Some Sun Grid Engine shortcuts to include in .bashrc

qsub_script.sh

# .bashrc

# simple qsub: assings 8GB memory for 1 hour. Call with: $ nq8 script.sh
alias nq8='qsub -l h_rt=01:00:00 -l tmem=8.0G -l h_vmem=8.0G -l vf=4.0 -l s_stack=10240 -R y -j y -S /bin/csh -b y -cwd -V'

# Shell function to echo the current time along with status updates
echoStatusTime() {
	STATUS_TEXT=$1
	NOW=$(date +%T)
	DATE=$(date +%F)
	echo "[${DATE} ${NOW}] ${STATUS_TEXT}"
}

function qdm() {
      # Delete a numbered range of jobs
			delfirst=$1
			dellast=$2
			deldiff=$[dellast - delfirst]
			
			echo "deleting multiple queued jobs: ${delfirst} through ${dellast} ..."
			
			for i in `seq 0 ${deldiff}`; do delthisnum=$[delfirst + i]; qdel ${delthisnum}; done
			
			echo "... completed $[deldiff + 1] deletions."
		}
		
# Shell function to check and make directories if they don't already exist
makeDirs() {
	# Check directories
	for dirToMake in "$@"
		do
			if [ ! -d ${dirToMake} ]
				then
					mkdir ${dirToMake}
					echoStatusTime "Created directory, ${dirToMake}"
			fi
			
			# if it still doesn't exist...
			if [ ! -d ${dirToMake} ]
				then
					echoStatusTime "Unable to create the ${dirToMake} folder!"
			fi
	done
	
	sleep 0
}
		
# Compute a script's total runtime with this and completeFunc
time_start=`date +%s`
		
completeFunc() {
	time_end=`date +%s`
	time_diff=$(( ${time_end} - ${time_start} ))

	echo ""
	echo "*******************************************************************************"
	echoStatusTime "Complete. Took ${time_diff} seconds total."
	echo "*******************************************************************************"
	echo ""
}
		
# Generate a random number for qsubFunc which is consistent for the whole run of the calling script. This doesn't need to be referenced in the calling script; it is appended to job names in qsubFunc. Hopefully this means simultaneous runs of the same script won't conflict.
randNum=$[ ( $RANDOM % 1000 ) ]

logDir=/home/${USER}
		
# Function to generate a qsub. This can be run and submitted in one line with eg. `qsubFunc 2 12 echo Hello world`. The user can specify the name of the job and the name of a previous job to wait for. Subsequent qsubFuncs can be run with $4 == $name_string to wait for _this_ job. If the logDir hasn't been created then output will be into the current directory.
#
# Eg. Test 1: > qsubFunc 2 8 "name_one" # sets up the function
#             > ${QSUB_CMD} echo "Hello world" # runs it
#     Test 2: > `qsubFunc 2 8 "name_two" ${wait_job_name}` echo "Goodbye" # runs dependent job.
# If nothing depends on run 1 then it may also be called in one line with `quotes` as run 2. The `quotes` cause ${this_name} to be unavailable.
# 
# ${timeNow} is now included below: there's no need for the job -Name to have it ($3 cannot begin with a number anyway) and it complicates matters if ${wait_job_name} doesn't include it anyway. So using it for the -output file name alone. This also cleans up scripts using this function. The general format for -Name should be -N script_purpose_image_name_${timeNow} as image names could begin with a number as well.
# NB wait_job_name seems to be persistent between scripts. Another issue is that, in loops, if the first qsub in the loop has no wait_job_name but is skipped (if the output already exists, say), then the second qsub (with a wait_job_name) will just wait for the last job in the previous loop iteration. Have to clear wait_job_name="" explicitly at the beginning of the loop or use specific job names, in this case.
qsubFunc() {

	hrs=$1
	mem=$2
	
	# Needs to be reset otherwise it is persistent between jobs!
	unset hold_name_string
	
	# Set default number of cores to use and wait for (more: longer wait)
	numCores=4
	
	if [ $# -gt 2 ]
		then
			name_string="-N $3_${randNum}"
			
			# subsequent jobs can use this variable to wait for this job (if this function is called outside of ``s). If this is used, _${randNum} will be appended by hold_name_string, so no need to add it here.
			wait_job_name="$3"
			
			if [ -d "${logDir}" ]
				then
				
					timeNow=`date +"%F-%H%M%S"`
					
					outfile_name_string="-o ${logDir}/${timeNow}_${3}.txt"
					error_name_string="-e ${logDir}/${timeNow}_${3}_error.txt"
			fi
			
			if [ $# -gt 3 ]
				then
					hold_name_string="-hold_jid $4_${randNum}"
			fi
	fi
	
	# Floating-point division of memory between cores
	memresult=$(echo "$mem / $numCores" | bc -l)
	mem=${memresult:0:4}
	
	QSUB_CMD="qsub -l h_rt=0${hrs}:00:00 -l tmem=${mem}G -l h_vmem=${mem}G -l s_stack=10240 -R y -j y -S /bin/csh -b y -wd /home/${USER} -pe smp ${numCores} -V ${hold_name_string} ${outfile_name_string} ${name_string}"
	
	echo ${QSUB_CMD}

}

# To submit Matlab scripts, for example, see matlab_np.sh (also in Gist)
# qsubFunc 2 10 "job_name"
# ${QSUB_CMD} ${SCRIPTS_DIR}/matlab_np.sh matlab_scipt_name argument1 arg2 arg3