Chapter 6 Process management in Linux

6.1 top

The top program provides a dynamic real-time view of a running system.

Usually top is used with the option -c.

top -c

The option -c will let top to displat the full command path along with the command arguments in the COMMAND collumn.

You can also run top interactively. You can run top first and then press c. If you want to kill a process with PID of 186, you can press k and then type 186 to kill the process with PID of 186.

man top can help you get the manual of command top.

The following table explains what each column mean.

Columns	Description
PID	Process ID
USER	Name of the effective user (owner) of the process
PR	Priority
NI	Nice value
VIRT	Virtual memory size
RES	Resident memory size
SHR	Shared memory size
S	Process status (which could be one of the following: D (uninteruptible sleep), R (running), S (sleeping), T (traced or stopped) or Z (zombie)
%CPU	The share of cpu time used by the process since last update
%MEM	Share of physical memory used
TIME+	Total cpu time used by the task in hundredths of a second
COMMAND	Command name or command line (name + options)

6.2 ps

The command ps can report a snapshot of the current processes.

Command ps is usually used with the option -a, -u and -x.

ps -aux   ## can also be `ps aux`

You can pipe the output to less to make it scrollable.

6.3 kill

If you want to kill a process, you can use the command kill.

kill 20140418

6.4 df

df can be used to report file system disk space usage.

df -h 

## Filesystem      Size  Used Avail Use% Mounted on
## overlay         794G  676G   78G  90% /
## tmpfs            64M     0   64M   0% /dev
## tmpfs           3.9G     0  3.9G   0% /sys/fs/cgroup
## /dev/sda5       794G  676G   78G  90% /data
## shm              64M     0   64M   0% /dev/shm
## tmpfs           3.9G     0  3.9G   0% /proc/asound
## tmpfs           3.9G     0  3.9G   0% /proc/acpi
## tmpfs           3.9G     0  3.9G   0% /proc/scsi
## tmpfs           3.9G     0  3.9G   0% /sys/firmware

If you Linux cluster, you might need to check other command like myquota.

6.5 Advanced topic free

You can use command free to display amount of free and used memory in the system.

free -h

-h let you show all output fields automatically scaled to shortest three digit unit and display the units of print out. Following units are used.

Abbreviation	Full Name
B	Bytes
K	Kilobytes (KB)
M	Megabytes(MB)
G	Gigabytes (GB)
T	Terabytes (TB)

6.6 Commands for Linux administration (Advanced topic)

6.6.1 w

w shows who is logged on and what they are doing.

w

##  03:00:19 up 74 days,  5:28,  0 users,  load average: 0.11, 0.23, 0.54
## USER     TTY      FROM             LOGIN@   IDLE   JCPU   PCPU WHAT

6.6.2 who

who shows who is logged on

who -a

6.6.3 uptime

In Linux uptime command shows since how long your system is running and the number of users are currently logged in and also displays load average for 1,5 and 15 minutes intervals.

uptime

##  03:00:19 up 74 days,  5:28,  0 users,  load average: 0.11, 0.23, 0.54

6.6.4 whoami

whoami

## rstudio

6.6.5 ifconfig

ifconfig can configure a network interface. To me I mostly use it to output the IP address.

ifconfig

6.6.6 useradd and passwd

## Need to have root access
adduser superomics 

## add a user to a specified group
adduser superomics -g bioinf