batch_sub

#!/bin/bash
#
# Submit a whole bunch of runs at once

usage="batch_sub -stlrdb [-nhepxyz1]\n\n

Following flags to select type of batch job \n
	-s submit batch job \n 
	-t tar runs and send to warwick \n 
	-l list runs \n 
	-r restart runs \n
	-d delete runs \n
	-b basename of runs \n\n

Following flags for submitting: \n
	-n number of processors \n
	-h number of hours \n
	-e equilibrium file \n
	-p proffile file \n
	-x first index \n
	-y second index \n
	-z date of runs in format ddMmm \n\n

Use -1 to do dry run"

# Save the command line arguments
str=''
for i in  `seq 1 $#`
do
    str=${str}":"${!i}
done
cla=`echo $str | tr ":" " "`

# Default arguments
basename= 		
equname="" 		
profname="" 		
N= 			
SCALE= 			
date= 			

nproc=128
hours=1

# Flags for submission script
flags=

# Need to do getopts twice - once for the submission script, once for the batch commands.
# The catch-all (*) option for first getopts will wipe all the flags we don't use first time 
# round. So, keep track of flags needed for second getopts
str=		

# Get parameters needed to do batch job
while getopts :n:h:v:b:e:p:x:y:z:stlrd1 OPT; do
    case $OPT in
# First set of flags are for submission part
	n|+n) nproc=$OPTARG
	    flags="${flags} -n $nproc";;
	h|+h) hours=$OPTARG
	    flags="${flags} -h $hours";;
	v|+v) version=$OPTARG
	    flags="${flags} -v $version";;
	e|+e) equname=$OPTARG
	    # check an equilibrium file has been given
	    if [[ -z $equname ]]; then
		echo "Equilbrium file flag used, but no equilibrium file given"
		echo $usage
		exit
	    fi
	    flags="${flags} -e ${equname}";;
	p|+p) profname=$OPTARG
	    # check a profile file has been given
	    if [[ -z $profname ]]; then
		echo "Profile file flag used, but no profile file given"
		echo $usage
		exit
	    fi
	    flags="${flags} -p $profname";;
# Next set of flags are for batch part
	b|+b) basename=$OPTARG;;
	x|+x) N=$OPTARG;;
	y|+y) SCALE=$OPTARG;;
	z|+z) date=$OPTARG;;
# Next set of flags are for batch commands - used in second getopts later
	s) str=${str}s;;
	t) str=${str}t;;
	l) str=${str}l;;
	r) str=${str}r;;
	d) str=${str}d;;
	1) str=${str}"1";;
# Help and catch-all
	\? ) echo -e $usage
	    exit 1;;
	: ) echo "Option -$OPTARG requires an argument." >&2
	    echo -e $usage
	    exit 1;;
	*) echo -e $usage
#	    echo "usage: ${0##*/} [+-nhbepxy} [--] ARGS..."
	    exit 2;;
    esac
done
shift $(( OPTIND - 1 ))
OPTIND=1

# Make sure basename has been set
if [[ -z $basename ]]; then
    echo "Missing basename. "
    echo -e $usage
    exit
fi

# WARNING! Will need to change this part if format of basename/scan is different
# Make list of filenames
FILENAME=`for n in $N; do
    for scale in $SCALE; do
	echo -n "${basename}_n${n}_scale_${scale} "
    done
done`

# Select and run batch job
while getopts :n:h:b:e:p:x:y:z:stlrd1 OPT "-${str}"; do
    case $OPT in
	s|+s)# Submit
	    echo "submit!"
	    for filename in $FILENAME
	    do
		echo "subnemo -i ${filename} ${flags}"
		subnemo -i ${filename} ${flags}
	    done
	    ;;
	t|+t)# Tar up jobs and scp them to Warwick
	    echo "tar!"
	    # Need to have a file to create tarball in first place
	    touch fish_food
	    # Name of tarball - .tgz extension is tar + gzip
	    tarname=${basename}_${date}.tar
	    tar -cf ${tarname} fish_food
	    # Add the input file, hdf5 output and STD_OUT file to tarball
	    for filename in $FILENAME
	    do
		dirname=${filename}_${date}*
		tar -rvf ${tarname} ${dirname}/input ${dirname}/orb5_res.h5 ${dirname}/hpcff_nemorb_${version}.o
	    done
	    rm fish_food
	    # Show the filesize of the tarball before sending it
	    ls -Alh ${tarname}
	    notify-send "ENTER PASSWORD FOR SCP" &
	    scp ${tarname} phrebb@alya.space.warwick.ac.uk:/storage/space2/phrebb/nemo/runs/$(date +%b%Y)/ && notify-send "Finished scp" || notify-send "scp broke"
	    ;;
	r|+r)# Restart
	    echo "restart!"
	    for filename in $FILENAME
	    do
		dirname=${filename}_${date}*
		cd ${WORK}/${dirname}
		sed -i 's/\(nlres[ ]*=[ ]*\)f/\1t/' input
		msub ${filename}.pbs
	    done
	    ;;
	l|+l)# List directories conforming to the given template
	    echo "list!"
	    for filename in $FILENAME
	    do
		echo "looking for: " $filename
		ls | grep ${filename}
	    done
	    ;;
	d|+d)# Delete directories
	    echo "delete!"
	    for filename in $FILENAME
	    do
		echo ${filename}_${date}*
		rm -r ${filename}_${date}*
	    done
	    ;;
	1) # Dry run - print out lots of info!
	    echo "Dry run!"
	    for filename in $FILENAME
	    do
		# List directories/filenames
		dirname=${filename}_${date}*
		echo $filename
		cd ${WORK}/${dirname}
		pwd
		# List .pbs files needed for restart and show what would be changed for restart
		echo -n ".pbs file: "		
		ls ${filename}.pbs
		sed -n 's/\(nlres[ ]*=[ ]*\)f/\1t/p' input
		# How would submission script be called
		echo "subnemo -i ${filename} ${flags}"
	    done
	    ;;
# Already sorted these above, but need to preserve them from the catch-all
	n|+n);; 
	h|+h);;
	b|+b);;
	e|+e);;
	p|+p);;
	x|+x);;
	y|+y);;
	z|+z);;
	*)
	    echo $OPTARG
	    echo -e $usage #"usage: ${0##*/} [+-stlr} [--] ARGS..."
	    exit 2;;
    esac
done
shift $(( OPTIND - 1 ))
OPTIND=1