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--- hpc:numericserveruser:hpc_numericserver:batch_job_scripts:good_practice [2019/11/20 00:37] – kraus
+++ hpc:numericserveruser:hpc_numericserver:batch_job_scripts:good_practice [2020/02/14 18:05] (aktuell) – kraus
@@ Zeile 1: / Zeile 1: @@
+===== Good Practice - Available parameters =====
+**(please also cf. ''man qsub'')**
+=== Example header for a batch job script: ===
+<code>
+#!/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]
+</code>
+(where <nowiki>"|"</nowiki> signifies **exclusive OR** and all lines beginning with **#$** are directives interpreted the batch job scheduler)\\
+\\
+=== Detailed description of the batch job directives: ===
+<code>
+#!/bin/bash --login
+</code>
+<file>
+## invoke an appropriate **login** shell
+</file>
+\\
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\\
+\\
+<code>
+#$ -N [jobname]
+</code>
+<file>
+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)
+</file>
+\\
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\\
+\\
+<file>
+The next directives ask for host resources your job needs, please choose carefully
+</file>
+<code>
+#$ -l mem_free=[xxxM]|[yyyG]
+</code>
+<file>
+sum of resident/physical memory in Mebibytes or Gibibytes used by all processes within your job
+</file>
+<code>
+#$ -l h_rt=[HH:MM:SS]
+</code>
+<file>
+hard runtime/wall clock time limit of your job in **HOURS:MINS:SECS**
+</file>
+\\
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\\
+\\
+<code>
+#$ -q [name_of_job_queue]
+</code>
+<file>
+(special) queue the job is to be scheduled (**parameter generally not needed**)
+</file>
+<code>
+#$ -pe [name_of_parallel_env] [no_of_cpu_cores]    (possible parallel environments are mp (runs on a single node) and ompi (multiple nodes)
+</code>
+<file>
+(special) parallel environment and number of cores for your job
+</file>
+\\
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\\
+\\
+<code>
+#$ -cwd
+</code>
+<file>
+change to (current) directory, where your input files reside
+</file>
+\\
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\\
+\\
+<code>
+#$ -o stdout.out
+</code>
+<file>
+file where stdout of shell is redirected
+</file>
+<code>
+#$ -e stderr.out
+</code>
+<file>
+file where stderr of shell is redirected
+</file>
+<code> #$ -j [no|yes] </code>
+<file>
+stderr and stdout should (yes) or shouldn't (no) be redirected to same file/merged
+</file>
+\\
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\\
+\\
+<code>
+#$ -m [n|b|e|e,b,...]
+</code>
+<file>
+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
+</file>
+<code>
+#$ -M [name_of_your_mailbox]
+</code>
+<file>
+only needed when mails should be send
+</file>
+\\
+<WRAP rightalign>
+date of revision: 02-14-2020 © kraus
+</WRAP>