===== Good Practice - Available parameters ===== **(please also cf. ''man qsub'')** === Example header for a batch job script: ===


#!/bin/bash --login
#$ -N [jobname]
# job resources
#$ -l mem_free=[xxxM]|[yyyG]
#$ -l h_rt=HH:MM:SS
#$ -q [name_of_job_queue]
#$ -pe [name_of_parallel_env] [no_of_cpu_cores]
# cd to execution path
#$ -cwd
# mail stuff
#$ -o stdout.out
#$ -e stderr.out
#$ -j [no|yes]
#$ -m [n|b|e|e,b,...]  
#$ -M [name_of_your_mailbox]

(where "|" signifies **exclusive OR** and all lines beginning with **#$** are directives interpreted the batch job scheduler)\\ \\ === Detailed description of the batch job directives: ===


#!/bin/bash --login

## invoke an appropriate **login** shell \\ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\\ \\


#$ -N [jobname]

freely choose your own job name (gotcha: string is not(!) allowed to start with a numerical character and special characters like #, @, ? and * are not(!) permitted) \\ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\\ \\ The next directives ask for host resources your job needs, please choose carefully


#$ -l mem_free=[xxxM]|[yyyG]

sum of resident/physical memory in Mebibytes or Gibibytes used by all processes within your job


#$ -l h_rt=[HH:MM:SS]

hard runtime/wall clock time limit of your job in **HOURS:MINS:SECS** \\ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\\ \\


#$ -q [name_of_job_queue]

(special) queue the job is to be scheduled (**parameter generally not needed**)


#$ -pe [name_of_parallel_env] [no_of_cpu_cores]    (possible parallel environments are mp (runs on a single node) and ompi (multiple nodes)

(special) parallel environment and number of cores for your job \\ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\\ \\


#$ -cwd

change to (current) directory, where your input files reside \\ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\\ \\


#$ -o stdout.out

file where stdout of shell is redirected


#$ -e stderr.out

file where stderr of shell is redirected #$ -j [no|yes] stderr and stdout should (yes) or shouldn't (no) be redirected to same file/merged \\ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\\ \\


#$ -m [n|b|e|e,b,...]

mails about job status changes (n, no mail; b, beginning; e, end; ...) are send to the address given in [name_of_mailbox] or no mails (n) are send


#$ -M [name_of_your_mailbox]