LocalSubmission

Direct submission to local queue on the T2_BE_IIHE cluster

You first need to have read the Cluster_Presentation. Only then should you try to follow this page.

Aim

• The aim of this page is to provide a brief introduction/workbook on how to submit to the local cluster.
• The batch system allows to send executable code to the T2B cluster.
• This procedure can be used to run any code, even those needing access to files on the Storage Element (SE) maite.iihe.ac.be or directly through /pnfs.
• It is useful to use this procedure to not overload the User Interfaces (UIs, = mX machines).

Procedure

• Log in to an UI

ssh mshort.iihe.ac.be

• Make a directory and prepare an executable.

mkdir directsubmissiontest
cd directsubmissiontest/
emacs script.sh&

• Paste following code into script.sh. (see Attachemnt section below)

• Execute the following command to submit the script to the local queue

qsub -q express -o script.stdout -e script.stderr script.sh

• Follow the progress of your job on the UI

qstat -u $USER

• Your job are finished if you don't see it anymore with qstat. You should now be able to find your output files in the directory you've created:

> ls /user/$USER/directsubmissiontest
    script.stdout script.stderr

More details: some comments and FAQ

Comments

• In case you would like to access a root file you should copy it to the $TMPDIR (=/scratch/jobid.cream02.ac.be/) space on the workernode.
  • /scratch is the native disk of the workernode and is several 100 GBs big.
  • Each job is allotted a working directory that is cleaned automatically at the end of the job. This directory is stored in the variable $TMPDIR
  • Do not read root files from /user. This directory is not physically located on the workernode, it is mounted from the fileserver. Doing this will put a big load on the fileserver potentially causing the UIs to be slow.

****** IMPORTANT *******
If you use the local submission, please notice that you potentially can slow down our site. So please, copy all the files you will use during the job to $TMPDIR to avoid this.

dccp dcap://maite.iihe.ac.be/pnfs/iihe/..../MYFILE $TMPDIR/

FAQ

How to set CMSSW environment in a batch job

Add the following lines to your script :

pwd=$PWD
source $VO_CMS_SW_DIR/cmsset_default.sh                          # make scram available                                                                                                                                                             
cd /user/$USER/path/to/CMSSW_X_Y_Z/src/                          # your local CMSSW release                                                                                                                                                         
eval `scram runtime -sh`                                         # don't use cmsenv, won't work on batch                                                                                                                                            
cd $pwd

How to make your proxy available during batch jobs (for instance to write to /pnfs)

• Create a proxy with long validity time:

voms-proxy-init --voms MYEXPERIMENT--valid 192:0

• Copy it to /user

cp $X509_USER_PROXY /user/$USER/

• In your sh script you send to qsub, add the line:

export X509_USER_PROXY=/user/$USER/x509up_$(id -u $USER)    # Or the name of the proxy you copied before if you changed the name

• Then technically, to copy a file made in your job in the /scratch area, you just do:

gfal-copy file://$TMPDIR/MYFILE srm://maite.iihe.ac.be:8443/pnfs/iihe/MY/DIR/MYFILE

Stop your jobs

If for some reason, you want to stop your jobs on the server, you can use this procedure: qstat -u $USER

This will give you a list of jobs running with thier ID's. f.i.

394402.cream02            submit.sh        odevroed               0 R localgrid

Now, use the ID to kill the job with the qdel command: qdel 394402.cream02

Your job will now be removed.

Attachments

• script.sh

#!/bin/bash          

##Some general shell commands
STR="Hello World!"
echo $STR    
echo ">> script.sh is checking where it is"
pwd
echo ">> script.sh is checking how much disk space is still available"
df -h
echo ">> script.sh is listing files and directories in the current location"
ls -l
echo ">> script.sh is listing files and directories in userdir on storage element"
ls -l /pnfs/iihe/cms/store/user/$USER

echo ">> go to TMPDIR"
cd $TMPDIR
echo ">> ls of TMPDIR partition"
ls -l

##Create a small root macro

echo "{
  //TFile *MyFile = new TFile(\"testfile.root\",\"RECREATE\"); 
  //MyFile->ls();
  //MyFile->Close(),
  TFile* f=TFile::Open(\"dcap://maite.iihe.ac.be/pnfs/iihe/cms/store/user/$USER/testfile.root\");
  f->ls();
  f->Close();
} 
" > rootScript.C

cat rootScript.C


echo ">> execute root macro"
root -q -l -b -n rootScript.C

echo ">> ls of TMPDIR"
ls -l