C2110 UNIX and programming Lesson 3 / Module 1 -1C2110
UNIX and programming
Petr Kulhanek
kulhanek@chemi.muni.cz
National Center for Biomolecular Research, Faculty of Science
Masaryk University, Kamenice 5, CZ-62500 Brno
Lesson 3 / Module 1
PS / 2020 Distance form of teaching: Rev1
C2110 UNIX and programming Lesson 3 / Module 1 -2-
Processes
C2110 UNIX and programming Lesson 3 / Module 1 -3Internal
Scheme of a Computer
north
bridge
north
bridge
south
bridge
south
bridgeUSB
mouse, keyboard
real time clock
SATA controllers
hard drives
BIOS
graphics
system
memory
memory controller
peripherals with fast access
via PCI Express
network
(ethernet)
sound
PCI bus
computational cores (CPU core)
processor
number of CPU cores > 1
= SMP computer
Operating system ensures running
of programs (processes) on the
processors and optimal use of
other resources (memory, disk
capacity). Multitasking technique
is used in management of
processes.
C2110 UNIX and programming Lesson 3 / Module 1 -4Process
and Multitasking
Process in informatics is the name for a running computer program. The process is located
in the computer operating memory as the sequence of machine instructions executed by
the processor. It contains not only the code of the executed program, but also dynamically
changing data that the process processes. One program can run on the computer as
multiple processes with different data (for example, a web browser running multiple times
that displays different pages). Management of processes is performed by the operating
system, which ensures their separate running, allocates them computer system resources
and allows the user to manage processes (start, stop, etc.).
Multitasking in computer science indicates the ability of the operating system to perform
several processes simultaneously (at least seemingly). The core of the operating system
very quickly switches processes running on the processor or processors (so-called change
of context), so that the computer user has the impression that they are running at the
same time.
edited from wikipedia.org
C2110 UNIX and programming Lesson 3 / Module 1 -5SMP
- Symmetric Multiprocessing
memory
processor
Symmetric multiprocessing (SMP) in infomatics is a type of multiprocessor systems in
which all processors of the computer are equivalent. Increasing the number of processors
that share the same operating memory on the computer leads to increase of computer
performance, although not in a linear way, because part of the power is consumed for
overhead (locking data structures, controlling processors and their communication with
each other).
computational core (CPU core)
In the past, the performance of processors increased, in addition to better architecture,
also by speed of instruction processing (processor frequency), which nowadays encounters
physical limitations of the technology used (reliability, heat loss, ...). Another direction was
the introduction of more computing cores (approximately since 2005 for x86 architecture)
on one physical chip. Today's computers now commonly have more than one processor.
CPU - central processing unit
edited from wikipedia.org
C2110 UNIX and programming Lesson 3 / Module 1 -6Overview
of Running Processes
Processes can be listed with the following commands:
ps lists the processes running in the given terminal or according to the specified
specifications
(ps -u user_name)
top continuously displays processes sorted by their CPU load (end with q key)
pstree a list showing the hierarchy of processes
$ ps
PID TTY TIME CMD
8763 pts/5 00:00:00 bash
8852 pts/5 00:00:00 gimp
8857 pts/5 00:00:00 ps
process number
the terminal in which the process is running
consumed machine time
name of the running command
C2110 UNIX and programming Lesson 3 / Module 1 -7Overview
of Running Processes - top
By command top, it is possible to monitor running processes at regular intervals. The
command is terminated by the key q (quit).
top - 13:05:58 up 16 days, 2:27, 2 users, load average: 2.95, 3.10, 3.03
Tasks: 150 total, 3 running, 147 sleeping, 0 stopped, 0 zombie
%Cpu(s): 0.3 us, 0.1 sy, 10.6 ni, 88.9 id, 0.1 wa, 0.0 hi, 0.0 si, 0.0 st
KiB Mem: 8138412 total, 8005624 used, 132788 free, 210168 buffers
KiB Swap: 4194300 total, 168 used, 4194132 free. 7239188 cached Mem
PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
3351 ivo 39 19 46784 29872 772 R 100.0 0.4 24:16.67 sc
30745 root 20 0 51732 1228 400 S 13.0 0.0 8:15.87 systemd-udevd
1 root 20 0 104664 4984 2736 S 6.5 0.1 6:36.74 init
383 root 20 0 19596 948 628 S 6.5 0.0 4:30.06 upstart-udev-br
2 root 20 0 0 0 0 S 0.0 0.0 0:00.70 kthreadd
process
number
process owner
priority
state: S - sleeping, R - running,
D - uninterruptable sleep (waiting for a device)
memory CPU and memory
usage CPU time consumed
program name
CPU load in a fraction (1.0 = 100%)
in the last 1, 5 and 15 minutes
system response may be slow
if swap memory is used
C2110 UNIX and programming Lesson 3 / Module 1 -8Run
Commands and Applications
1. The path to the command is first searched in the table with already used commands:
$ hash
hits command
1 /bin/rm
3 /bin/ls
2. If the command is not found, it is searched in the directories specified in the system
variable PATH, which are separated by a colon.
$ echo $PATH
3. If the command is not found, an error is indicated. Otherwise, the command is run and
the path is stored in a table.
directory search order
The table can be deleted with the command:
$ hash -r
In order to run a command, shell needs to know the way to the file that contains a binary
program or script.
$ prt
bash: prt: command not found
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:
/bin:/usr/games:/usr/local/games:/snap/bin:/usr/bin
C2110 UNIX and programming Lesson 3 / Module 1 -9Modification
of PATH variable
Manual change of variable PATH
$ export PATH=/moje/cesta/k/mym/prikazum:$PATH
separator sign
The path to the directory containing the
commands that I want to be accessible
without specifying the path.
The path is always stated absolutely! (listing
relative paths is a safety risk) The original value of the variable PATH
(required to find system commands)
Automated change of variable PATH
The automated change of the PATH variable (and possibly other system variables) is
performed by the command module.
$ module add vmd This will be disucessed in Lesson 4
C2110 UNIX and programming Lesson 3 / Module 1 -10Path
to a command or application, if it exists, can be found by the command type or
whereis
$ type ls
ls is aliased to ‘ls --color=auto’
$ whereis ls
ls: /bin/ls /usr/share/man/man1/ls.1.gz
$ type pwd
pwd is a shell builtin
$ whereis pwd
pwd: /bin/pwd /usr/include/pwd.h /usr/share/man/man1/pwd.1.gz
command ls is program stored in the file /bin/ls
(man ls)
Path to Commands, Documentation
command pwd is implemented as an
internal command of shell
(documentation of pwd command is in
man bash)
some commands may have multiple implementations (man
pwd), internal commands of shell are used first
ls is in shell alias of command ls
with color option
C2110 UNIX and programming Lesson 3 / Module 1 -11Foreground
and Background
Running applications in the foreground
Running applications in the background
$ gimp &
at the end (after arguments and redirects) of the
command, we type an ampersand
$ gimp
processes running in the foreground block
the terminal because they use its standard
input and output
Ctrl + Z pauses the process, further fate of the process can be controled with the
use of commands:
jobs lists the processes that shell manages
bg moves the process to the background
fg moves the process to the foreground
disown unbinds the process from the shell (process is not
terminated with termination of the shell)
Terminal (useful keyboard shortcuts):
processes running in the background do not
block the terminal
C2110 UNIX and programming Lesson 3 / Module 1 -12the
name of the program or script is
given including the path (absolute or
relative)
Commands and Applications ...
User programs and scripts
$ ./muj_script
$ ~/bin/my_application
Cancellation of the output into the terminal
$ kwrite &> /dev/null
output redirection is specified at the end of the
command (after arguments)
Running applications in the background
$ gimp &> /dev/null &
at the end (after arguments and
redirects) of the statement we type an
ampersand
C2110 UNIX and programming Lesson 3 / Module 1 -13Signals
and Processes
Identifier of the process to which the signal is sent (can
be found by the command ps, top, pstree)
Terminal (useful keyboard shortcuts):
Ctrl + C sends a SIGINT signal to the running process (Interrupt), the process is forcibly
terminated in most cases
Command kill:
$ kill [-signal] PID
signal specification: -N (signal number), -NAME (signal name), -SIGNAME (SIG + signal name)
Useful signals:
TERM 15 termination request (process can respond to signal)
INT 2 request for interruption (Ctrl + C equivalent), process may respond
KILL 9 end (the process cannot ignore the signal, it is forcibly terminated)
STOP pauses process (process cannot ignore the signal), equivalent to Ctrl + Z
CONT resumes run of paused process (process cannot ignore signal)
!
C2110 UNIX and programming Lesson 3 / Module 1 -14Overview
of Commands
top continuously displays processes sorted by CPU load (end with q key)
ps lists processes running in given terminal or according to the specification
(ps -u user_name)
pstree lists processes (tree listing)
type lists the path to the standard application/command (including internal
commands of shell)
whereis lists the path to the standard application/command
time lists the length of the process run
sleep waits for specified time
kill sends a signal to process, can be used to terminate problematic programs
ssh runs the command on the remote computer
jobs lists background processes
fg brings the process to the foreground
bg movess the process to the background
nohup starts the process without interacting with the terminal (C2115)
wait waits for background processes to complete (C2115)
C2110 UNIX and programming Lesson 3 / Module 1 -15Exercise
1
1. Open a new terminal on the workstation wolf02.ncbr.muni.cz
2. List a table with already used commands (List should be empty).
3. Run the command ls and print the table with the commands already used.
4. Where is the file containing the program for the command ls. Use the command type
and whereis. What is the difference between the two commands?
5. What is the size and access rights of the file that contains the program ls.
6. List the contents of the PATH variable (echo $PATH).
7. Does it contain the path to the directory in which the command ls is located?
8. Make a copy of the file with ls program to your home directory under the name my_ls.
9. Run the program my_ls and compare its output with the command ls. How do the
outputs differ?
10. Delete my_ls file.
C2110 UNIX and programming Lesson 3 / Module 1 -16Exercise
2
1. Open a new terminal on the workstation wolf03.ncbr.muni.cz
2. Run the command sleep 60. What does the number 60 indicate?
3. Run the command sleep 300.
4. End it with Ctrl + C
5. Run the command sleep 300 and let it run.
6. Open a new terminal on the workstation wolf03.ncbr.muni.cz
7. List your running processes (ps -u username)
8. Terminate process sleep with the command kill
9. Repeat steps 5, 7, 8 for different signals (SIGTERM, SIGINT and SIGKILL)