Add 'computing_qsub'

computing_qsub.md

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+# qsub on sigma0
+Connect to sigma0 with SLC6 as OS
+```shell
+ssh -p 28 -X -o ServerAliveInterval=60 -C -c aes128-ctr -m hmac-sha1 <username>@sigma0.physi.uni-heidelberg.de
+
+```
+
+# Setup your local environment 
+The simplest way.
+```shell
+source /cvmfs/lhcb.cern.ch/lib/LbEnv
+lb-run Urania/latest bash
+```
+## to submit a few jobs (about 2-50) that take more than a couple minutes each
+Build a bash script that creates job specific bash-scripts and submits the jobs from individual job folders.
+
+```sh
+#!/bin/bash
+#set -x #echo on
+# A sample Bash script
+echo 'Running Script'
+workdir=/work/username/workfolder
+#a, x, and y are some variables that I want to loop over with my executable
+a=27
+x=$(($a + 1))
+    for ((y=0; y<=$a; y=y+2))
+    do
+	i=$((i+1))
+	mkdir -p $workdir/jobs/runjob$i  
+	rm -rf $workdir/jobs/runjob$i/*  #cleanup old jobs
+	touch $workdir/jobs/runjob$i/runjob$i.sh #create the job bash script
+	echo "#!/bin/bash" >> $workdir/jobs/runjob$i/runjob$i.sh
+	echo "$workdir/my_executable $a $x $y" >> $workdir/jobs/runjob$i/runjob$i.sh
+	cd  $workdir/jobs/runjob$i
+	echo "submitting--> $workdir/my_executable $a $x $y as ./runjob$i.sh" #output to check everything is being calculated as you want
+	qsub -V -b n -l os=slc6 -l ujl=20 -cwd -j yes ./runjob$i.sh # submit the job.  -V passes the current environment 
+	sleep 2 #be nice to the submission system
+   done
+exit 1
+```
+
+## to submit a few hundred jobs use the array feature of qsub
+‘qsub’ command combined with the -t option allow for the submission of an ‘array’ of jobs. When a job is launched via ‘qsub -t n[-m[:s]]’ you will have the environment variables SGE_TASK_ID and SGE_TASK_FIRST,  and if you add m you will have SGE_TASK_LAST, and if you add s you will have SGE_TASK_STEPSIZE. So -t sets the ‘index numbers’ associated with the job, like so:
+   - n is the first index number
+   - m is the last index number (optional)
+   - s is the step size (optional, defaults to 1)
+
+***runarray_jobcreater.sh***
+```sh
+#!/bin/bash
+#set -x #echo on
+# A sample Bash script
+echo 'Running Script'
+workdir=/work/username/workfolder
+#a, x, and y are some variables that I want to loop over with my executable
+a=2700
+x=$(($a + 1))
+    for ((y=0; y<=$a; y=y+2))
+    do
+	i=$((i+1))
+	mkdir -p $workdir/jobs/ 
+	rm -rf $workdir/jobs/*  #cleanup old jobs
+	echo "$a $x $y" >> $workdir/jobs/parameters.$i #make a unique parameter file for each task so that we can use the $SGE_TASK_ID to easily reference
+    done
+
+cd  /$workdir/jobs/
+#submits $i jobs as an array of jobs to the queue  "-t 1-$i"
+#-V passes the current environment
+#
+qsub -t 1-$i -V -b n -l os=slc6 -l ujl=20 -cwd -j yes ./runarray.sh
+exit 1
+```
+
+***runarray.sh***
+```sh
+#!/bin/bash
+#
+#
+workdir=/work/username/workfolder
+
+echo "Task id is $SGE_TASK_ID" 
+
+#executes a version of your executable that will read in the parameter file that you have specifically created for this
+$workdir/my_executable $workdir/jobs/parameters.$SGE_TASK_ID
+```
+
+_imported from lhcbmedia wiki_
+ If you want to submit jobs to only some of the machines on our cluster(e.g. leave one machine free for other users), you can specify it the queues options(chosing also a machines): 
+```
+qsub -masterq fgslc5.q@nu*,fgslc5.q@lambda*,fgslc5.q@alpha*,fgslc5.q@beta*,fgslc5.q@gamma*,fgslc5.q@eta*,fgslc5.q@delta*,fgslc5.q@lhcb-raid03*
+```