Re: Inserting Parallel argument into command script

[Ernst, Kevin]

(reply below)

On 18.06.20 at 19:49, Miriam Dixon wrote:
> parallel runSim.sh --projAngles {1} ::: 0 45 90 135
>
> This seemed to work, in that it started my runSim.sh, but it didn't 
> use the value from projAngles within the script,
> time=$(bc -l <<< "$projAngles*$timePerProjection")
>
> Is there a way in the script or in parallel to insert the particular 
> projAngles value for that run, and use it to calculate the next step?

Hi Miriam,

Your 'parallel' command seems perfectly fine (you /could/ leave out the 
"1" in the "{}" as it's optional when there's only one argument, but 
that's up to you). Perhaps it's a shell scripting error?

Doing my best to imagine what the inside of your 'runSim.sh' script 
might look like, I came up with this:

     #!/bin/bash
     timePerProjection=10
     projAngles=${2:?Missing argument}
     time=$(bc -l <<< "$projAngles*$timePerProjection")
     echo $time

And running Parallel 20200122, I get (what I expected to be) the proper 
result

     $ parallel ./runSim.sh --projAngles {1} ::: 0 45 90 135
     0
     450
     900
     1350

It might help to just put

     echo $projAngles
     exit

somewhere early on in your script, just so you can be sure that the 
variable is being assigned properly given the option to the 
'--projAngles' command-line argument.

Also, adding 'set -u' at the top of your script will cause it to 
terminate (with an error message) any time a variable is used without 
being defined first. I add this to the top of all of my Bash scripts, 
for sanity's sake.

Lastly, as an aside, I find the '--dry-run' option to Parallel itself 
really handy when I'm preparing to run something with Parallel.

Hope this helps.

—Kevin