Control Flow

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This page continues the Bash scripting tutorial by introducing conditionals, loops, and common control-flow patterns. These constructs allow scripts to make decisions, repeat tasks, and automate complex workflows.

In Bash, commands return an exit code:

0 → success (true)
non-zero → failure (false)

ls /tmp        # success → exit code 0
ls /nope       # failure → exit code != 0

You can check the last exit code with:

echo $?

This is the foundation for conditionals in shell scripts.

Conditionals

Basic `if`/`else` statements

if command; then
  echo "Command succeeded"
else
  echo "Command Failed!"
fi

Test Expressions

Test	Meaning
`-f file`	Regular file exists
`-d dir`	Directory exists
`-e path`	Path exists
`-r file`	Readable
`-w file`	Writable
`-x file`	Executable

if [[ -d "$SCRATCH" ]]; then
  echo "Scratch directory exists"
fi

String Tests

Test	Meaning
`-z str`	String is empty
`-n str`	String is not empty
`str1 == str2`	Equal
`str1 != str2`	Not equal

if [[ -z "$1" ]]; then
  echo "Usage: $0 <filename>"
  exit 1
fi

Numeric Comparisons

Operator	Meaning
`-eq`	equal
`-ne`	not equal
`-lt`	less than
`-le`	less or equal
`-gt`	greater than
`-ge`	greater or equal

if [[ "$N" -gt 10 ]]; then
  echo "Large job"
fi

Logical Operators

Operator	Meaning
`&&`	AND
`\|\|`	OR
`!`	NOT

if [[ -f input.dat && -d /path/to/data ]]; then
  echo "Input file and Data directory present!"
fi

Loops

Basic For loop

for x in a b c; do
  echo "$x"
done

Loop Over Files

for f in *.py; do
  echo "Processing $f"
  python $f
done

Numeric Loop

for i in {1..5}; do
  echo "Iteration $i"
done

Alternatively,

for ((i=1; i<=5; i++)); do
  echo "$i"
done

`while` Loops

While loops are also available in bash. Note that this example uses an expression to increment count.

count=0
while [ "$count" -lt 5 ]; do
  echo "$count"
  ((count++))
done

Reading files with `while`

One of the most common uses of a while loop is using a file. Note that this example uses a < to read input from a file. We'll talk more about this in the pipes section!

while read -r line; do
  echo "$line"
done < input.txt

Examples

#!/bin/bash

if [[ -z "$SLURM_JOB_ID" ]]; then
  echo "Must be run inside Slurm"
  exit 1
fi

for gpu in $(nvidia-smi --query-gpu=index --format=csv,noheader); do
  echo "GPU $gpu active"
done

for input in $(ls -d ./replicate*); do 
  sbatch myjob.sub $input
  sleep 0.1
done

Common Pitfalls

Warning

Spaces matter: [ "$x" = 1 ], not ["$x"=1]
Use quotes to avoid word splitting
Remember: 0 means success
If a command fails, bash will continue to move on through the script!

Next Section: Pipes