file): dteam

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

COMPUTING ELEMENT IDs LIST

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

adc0015.cern.ch:2119/jobmanager-lcgpbs-infinite

adc0015.cern.ch:2119/jobmanager-lcgpbs-long

adc0015.cern.ch:2119/jobmanager-lcgpbs-short

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

Command Line Interface (cont.)



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Command Line Interface

• Job Submission– Perform the job submission to the Grid.

$ glite-job-submit [options] <jdl_file>

--vo <vo name> : perform submission with a different VO than the UI default one.

--output, -o <output file> save jobId on a file.--resource, -r <resource value> specify the

resource for execution. --nomsgi neither message nor errors on the stdout

will be displayed.



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If the submission is successful, the output is similar to:

glite-job-submit test.jdl

======================glite-job-submit Success =======================

The job has been successfully submitted to the Network Server.

Use glite-job-status command to check job current status.

Your job identifier (edg_jobId) is:

- https://lxshare0234.cern.ch:9000/rIBubkFFKhnSQ6CjiLUY8Q

===================================================================

In case of failure, an error message will be displayed instead, and an exit status different form zero will be retured.




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If the command returns the following error message:

**** Error: API_NATIVE_ERROR ****

Error while calling the "NSClient::multi" native api

AuthenticationException: Failed to establish security context...

**** Error: UI_NO_NS_CONTACT ****

Unable to contact any Network Server

it means that there are authentication problems between the UI and the Network Server (check your

proxy or have the site administrator check the certificate of the server).

(applies to UIPnP)




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After a job is submitted, it is possible to see its status using the glite-job-status command.

glite-job-status https://lxshare0234.cern.ch:9000/X-ehTxfdlXxSoIdVLS0L0w

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

BOOKKEEPING INFORMATION:

Printing status info for the Job:

https://lxshare0234.cern.ch:9000/X-ehTxfdlXxSoIdVLS0L0w

Current Status: Ready

Status Reason: unavailable

Destination: lxshare0277.cern.ch:2119/jobmanager-pbs-infinite

reached on: Fri Aug 1 12:21:35 2003

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




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The option -i <file path> can be used to specify a file with a list of job identifiers (saved previously with the -o option of glite-job-submit).

glite-job-status -i jobs.list---------------------------------------------------------------------------------------------------1 : https://lxshare0234.cern.ch:9000/UPBqN2s2ycxt1TnuU3kzEw2 : https://lxshare0234.cern.ch:9000/8S6IwPW33AhyxhkSv8Nt9A3 : https://lxshare0234.cern.ch:9000/E9R0Yl4J7qgsq7FYTnhmsA4 : https://lxshare0234.cern.ch:9000/Tt80pBn17AFPJyUSN9Qb7Qa : allq : quit---------------------------------------------------------------------------------------------------Choose one or more edg_jobId(s) in the list - [1-4]all:

If the - -all option is used instead, the status of all the jobs owned by the user submitting the command is retrieved.




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The --status <state> (-s) option makes the command retrieve only the jobs that are in the specified state, and the --exclude

<state> (-e) option makes it retrieve jobs that are not in the specified state.

This two lasts options are mutually exclusive, although they can be used with --from and --to.

Example: All jobs of the user that are in the state DONE or RUNNING are retrieved.

glite-job-status --all -s Done -s Running

Example: All jobs that were submitted before the 17:35 of the current day, and that were not in the Cleared state are retrieved.

glite-job-status --all -e Cleared --to 17:00




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A job can be canceled before it ends using the command glite-job-cancel.

glite-job-cancel https://lxshare0234.cern.ch:9000/dAE162is6EStca0VqhVkog

Are you sure you want to remove specified job(s)? [y/n]n :y

=================== glite-job-cancel Success====================

The cancellation request has been successfully submitted for the following job(s)

- https://lxshare0234.cern.ch:9000/dAE162is6EStca0VqhVkog

===========================================================




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After the job has finished (it reaches the DONE status), its output can be copied to the UI

glite-job-output https://lxshare0234.cern.ch:9000/snPegp1YMJcnS22yF5pFlg

Retrieving files from host lxshare0234.cern.ch*****************************************************************JOB GET OUTPUT OUTCOMEOutput sandbox files for the job:- https://lxshare0234.cern.ch:9000/snPegp1YMJcnS22yF5pFlghave been successfully retrieved and stored in the directory:/tmp/jobOutput/snPegp1YMJcnS22yF5pFlg*****************************************************************

By default, the output is stored under /tmp, but it is possible to specify in which directory to save the

output using the - -dir <path name> option.




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Exercises

EGEE Tutorial, Melbourne, 30.01..2006


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hello.jdl

Type = "Job";JobType = "Normal";Executable = "/bin/echo";StdOutput = "hello.out";StdError = "hello.err";OutputSandbox = {"hello.err","hello.out"};Arguments = "Hello World";RetryCount = 7;

Create JDL file similar to:



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Exercises

• Check where hello.jdl can be executed• Run the hello world example• Submit multiple times• Cancel a job• Check output



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Exercises

• Simple job submission

– cp hello.jdl exercise1.jdl

– Modify exercise1.jdl file Instead of running hostname command, run a bash

script you have just created (yourscript.sh).

– Submit the job, check its status and when done retrieve the output

Create a bash script which displays hostname and current date

Test script locally

Save the script as yourscript.sh



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JDL – Examples

Type = "Job";JobType = "Normal";Executable = "/bin/bash";StdOutput = “std.out";StdError = “std.err";InputSandbox = {“yourscript.sh"};

OutputSandbox = {“std.err",“std.out"};Arguments = "yourscript.sh";

#!/bin/bash/bin/hostname/bin/date

exercise1.jdl

yourscript.sh



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JDL – Requirements

#Insert a requirement to parse only the short queues.Requirements = (other.GlueCEPolicyMaxWallClockTime >

720);

#Insert a requirement to parse only the long queues.Requirements = (other.GlueCEPolicyMaxWallClockTime >

1440);

#Insert a requirement to parse only the infinite queues.

Requirements = (other.GlueCEPolicyMaxWallClockTime > 2880);

#Insert a requirement to stear the execution on a particular CE Queue.

Requirements = other.GlueCEUniqueID == "grid010.ct.infn.it:2119/jobmanager-lcgpbs-long";



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Exercises

• Simple job using Requirements– Modify exercise1.jdl file so that user with a even

workstation number will submit their job on a “long” queue, and the other to an “infinite” one

– Verify the list of CE suitable for this job execution– Submit the job, check its status and retrieve the output



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JDL with Requirements

Type = "Job";JobType = "Normal";Executable = "/bin/sh";Arguments = "start_povray_cubo.sh";StdOutput = "povray_cubo.out";StdError = "povray_cubo.err";InputSandbox =

{"start_povray_cubo.sh","cubo.pov"};OutputSandbox =

{"povray_cubo.out","povray_cubo.err","cubo.png"};

Requirements = Member("POVRAY-3.5",other.GlueHostApplicationSoftwareRunTimeEnvironment);



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start_povray_cubo.sh

#!/bin/bashmv cubo.pov OBJECT.POV #rename input file/usr/bin/povray

/usr/share/povray-3.5/ini/res800.ini #run povray

mv OBJECT.png cubo.png #rename output file



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Exercises

• Modify povray_cubo.jdl, specifying the resource for execution into the jdl file

• Check job status and when done retrieve the output

• Display .png file obtained as output, using ImageMagick (if possible – transfer file on Windows machines or leave out this step)



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Run an ls command on the selected resource.[ Executable = "ls.sh"; Arguments = "-alt"; StdError = "stderr.log"; StdOutput = "stdout.log"; InputSandbox = "ls.sh"; OutputSandbox = {"stderr.log", "stdout.log"}; ]

ls.sh#!/bin/bash /bin/ls $1

Exercises



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Type = "Job"; JobType = "MPICH"; Executable = "MPItest.sh"; Arguments = "cpi 2"; NodeNumber = 2; StdOutput = "test.out"; StdError = "test.err"; InputSandbox = {"MPItest.sh","cpi"}; OutputSandbox = {"test.err","test.out","executable.out"};Requirements = other.GlueCEInfoLRMSType == "PBS" ||

other.GlueCEInfoLRMSType == "LSF";

mpi.jdl



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MPItest.sh

#!/bin/sh#

# this parameter is the binary to be executedEXE=$1# this parameter is the number of CPU's to be reserved

for parallel executionCPU_NEEDED=$2

# prints the name of the master nodeecho "Running on: $HOSTNAME"

if [ -f "$PWD/.BrokerInfo" ] ; then TEST_LSF=`edg-brokerinfo getCE | cut -d/ -f2 | grep

lsf`else TEST_LSF=`ps -ef | grep sbatchd | grep -v grep`fi



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MPItest.sh (cont.)

if [ "x$TEST_LSF" = "x" ] ; then # prints the name of the file containing the nodes

allocated for parallel execution echo "PBS Nodefile: $PBS_NODEFILE" # print the names of the nodes allocated for parallel

execution cat $PBS_NODEFILE HOST_NODEFILE=$PBS_NODEFILEelse # print the names of the nodes allocated for parallel

execution echo "LSF Hosts: $LSB_HOSTS" # loops over the nodes allocated for parallel

execution HOST_NODEFILE=`pwd`/lsf_nodefile.$$

for host in ${LSB_HOSTS} do host=`host $host | awk '{ print $1 } '` echo $host >> ${HOST_NODEFILE} donefi



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# prints the working directory on the master nodeecho "Current dir: $PWD"

for i in `cat $HOST_NODEFILE` ; do echo "Mirroring via SSH to $i" # creates the working directories on all the nodes

allocated for parallel execution ssh $i mkdir -p `pwd` # copies the needed files on all the nodes allocated

for parallel execution /usr/bin/scp -rp ./* $i:`pwd` # checks that all files are present on all the nodes

allocated for parallel execution echo `pwd` ssh $i ls `pwd` # sets the permissions of the files ssh $i chmod 755 `pwd`/$EXE ssh $i ls -alR `pwd`done

MPItest.sh (cont.)



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# execute the parallel job with mpirunecho "*********************************"echo "Executing $EXE"chmod 755 $EXEmpirun -np $CPU_NEEDED -machinefile $HOST_NODEFILE

`pwd`/$EXE > executable.outecho "*********************************"

MPItest.sh (cont.)



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Exercises

Modify c_sample.c file as follow:

#include <stdio.h>int main(int argc, char **argv){

printf("\n\n\n");printf("Hello !\n");

printf("Welcome to EGEE Tutorial, Melbourne\n\n\n");

exit(0);}

This exercise allows user to submit a C program.



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Compile your script using make.

Submit the c_sample.jdl job to the grid using the glite-job-submit c_sample.jdl command.

Inspect the status and retrieve its output when the job is finished.

Exercises (cont.)



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Exercises

Modify c_sample.c file as follow:

#include <stdio.h>int main(int argc, char **argv){ char *name = argv[1]; printf("\n\n\n"); printf("Hello !\n"); printf("Welcome to EGEE Tutorial\n\n\n"); exit(0);}



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Exercises (cont.)

Compile your script with make.

Modify the start_c_sample.sh script as follow:

#!/bin/shchmod 777 c_sample./c_sample $1

Modify c_sample.jdl’s Arguments as follow:Arguments = "start_c_sample.sh <Your Name>";

Submit, inspect the status and retrieve its output when the job is finished.



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Questions…



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DataGrid Accounting System

Giuseppe La Rocca



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Exercise

View user Credits



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$ dgas-check-balance

User: Giuseppe La RoccaE-mail:: [email protected]: /C=IT/O=GILDA/OU=Personal Certificate/L=INFN

Catania/CN=Giuseppe La Rocca/[email protected]

Assigned credits (0=infinite): 0Booked credits: 0Used credits: 451Used wall clock time (sec): 1187Used CPU time (sec): 264Accounted jobs: 22



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View CE Price

Exercise



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Usage: dgas-check-ce-price <CE name>:2119/jobmanager-lcgpbs-<queue>

Example: dgas-check-ce-price grid010.ct.infn.it:2119/jobmanager-lcgpbs-short

Price Authority queried at: Thu Oct 20 18:43:39 CEST 2005

Computing Element: grid010.ct.infn.it:2119/jobmanager-lcgpbs-short

Price (credits for 100 CPU secs): 170



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Questions…

INFSO-RI-508833 Enabling Grids for E-sciencE GILDA WMS Praticals Ruediger Berlich /...

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