gSSwrapper

#!/bin/tcsh -f
# usage: gSSwrapper cell#start cell#end #surr/set #sets filename [cstep dbflag]

# set arguments
@ cellstart = $1
@ cellend = $2
@ surrperset = $3
@ sets = $4
set basename = $5

if( $6 == "" ) then
	set cstep = 100
else
	set cstep = $6
endif
if( $7 == "") then
	set dbflag = 0
else
	set dbflag = $7
endif

# set loop variables
@ setn = 1

while( $setn <= $sets )
	@ celln = $cellstart
	while( $celln <= $cellend )
		# if first time through, check to see if directory exists
		if(($setn == 1) && !(-e cell$celln)) then
		    mkdir cell$celln
		    ln -s ../rfd.mat .
		endif
		set gSSout = "gSSs${setn}c${celln}"
		# save hostname in $gSSout as well as the standard out in case there were errors
		echo 'hostname; unset DISPLAY; cd $PBS_O_WORKDIR/cell${celln};'"hostname > $gSSout; ../gSS $celln $surrperset ${basename}S${setn}C${celln} $cstep $dbflag >> $gSSout 2>&1" | qsub -V -l nodes=1 -j oe -o $PWD/cell$celln/qsubs${setn}c${celln} -N gSS -
		@ celln++
	end
	@ setn++
end