Re: Inserting Parallel argument into command script

[Shlomi Fish]

Hi Miriam,

Please reply to list:

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On Fri, 19 Jun 2020 11:49:22 +1200
Miriam Dixon <miriam.gatemc@gmail.com> wrote:

> Hi,
> 
> I am very new to Parallel, Linux, and computing in general but I need to
> use it for my Masters Thesis, so I am doing my best to learn quickly.
> 

Welcome aboard!

> For my project, I am running a simulation using GATE, and I have a shell
> script to run the simulation for each of four different projection angles.
> I want to run each projection angle simulation on a different core, to
> speed things along and use the computer memory efficiently. I tried to do
> this by pulling projAngles out of my script and calling it as a parallel
> argument.
> 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")
> 

As far as I know "--projAngles" in the shell script's command line arguments
does not automatically propagate to a shell variable. E.g:

```
[shlomif@telaviv1 ~]$ cat miriam-test.bash                  
#! /bin/bash
#
# miriam-test.bash
# Copyright (C) 2020 Shlomi Fish <shlomif@cpan.org>
#
# Distributed under the terms of the MIT license.
#
echo "argv = < $@ >"
echo "projAngles = < $projAngles >"
[shlomif@telaviv1 ~]$ bash miriam-test.bash --projAngles 500
argv = < --projAngles 500 >
projAngles = <  >
[shlomif@telaviv1 ~]$ projAngles=500 bash miriam-test.bash  
argv = <  >
projAngles = < 500 >
[shlomif@telaviv1 ~]$  
```

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> 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?
> 

Either parse the cmd line arguments (using $1 / shift / $@ / etc.) or pass them
to the script using https://en.wikipedia.org/wiki/Environment_variable .

> Cheers,
> Miriam



-- 

Shlomi Fish       https://www.shlomifish.org/
Star Trek: “We, the Living Dead” - https://shlom.in/st-wtld

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