Hi,
Am 03.03.2014 um 16:05 schrieb Pablo Escobar:
> Hi guys
>
> I am running this submit script which works fine and generates a new file
> "myout.txt" which contains the string "test"
>
> #!/bin/bash
> #$ -N test
> #$ -l h_vmem=1G
> #$ -cwd
> echo "test" > myout.txt
>
>
> But when I try to do the same in an array job it's not working :?
>
> This is my submit script:
>
> #!/bin/bash
> #$ -N testArray
> #$ -l h_vmem=1G
> #$ -cwd
> #$ -t 1-1
> SEEDFILE=$PWD/cmd.txt
> SEED=$(cat $SEEDFILE | head -n $SGE_TASK_ID | tail -n 1)
SEED=$(sed -n ${SGE_TASK_ID}p $SEEDFILE)
might be shorter.
> $SEED
>
>
> This is my cmd.txt:
>
> $ cat cmd.txt
> echo "test" > myoutput.txt
>
> But when submitting this intead of getting a new file "myoutput.txt" I get
> the normal grid engine STDOUT file wich contains everything right after the
> "echo" command:
>
> $ cat testArray.o1769682.1
> "test" > myoutput.txt
>
> I have tried to redirect stdout and stderr with &>, also tried "qsub -o
> /dev/null -j y" and a few other variantes without luck
This happens, as bash is not re-interpreting the content of the string again
(it knows about the ">" only after it expanded $SEED already). What will do it:
eval $SEED
NB: http://mywiki.wooledge.org/BashFAQ/048
-- Reuti
> any clue about how I can manage to get standar stdout redirections working in
> an array job? I know I could use -o and -e but my users WANT to do it like
> this....
>
> thanks in advance for any help.
> Pablo.
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