While loop stops reading after the first line in Bash

Question

I have the following shell script. The purpose is to loop thru each line of the target file (whose path is the input parameter to the script) and do work against each line. Now, it seems only work with the very first line in the target file and stops after that line got processed. Is there anything wrong with my script?

#!/bin/bash
# SCRIPT: do.sh
# PURPOSE: loop thru the targets 

FILENAME=$1
count=0

echo "proceed with $FILENAME"

while read LINE; do
   let count++
   echo "$count $LINE"
   sh ./do_work.sh $LINE
done < $FILENAME

echo "\ntotal $count targets"

In do_work.sh, I run a couple of ssh commands.

Factotum

Are you sure it's exactly the code that stops after the first line? – Dichy

Your script is fine, but there might be something wrong with the do_work.sh – Calathus

Yes, it could eat up all input, or it could be invoked as source and simply exit or exec. But this code doesn't look genuine, the OP would notice that echo requires -e to display line feed properly... – Dichy

Does do_work.sh run ssh by any chance? – Illustration

yes, do_work.sh runs a couple ssh commands. anything special about that? – Factotum

Better you show the do_work.sh source and also run do.sh with set -x to debug. – Thorathoracic

Answer 1

The problem is that do_work.sh runs ssh commands and by default ssh reads from stdin which is your input file. As a result, you only see the first line processed, because the command consumes the rest of the file and your while loop terminates.

This happens not just for ssh, but for any command that reads stdin, including mplayer, ffmpeg, HandBrakeCLI, httpie, brew install, and more.

To prevent this, pass the -n option to your ssh command to make it read from /dev/null instead of stdin. Other commands have similar flags, or you can universally use < /dev/null.

Illustration

Very useful, helped me to run this zsh oneliner: cat hosts | while read host ; do ssh $host do_something ; done – Backsight

@Backsight You still want to avoid the useless cat. You'd think a rodent in particular would be wary of this. – Racket

while read host ; do $host do_something ; done < /etc/hosts would avoid it. That's quite a life saver, thanks! – Backsight

httpie is another command that reads STDIN by default, and will suffer from the same behavior when called inside a bash or fish loop. Use http --ignore-stdin or set standard input to /dev/null as above. – Weighin

What will be the solution for gcloud compute ssh case? – Seemly

Answer 2

A very simple and robust workaround is to change the file descriptor from which the read command receives input.

This is accomplished by two modifications: the -u argument to read, and the redirection operator for < $FILENAME.

In BASH, the default file descriptor values (i.e. values for -u in read) are:

• 0 = stdin
• 1 = stdout
• 2 = stderr

So just choose some other unused file descriptor, like 9 just for fun.

Thus, the following would be the workaround:

while read -u 9 LINE; do
   let count++
   echo "$count $LINE"
   sh ./do_work.sh $LINE
done 9< $FILENAME

Notice the two modifications:

1. read becomes read -u 9
2. < $FILENAME becomes 9< $FILENAME

As a best practice, I do this for all while loops I write in BASH. If you have nested loops using read, use a different file descriptor for each one (9,8,7,...).

Heraldic

Thanks! this is actually the best solution here IMO – Papism

Thank you very much! This looks also like the best solution for me right know because with this one you don't need to find the problematic command if you have larger scripts. – Constitutionality

This is a really nice trick. It can be quite a surprise that arbitrary commands end up reading stdin. In my case it was sloccount. This is general solution that doesn't require reading command specific man pages (if any). – Heda

This is IMHO a better solution than the accepted one. There are other commands besides ssh that read stdin, messing up the while loop. This solution, to use a different file descriptor, allowed me to keep existing called infrastructure in the loop the same. This allowed me to avoid having to test interactions with sshpass, or other programs in the loop that might affect stdin. Thanks!! – Intrastate

Thanks! this worked for me, saves amended the many ssh commands i had. Although i tried the preferred solution of Dogbane, adding the -n and </dev/null also worked in my case, but i prefer this one as its just changing the while loop. A very tidy solution that i will try to commit to memory! – Menorca

The -u option to read is a bashism; to make this portable to shells other than bash, just use while read LINE <&9; do. – Steiermark

Answer 3

More generally, a workaround which isn't specific to ssh is to redirect standard input for any command which might otherwise consume the while loop's input.

while read -r line; do
   ((count++))
   echo "$count $line"
   sh ./do_work.sh "$line" </dev/null
done < "$filename"

The addition of </dev/null is the crucial point here, though the corrected quoting is also somewhat important for robustness; see also When to wrap quotes around a shell variable?. You will want to use read -r unless you specifically require the slightly odd legacy behavior you get for backslashes in the input without -r. Finally, avoid upper case for your private variables.

Another workaround of sorts which is somewhat specific to ssh is to make sure any ssh command has its standard input tied up, e.g. by changing

ssh otherhost some commands here

to instead read the commands from a here document, which conveniently (for this particular scenario) ties up the standard input of ssh for the commands:

ssh otherhost <<'____HERE'
    some commands here
____HERE

Racket

Answer 4

ssh -n option prevents checking the exit status of ssh when using HEREdoc while piping output to another program. So use of /dev/null as stdin is preferred.

#!/bin/bash
while read ONELINE ; do
   ssh ubuntu@host_xyz </dev/null <<EOF 2>&1 | filter_pgm 
   echo "Hi, $ONELINE. You come here often?"
   process_response_pgm 
EOF
   if [ ${PIPESTATUS[0]} -ne 0 ] ; then
      echo "aborting loop"
      exit ${PIPESTATUS[0]}
   fi
done << input_list.txt

Cauldron

This doesn't make sense. The <<EOF overrides the </dev/null redirection. The << redirection after the done is wrong. – Racket

Answer 5

This was happening to me because I had set -e and a grep in a loop was returning with no output (which gives a non-zero error code).

Rain

You beauty, just saved my afternoon – Goshawk

Perhaps see #19622698 for more details about set -e – Racket

Answer 6

I had a similar problem but I was not reading from a file but from a bash variable containing some csv data, so the file descriptor thing did not work for me.
My solution was to feed some empty input into the program that was stealing data from stdin via
echo -n | input_stealing_program

Example:

csv_data="Germany,Berlin
France,Paris
Enland,London"

# Set IFS to comma for parsing CSV
IFS=','

while read -r country capital; do
    echo -n | input_stealing_programm $country $capital
done <<< "$csv_data"

An alternative would be input_stealing_program < /dev/null

Meilen