Thank you, after reading your $EID not available comment it made me think in terms of bash and im now executing the script as sudo and it seems to work.

system("sudo -u $var1 /net/watusi/usr1/scripts/submitjobs.sh");
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here $var1 is jjack, file /net/watusi/usr1/scripts/submitjobs.sh below

#!/bin/sh -p
. /net/watusi/usr1/lsf8.0/conf/profile.lsf
bsub -q lxpt64_2cpu -o /dev/null -e /dev/null  sleep 10
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All these jobs are now being submitted into LSF with the Effective user id I wanted