What does this bash line do? (HPC)

Asked Sep 19 '16 at 20:03

Active Sep 19 '16 at 20:03

Viewed 39 times

The context here is a Beowulf HPC cluster. I will simplify the code:

for img in $images; do
    script=$(mktemp)
    cat > $script <<EOF ######## What does this line do?
    module load mymodule
    my_processing -with $img
    EOF

    # cat $script
    # qsub $script
done

The script can be printed to screen to verify all paths have been resolved correctly by uncommenting the cat $script line, and similarly submitted as a job by uncommenting the qsub $script line. I have basic understanding of the > operator, but to my understanding it is cating nothing into the $script... Obviously that's not what's really happening because this all works.

asked Sep 19 '16 at 20:03

reas0n

1

it's a heredoc (`< $script`) – Marc B Sep 19 '16 at 20:04
1

Manual: https://www.gnu.org/software/bash/manual/bashref.html#Here-Documents – Benjamin W. Sep 19 '16 at 20:07
Open `man bash` and search on `<<` and you find a detailed explanation of here-documents. – John1024 Sep 19 '16 at 20:13
So the file descriptor in this case is `cat > $script`? – reas0n Sep 19 '16 at 20:15
It writes the 2 lines between `cat` and `EOF` into the file `$script`. – Mark Setchell Sep 19 '16 at 20:21
I know what it does, just confused on the how... – reas0n Sep 19 '16 at 20:23
`>` is redirection. It sends the output to `$script`. `<<` starts a here-document. – John1024 Sep 19 '16 at 20:25
Got it. I didn't realize I could run `cat > $file`, I just thought you always had to have something before the `>`. Thanks. – reas0n Sep 19 '16 at 20:27
When used without an argument, `cat` copies stdin to stdout. The here-document counts as stdin. – John1024 Sep 19 '16 at 20:40
1

`cat` is the simplest case of a class of programs called *filter programs*. They process filenames specified as parameters or, if none are specified, read from standard input. https://en.wikipedia.org/wiki/Filter_(software)#Unix – cdarke Sep 19 '16 at 21:25

What does this bash line do? (HPC)

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