Modules not loaded into environment [duplicate]

Question

I have the following line in my .bashrc file:

cat "$HOME/.module_list" | while read m; do echo "Loading module $m..."; module load "$m"; done

where $HOME/.module_list is a file that contains the name of a module to load on each row. When .bashrc is sourced, the line goes through each module in the list one by one and seemingly loads them, but afterwards, when I do module list, none of the modules are loaded.

Does this line create a new scope into which the modules are loaded, which is then terminated as soon as the line finishes, or why aren't the modules still loaded afterwards? How can I successfully load all modules from the list and still have them be loaded afterwards?

by default commands after the pipeline (|) would run in a subshell and its env would be gone when the | command completes. — sexpect - Expect for Shells
– sexpect - Expect for Shells, Commented Jun 7, 2022 at 16:28
See BashFAQ/024 (I set variables in a loop that's in a pipeline. Why do they disappear after the loop terminates? Or, why can't I pipe data to read?). — pjh
– pjh, Commented Jun 7, 2022 at 16:39
Also see Append to an array variable from a pipeline command, A variable modified inside a while loop is not remembered, and Capturing output of find . -print0 into a bash array. — pjh
– pjh, Commented Jun 7, 2022 at 16:40

Fravadona · Accepted Answer · 2022-06-07 16:26:03Z

1

A simple solution is to load your modules names into an array:

#!/bin/bash

readarray -t modules < ~/.module_list

module load "${modules[@]}"

An other solution is to use a while read loop, making sure to avoid the |:

#!/bin/bash

while IFS='' read -r m
do
    module load "$m"
done < ~/.module_list

edited Jun 7, 2022 at 16:26

answered Jun 7, 2022 at 16:20

Fravadona

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4 Comments

HelloGoodbye Over a year ago

Ok, thank you! In the second alternative, which command is it that gets ~/.module_list as input? I'm not that familiar with the < syntax.

Fravadona Over a year ago

The whole while loop (i.e. each command in it) will "share" the content of ~/.module_list as input; in this aspect, it's 100% equivalent to cat ~/.module_list | while

HelloGoodbye Over a year ago

Also, what is IFS in the second alternative?

Fravadona Over a year ago

It's not really needed here, it's just a habit of mine. Setting IFS to the empty string in the read command is for making sure that the leading/trailing blanks characters are not stripped from the line

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