SSH session termination on script error when sourcing multiple sub-scripts

Question

I'm facing an issue with SSH on a server. Running individual scripts (source s01.sh, etc.) works fine, with errors displayed in the console. However, when using a master script to source these scripts, the SSH connection unexpectedly terminates upon encountering an error. The master script master.sh is as follows:

#!/bin/bash
set -e

source s01.sh
source s02.sh
Rscript s03.R
source s04.sh

I source the master script in interactive SSH session using

source master.sh

With set -e, I expect the script to stop at errors, but instead, it's causing the entire SSH session to drop. This only happens with the combined script, not with individual sourcing. Why does this occur, and how can I keep the SSH session from closing on script errors?

I am aware this might involve SSH server configurations, but I'm unsure which settings to investigate.

Answer 1

The reason this is happening is because you are sourcing the master script. I can reproduce the behavior you describe using these two toy examples:

terdon@oregano ~ $ cat ~/scripts/foo.sh
#!/bin/bash
set -e
source /home/terdon/scripts/bar.sh
echo "done!"

terdon@oregano ~ $ cat ~/scripts/bar.sh
#!/bin/bash

echo "start"
false

Now, if I open a new terminal and run . ~/scripts/foo.sh (note that source is a non-portable bash alias to the standard . command, so . foo is the same as source foo), the terminal I opened just exits. And if I try it in an ssh session, the ssh session exits. Why? Because sourcing means executing the commands and applying them to the current session. So since one of the scripts causes an error (the command false just exits with 1), the set -e causes the session to exit. It doesn't just kill the script because you have told it to apply the commands to the current shell session by sourcing instead of executing.

However, from your example, it looks like you don't need to source the master script, all you want is to source the other scripts which presumably are setting up the environment needed by your R script. So just execute instead of sourcing and you should be fine:

/path/to/master.sh

Or, if you haven't made it executable:

bash /path/to/master.sh

See this post for more on sourcing vs executing.