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--- doku:miscellaneous [2014/05/28 11:35] – created ir
+++ doku:miscellaneous [2021/05/13 17:49] (current) – removed goldenberg
@@ Line 1: / Line 1: @@
-====== Miscellaneous ======
-==== submitting a job from standard in (stdin) ====
-<code>
-echo "sleep 10" | qsub -N test
-</code>
-==== Redirecting output of jobs ====
-=== Within Grid Engine ===
-If nothing else is specified the output of GridEngine Jobs is written to four files:
-  * <job_name>.o<job_id>(.<task_id>): STDOUT of the job
-  * <job_name>.e<job_id>(.<task_id>): STDERR of the job
-  * <job_name>.po<job_id>(.<task_id>): STDOUT of parallel environment of the job
-  * <job_name>.pe<job_id>(.<task_id>): STDERR of parallel environment of the job
-This behaviour can be modified in the following way:
-  * '#$ -j y' joins STDOUT and STDERR, i.e. there will be a '.o' and a '.po' file
-  * '#$ -o /path/filname' sets the STDOUT to a certain filename, i.e one gets the file specified with '-o' plus a '.e' and a '.pe' file
-  * '#$ -e /path/filname' sets the STDERR to a certain filename, three files in analogy to the '-o' option
-  * combination of '-j' with '-o' is possible, '-e' is ignored if '-j' is used.
-When using the '-o' and '-e' options following pseudo variables can be used for specifying the path/filenames. NOTE: The
-variables can not be used as in a bash environment, i.e. using ${HOME} will not work.
-  * $HOME       home directory on execution machine
-  * $USER       user ID of job owner
-  * $JOB_ID     current job ID
-  * $JOB_NAME   current job name
-  * $HOSTNAME   name of the execution host
-  * $TASK_ID    array job task index number
-For further details see 'man qsub' on the login nodes of VSC.
-=== Ordinary shell redirection ===
-Since the job is executed in an shell environment, the output of any shell command can be redirected to any file:
-<code>
-echo hello > /path/file
-</code>
-==== Overcommitting memory of the compute nodes on VSC-2 ====
-By default only 32 GB of (the physically available) memory can be allocated by applications  on the compute nodes of VSC-2. Some applications however
-have to allocate larger amounts of memory than the physical limit (but although allocated, it is never used). For such cases a kernel parameter of the
-compute nodes can be changed in order to allow for overcommittment of the memory:
-<code>
-#$ -N test
-#$ -pe mpich 32
-#$ -l overcommit_mem=true
-</code>