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Bash shell tutorial

Training materials for using the bash (and zsh) shell.

View the Project on GitHub berkeley-scf/tutorial-using-bash

This project is maintained by berkeley-scf, the UC Berkeley Statistical Computing Facility.

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Managing processes

A process is a program that is being executed. Processes have the following attributes:

  • A lifetime.
  • A process ID (PID).
  • A user ID (UID).
  • A group ID (GID).
  • A parent process with its own ID (PPID).
  • An environment.
  • A current working directory.

Anytime you do something on the computer, one or more processes will start up to carry out the activity.

1 Monitoring

1.1 Monitoring processes

ps

Examining subprocesses of your shell with ps:

$ ps
PID   TTY          TIME CMD
19370 pts/3    00:00:00 bash
22846 pts/3    00:00:00 ps

Examining in more detail subprocesses of your shell with ps:

$ ps -f
UID        PID  PPID  C STIME TTY          TIME CMD
jarrod   19370 19368  0 10:51 pts/3    00:00:00 bash
jarrod   22850 19370  0 14:57 pts/3    00:00:00 ps -f

Examining in more detail all processes on your computer:

$ ps -ef
UID        PID  PPID  C STIME TTY          TIME CMD
root         1     0  0 Aug21 ?        00:00:05 /usr/lib/systemd
root         2     0  0 Aug21 ?        00:00:00 [kthreadd]
root         3     2  0 Aug21 ?        00:00:07 [ksoftirqd/0]
root         5     2  0 Aug21 ?        00:00:00 [kworker/0:0H]
<snip>
root     16210     1  0 07:19 ?        00:00:00 login -- jarrod
jarrod   16219 16210  0 07:19 tty1     00:00:00 -bash
jarrod   16361 16219  0 07:19 tty1     00:00:00 /bin/sh /bin/startx
<snip>

You can use the -u option to see percent CPU and percent memory used by each process. You can use the -o option to provide your own user-defined format; for example, :

$ ps -o pid,ni,pcpu,pmem,user,comm
PID    NI %CPU %MEM USER     COMMAND
18124   0  0.0  0.0 jarrod   bash
22963   0  0.0  0.0 jarrod   ps

To see the hierarchical process structure (i.e., which processes started which other processes), you can use the pstree command.

top

Examining processes with top:

$ top
top - 13:49:07 up  1:49,  3 users,  load average: 0.10, 0.15, 0.18
Tasks: 160 total,   1 running, 158 sleeping,   1 stopped,   0 zombie
%Cpu(s):  2.5 us, 0.5 sy, 0.0 ni, 96.9 id, 0.0 wa, 0.0 hi, 0.0 si, 0.0 st
KiB Mem : 7893644 total, 5951552 free, 1085584 used,  856508 buff/cache
KiB Swap: 7897084 total, 7897084 free,       0 used. 6561548 avail Mem

PID USER      PR  NI    VIRT    RES    SHR S  %CPU %MEM     TIME+ COMMAND
1607 jarrod   20   0 2333568 974888 212944 S  12.5 12.4  11:10.67 firefox
3366 jarrod   20   0  159828   4312   3624 R   6.2  0.1   0:00.01 top
   1 root     20   0  193892   8484   5636 S   0.0  0.1   0:01.78 systemd
<snip>

The first few lines show general information about the machine, while the remaining lines show information for each process.

  • The RES column indicates the amount of memory that a process is using (in bytes, if not otherwise indicated).
  • The %MEM shows that memory use relative to the physical memory available on the computer.
  • The %CPU column shows the proportion of a CPU core that the process is using (which can exceed 100% if a process is threaded).
  • The TIME+ column shows the amount of time the process has been running.

To quit top, type q.

You can also kill jobs (see below for further details on killing jobs) from within top: just type r or k, respectively, and proceed from there.

1.2 Monitoring memory use

One of the main things to watch out for is a job that is using close to 100% of memory and much less than 100% of CPU. What is generally happening is that your program has run out of memory and is using virtual memory on disk, spending most of its time writing to/from disk, sometimes called paging or swapping. If this happens, it can be a very long time, if ever, before your job finishes.

Note that the per-process memory use reported by top and ps may “double count” memory that is being used simultaneously by multiple processes. To see the total amount of memory actually available on a machine:

free -h

              total        used        free      shared  buff/cache   available
Mem:           251G        998M        221G        2.6G         29G        247G
Swap:          7.6G        210M        7.4G

You’ll generally be interested in the Memory row and in the total, used and available columns. The free column can be confusing and does not actually indicate how much memory is still available to be used, so you’ll want to focus on the available column.

2 Job Control

2.1 Foreground and background jobs

When you run a command in a shell by simply typing its name, you are said to be running in the foreground. When a job is running in the foreground, you can’t type additional commands into that shell session, but there are two signals that can be sent to the running job through the keyboard. To interrupt a program running in the foreground, use Ctrl-c; to quit a program, use Ctrl-\. While modern windowed systems have lessened the inconvenience of tying up a shell with foreground processes, there are some situations where running in the foreground is not adequate.

The primary need for an alternative to foreground processing arises when you wish to have jobs continue to run after you log off the computer. In cases like this you can run a program in the background by simply terminating the command with an ampersand (&). However, before putting a job in the background, you should consider how you will access its results, since stdout is not preserved when you log off from the computer. Thus, redirection (including redirection of stderr) is essential when running jobs in the background. As a simple example, suppose that you wish to run a Python script, and you don’t want it to terminate when you log off.

$ python code.py > code.pyout 2>&1 &

What does the inscrutable 2>&1 do? It says to send stderr to the same place as stdout, which in this case has been redirected to code.pyout.

If you forget to put a job in the background when you first execute it, you can do it while it’s running in the foreground in two steps. First, suspend the job using the Ctrl-z signal. After receiving the signal, the program will interrupt execution, but it will still have access to all files and other resources. Next, issue the bg command, which will start the stopped job running in the background.

2.2 Listing and killing jobs

Since only foreground jobs will accept signals through the keyboard, if you want to terminate a background job you must first determine the unique process id (PID) for the process you wish to terminate through either ps or top. Here we’ll illustrate use of ps again.

To see all processes owned by a specific user (e.g., jarrod), I can use the -U jarrod option:

$ ps -U jarrod

If I want to get more information (e.g., %CPU and %MEM), I can use add the -u option:

$ ps -U jarrod -u
USER       PID %CPU %MEM    VSZ   RSS TTY      STAT START    TIME COMMAND
jarrod   16116 12.0  6.0 118804  5080 tty1     Ss   16:25  133:01 python

In this example, the ps output tells us that this python job has a PID of 16116, that it has been running for 133 minutes, is using 12% of CPU and 6% of memory, and that it started at 16:25. You could then issue the command:

$ kill 16116

or, if that doesn’t work:

$ kill -9 16116

to terminate the job. Another useful command in this regard is killall, which accepts a program name instead of a process id, and will kill all instances of the named program (in this case, R):

$ killall R

Of course, it will only kill the jobs that belong to you, so it will not affect the jobs of other users. Note that the ps and kill commands only apply to the particular computer on which they are executed, not to the entire computer network. Thus, if you start a job on one machine, you must log back into that same machine in order to manage your job.

Finally, let’s see how to build up a command to kill firefox using some of the tools we’ve seen. First let’s pipe the output of ps -e to grep to select the line corresponding to firefox:

$ ps -e | grep firefox
16517 ?        00:10:03 firefox

We can now use awk to select the first column, which contains the process ID corresponding to firefox:

$ ps -e | grep firefox | awk '{ print $1 }'
16517

Finally, we can pipe this to the kill command using xargs or command substitution:

$ ps -e | grep firefox | awk '{ print $1 }' | xargs kill
$ kill $(ps -e | grep firefox | awk '{ print $1 }')

As mentioned before, we can’t pipe the PID directly to kill because kill takes the PID(s) as argument(s) rather than reading them from stdin.

3 Screen

Screen allows you to create virtual terminals, which are not connected to your actual terminal or shell. This allows you to run multiple programs from the command line and leave them all in the foreground in their own virtual terminal. Screen provides facilities for managing several virtual terminals including:

  • listing them,
  • switching between them, and
  • disconnecting from one machine and then reconnecting to an existing virtual terminal from another.

While we will only discuss its basic operation, we will cover enough to be of regular use. tmux is an alternative to screen.

Calling screen:

$ screen

will open a single window and you will see a new bash prompt. You just work at this prompt as you normally would. The difference is that you can disconnect from this window by typing Ctrl-a d and you will see something like this :

$ screen
[detached from 23974.pts-2.t430u]

tip

All the screen key commands begin with the control key combination Ctrl-a followed by another key. For instance, when you are in a screen session and type Ctrl-a ?, screen will display a help screen with a list of its keybindings.

You can now list your screen sessions :

$ screen -ls
There is a screen on:
	23974.pts-2.t430u       (Detached)

To reconnect :

$ screen -r

You can start multiple screen sessions. This is what it might look like if you have 3 screen sessions:

$ screen -ls
There are screens on:
	24274.pts-2.t430u       (Attached)
	24216.pts-2.t430u       (Detached)
	24158.pts-2.t430u       (Detached)

with the first session active on a machine.

To specify that you want to reattach to session 24158.pts-2.t430u, type:

$ screen -r 24158.pts-2.t430u

If you have several screen sessions, you will want to name your screen session something more informative than 24158.pts-2.t430u. To name a screen session gene-analysis you can use the -S option when calling screen:

$ screen -S gene-analysis

While there are many more features and keybindings available for screen, you’ve already seen enough screen to be useful. For example, imagine you ssh to a remote machine from your laptop to run an analysis. The first thing you do at the bash prompt on the remote machine is:

$ screen -S dbox-study

Then you start your analysis script dbox-analysis.py running:

$ dbox-analysis.py
Starting statistical analysis ...
Processing subject 1 ...
Processing subject 2 ...

If your study has 50 subjects and processing each subject takes 20 minutes, you will not want to sit there watching your monitor. So you use Ctrl-a d to detach the session and you will then see:

$ screen -S dbox-study
[detached from 2799.dbox-study]
$

Now you can log off your laptop and go home. Sometime after dinner, you decide to check on your job. So you ssh from your home computer to the remote machine again and type the following at the bash prompt:

$ screen -r dbox-study

You should then be able to see the progress of your analysis script, as if you had kept a terminal open the whole time.