One possible way to wrap akmc.pl and run it as a cronjob:

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akmc.sh (in muskoka)
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#!/bin/sh
export SGE_ROOT=/opt/gridengine
export SGE_ARCH=lx24-amd64
export SGE_CELL=default
export SGE_QMASTER_PORT=536
export SGE_EXECD_PORT=537
export PGI=/usr/local/pgi

export VTST_STDOUT=ll_out
export VTST_STDERR=ll_err
export VTST_BC=BBC
#export VTST_ZIP=bzip2

export PATH=.:/home/xulijun/bin/vtstscripts:/opt/gridengine/bin/lx24-amd64:/usr/local/bin:/bin:/usr/local/mpich/bin:$PATH

cd $1
/home/xulijun/bin/vtstscripts/akmc.pl

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crontab -e
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30 * * * * /home/xulijun/bin/akmc.sh  /home/xulijun/H_Mg/akmc2 > /home/xulijun/H_Mg/akmc2/akmc.log
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