1. WMS - Tecniche di scripting
Fabio Scibilia
INFN – Catania, Italy
Dipartimento di Ingegneria Informatica e delle Telecomunicazioni (DIIT), Catania, Marzo 2007

2. Preliminars LCG middleware gLite Tips and tricks
The workload is managed by the Resource Broker
Doesn’t support neither parametric jobs nor DAGs
Works fine
gLite
Support both the parametric and the DAG jobs
Under developing
Uses WMProxy to manage the workload
Will be available in a few months
Tips and tricks
Some ideas to use LCG middleware to support parametric jobs and DAGs while waiting for WMProxy stable release
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3. Exercise 1: Parametric jobs
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4. Exercise 1: The bash script (1/2)
A set of jobs differing for input files only
The bash script looks like this
#!/bin/sh
if [ "$2" = "" ]; then
echo "Usage: $0 begin end [step]"
echo " begin The first value of the sequence"
echo " end The last value of the sequence"
echo " step The step between two submissions"
exit 0 fi
joblist="jobs.list"
begin_index=$ // the first parameter of the script
end_index=$ // the second parameter of the script
if [ "$3" = "" ]; then
step=1;
else
step=$ // the third parameter of the script
. . .
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5. Exercise 1: The bash script (2/2)
# starts iterations
for ((index=$begin_index; index<=$end_index; index=$index+$step)) do
# we generate the input file automatically. Obviously it can be made by hand
inputfile="input$index.txt"
echo "creating input file $inputfile"
echo "The name of this input file is $inputfile" > $inputfile
# create the correspondent jdl file depending on the index
jdlfile="job$index.jdl“ # name of the jdl
echo "creating JDL file $jdlfile" (
echo 'Type="Job";'
echo 'JobType="Normal";'
echo 'Executable=“/bin/cat";'
echo "Arguments=\"$inputfile\";"
echo "StdOutput=\"stdout$index.txt\";"
echo "StdError=\"stderr$index.txt\";“
echo "InputSandbox={\"$inputfile\"};"
echo "OutputSandbox={\"stdout$index.txt\", \"stderr$index.txt\"};"
) > $jdlfile
edg-job-submit -o jobs.id $jdlfile # actual job submission
done # end of iterations
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6. Exercise 2: DAGs
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7. Exercise 2: DAG modelling
DAGs can be emulated with a simplified Petri net
A job is submitted only when activating jobs have terminated
Each transition bar corresponds to a bash script that
Waits for termination of activating job(s) by polling every minute
Collects the output
Submits next job(s) job 2 5 1 3 6 4
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8. Exercise 2: An example We emulate a simple split and merge DAG
Two states machine
Anyway, this example can be extended to any possible DAG
./submitter.sh: generates input[1..n].txt and submits jobs
./polling && ./last_job.sh: Implement the bar transion
input1.txt 1
./polling.sh: waits for jobs [1..n] completion, collect the output and creates the final input file
stdout
input2.txt
stdout
final_input
./last_job.sh: submits the last job and waits for its completion, downloading the output
final_output 2
last
stdout
input(n).txt n
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9. Exercise 2: ./submitter.sh
#!/bin/sh
if [ "$1" = "" ]; then
echo "Usage: $0 num-splits“ ; exit 0 fi
for ((index=1; index<= $1; index++)); do # for each job
echo "this is the content of input$index.txt" >> input$index.txt
( ## creates the jdl for this job
echo "Type=\"Job\";"
echo "JobType=\"Normal\";"
echo "Executable=\"/bin/cat\";"
echo "Arguments=\"input$index.txt\";"
echo "InputSandbox={\"input$index.txt\"};"
echo "StdOutput=\"stdout.txt\";"
echo "StdError=\"stderr.txt\";"
echo "OutputSandbox={\"stdout.txt\", \"stderr.txt\"};"
) > job$index.jdl;
edg-job-submit -o jobs.id job$index.jdl
done
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10. Exercise 2: ./submitter.sh output
dag]$ ./submitter.sh 2
The job has been successfully submitted to the Network Server.
Use edg-job-status command to check job current status. Your job identifier is: -
The job identifier has been saved in the following file:
/home/fscibi/tips_and_tricks/dag/jobs.id -
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11. Exercise 2: ./polling.sh (1/4)
#!/bin/sh
while read line; do
if [ "$line" != "###Submitted Job Ids###" ]; then
joblist="$joblist $line" fi
done < jobs.id
for job in $joblist; do
status="unknown"
finished="false"
while [ "$finished" = "false" ]; do # loops waiting for job completion
## Gets the status of the job
echo
echo "getting status of job $job"
output=`edg-job-status $job`
status=`echo "$output" | grep "Current Status" | awk '{print $3 }'`
echo "status = $status"
Luogo, Evento, dd.mm.aaaa

12. Exercise 2: ./polling.sh (2/4)
## depens on the status, decides what to do
case $status in
"Aborted“ )
echo "The job has been aborted on the CE"
finished="true" ;;
"Cleared“ )
echo "The job output sandbox has been already retrieved. I don't know where!"
"Done“ )
echo "Job $job Done!!! Downloading the output"
## executes and parses the output of edg-job-get-output
## to understand where the output has been stored
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13. Exercise 2: ./polling.sh (3/4)
edg-job-get-output --dir . $job | (pipes the edg-job-get-output to llok for job status
found="false"
while read line; do
if "$found" = "true“ ; then ## this line contains the dir path
dirpath=$line
echo "output sandbox stored at $dirpath"
break fi
if echo "$line" | grep -q "have been successfully retrieved and stored“ ;
then
found= "true" ## next line contains the dir path
done
if "$found" = "true“; then
filename=$dirpath/stdout.txt
echo "appending $filename to final_input"
cat $filename >> final_input )
finished="true" ;;
Luogo, Evento, dd.mm.aaaa

14. Exercise 2: ./polling.sh (4/4)*)
echo "sleeping 1 minute"
sleep 1m ;;
esac
done # while
done # for
dag]$ ./polling.sh
. . . (after a while)
getting status of job Od68j9IBOuJHGlUq-EfWTg
status = Done
Job Done!!! Downloading the output
output sandbox stored at /dag/fscibi_Od68j9IBOuJHGlUq-EfWTg
appending dag/fscibi_Od68j9IBOuJHGlUq-EfWTg/stdout.txt to final_input
getting status of job _-suh1wmmo1VvYJd_4AiLhA
output sandbox stored at /dag/fscibi_-suh1wmmo1VvYJd_4AiLhA
appending dag/fscibi_-suh1wmmo1VvYJd_4AiLhA/stdout.txt to final_input
Luogo, Evento, dd.mm.aaaa

15. Exercise 2: Submitting last job
. . ] cat last_job.sh
#!/bin/sh
## submits the last job
edg-job-submit -o last_job.id last_job.jdl
status=unknown
while [ "$status" != "Done" ]; do
echo "sleeping 30 seconds“
sleep 30s
output=`edg-job-status -i last_job.id`
status=`echo "$output" |
grep "Current Status" | awk '{print $3 }'`
echo "status = $status"
done
edg-job-get-output -i last_job.id --dir .
echo "Everything is Done !!! "
. . ] cat last_job.jdl
Type="Job";
JobType="Normal";
Executable="/bin/cat";
Arguments="-n final_input";
StdOutput="final_output";
StdError="stderr.txt";
InputSandBox={"final_input"};
OutputSandbox={"stderr.txt", "final_output"};
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16. Exercise 2: ./last_job.sh output
dag]$ ./last_job.sh
. . .
The job has been successfully submitted to the Network Server. -
sleeping 30 seconds (many times)
status = Scheduled (waiting for status Done)
sleeping 30 seconds
status = Done
Retrieving files from host: Output sandbox files for the job:
have been successfully retrieved and stored in the directory:
/home/fscibi/tips_and_tricks/dag/fscibi_q_rqVQpNFt0GshDn5MZHEw
"Everything is Done !!!
dag]$ cat fscibi_q_rqVQpNFt0GshDn5MZHEw/final_output
1 this is the content of input1.txt
2 this is the content of input2.txt
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17. References JDL (WMS Netrwork Server) JDL (WMS WMProxy)
JDL (WMS WMProxy)
Advanced BASH scripting
Gilda twiki pages
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18. Questions . . .
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