infso-ri-508833 enabling grids for e-science gilda wms praticals ruediger berlich /...
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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
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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 : melbourneXX@glite-tutor.ct.infn.it 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=emidio.giorgio@ct.infn.it
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=emidio.giorgio@ct.infn.it/CN=proxy
issuer : /C=IT/O=GILDA/OU=Personal Certificate/L=INFN/CN=Emidio Giorgio/Email=emidio.giorgio@ct.infn.it
identity : /C=IT/O=GILDA/OU=Personal Certificate/L=INFN/CN=Emidio Giorgio/Email=emidio.giorgio@ct.infn.it
type : proxystrength : 512 bitspath : /tmp/x509up_u513timeleft : 20:59:53VO : gildavsubject : /C=IT/O=GILDA/OU=Personal
Certificate/L=INFN/CN=Emidio Giorgio/Email=emidio.giorgio@ct.infn.it
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
Certificate/L=INFN/CN=Emidio Giorgio/Email=emidio.giorgio@ct.infn.it
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=emidio.giorgio@ct.infn.it 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.
Command Line Interface (cont.)
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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)
Command Line Interface (cont.)
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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
*************************************************************
Command Line Interface (cont.)
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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.
Command Line Interface (cont.)
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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
Command Line Interface (cont.)
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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
===========================================================
Command Line Interface (cont.)
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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.
Command Line Interface (cont.)
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Exercises
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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:: giuseppe.larocca@ct.infn.itSubject: /C=IT/O=GILDA/OU=Personal Certificate/L=INFN
Catania/CN=Giuseppe La Rocca/Email=giuseppe.larocca@ct.infn.it
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…
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