BCH709 Introduction to Bioinformatics: Process Management

Process Management

Managing processes is essential for running long bioinformatics analyses.

Step 1: View Running Processes

# Show your current processes
ps

  PID TTY          TIME CMD
12345 pts/0    00:00:00 bash
12400 pts/0    00:00:00 ps

# Show all processes (abbreviated output)
ps aux | head -5

USER       PID %CPU %MEM    VSZ   RSS TTY   STAT START   TIME COMMAND
root         1  0.0  0.1  16894  1340 ?     Ss   Jan19   0:02 /sbin/init
root         2  0.0  0.0      0     0 ?     S    Jan19   0:00 [kthreadd]
...

# Interactive view (press 'q' to quit)
top

Step 2: Run Commands in Background

# Start a long-running process (sleep simulates a long job)
sleep 60 &

[1] 12456

# List background jobs
jobs

[1]+  Running                 sleep 60 &

# Bring to foreground
fg %1
# Press Ctrl+C to stop, or Ctrl+Z to suspend

Step 3: Kill Processes

# Start a background process
sleep 300 &

[1] 12500

# Kill by job number
kill %1
jobs

[1]+  Terminated              sleep 300

# Or kill by PID
sleep 300 &
ps | grep sleep

12510 pts/0    00:00:00 sleep

kill 12510

Step 4: Keep Processes Running After Logout

# nohup keeps process running after you log out
nohup sleep 120 > mysleep.log 2>&1 &

[1] 12600

# Check it's running
jobs
ps aux | grep sleep

# You can now log out and the process continues!

Process Signals Reference