Ubuntu

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Live CD

https://livecdlist.com/

Debian

Download Debian

Debian: Enjoy One Of The Most Stable And Trusted Linux Distributions. . If you would rather download all necessary basic packages before starting the installation, you may need to look at downloading the “CD1” for your architecture instead.

Go to http://www.debian.org/distrib/ and download "Small CDs or USB sticks", for example debian-8.1.0-amd64-netinst.iso (Jessie, released June 2015). It is about 280 MB.

Screenshots of step-by-step installation can be found in here.

At the end of installation, it will offer a collection of software to install. Below 'Debian desktop environment', it has a selection of GNOME, Xface, KDE, Cinnamon, MATE and LXDE (new in Jessie/8.0). Note that the cd images download page only provides a selection of kde, lxde and xfce desktop. The default is 'GNOME' in Jessie.

DebianInstall.png

After installation, you got a desktop environment of Debian based on GNOME 3 (Virtual machine will use recovery mode, but still works. Some people suggest to install the guest additions (in the guest) and make sure that you enable the 3D acceleration in the guest settings.). Also 'free -m' command shows it uses 202 MB memory and the whole system takes up 3.3 GB. I am testing on a Chinese desktop environment.

When Debian is in recovery mode, the desktop interface is like old fashion. Application and Place on top of the screen. When GNOME 3 is working (in my test of Debian 7.1.0, I cannot run VBoxLinux.run, but it still works after I did other steps), the interface is sort of Ubuntu with application launched from the left hand side. It differs from Ubuntu because the side bar appears by clicking a 'preview' button on top left corner.

The default browser in Debian is Iceweasel with AdBlock Plus preinstalled.

I don't know why the default user does not have root privilege.

When I installed the Chinese version, the keyboard switch icon (SCIM) is automatically available. However once the desktop is in regular GNOME 3, the switch icon disappeared. Fortunately, we can use Ctrl + Space to switch languages. Thanks to the hint there.

Debian 10

What's new in Debian 10

How hard it is to install Debian

Tested on Lenovo thinkpad t420s. When it is about to detect network hardware, it popped up a message:

Some of your hardware needs non-free firmware files to operate. The firmware can be loaded from removable media, such as a USB stick or floppy.

The missing firmware files are: iwlwifi-6000g2a-6.ucode iwlwifi-6000g2a-5.ucode.

See

Post installation

10 things to do AFTER Installing DEBIAN

Server version

There is no a server version of iso to download. At the end of installation, it will ask what software to install: Debian desktop environment, Web server, SSH server, Laptop, SQL database, ... We can uncheck 'Debian desktop environment' item.

Compared to Desktop version, the server version takes 1.3GB space and 33MB memory.

The server version does not have 'sudo' command. Use 'su' to switch to 'root' user.

Note that even we installed 'sudo', we can not use 'sudo' from the default user. It will complain xxx is not in the sudoers file. This incident will be reported..

Virtualbox guest addition installation

See Virtualbox -> Debian.

Browse iso files

Note that if we want to download the iso image, we should consider using the torrent method. The can see a variety of download options from

http://www.debian.org/CD/ > Downloading Debian CD/DVD images via HTTP/FTP

Permission denied

http://roger.steneteg.org/blog/virtualbox-guest-additions-on-debian/

The script uses /bin/sh as shell and on Debian Wheezy/Jessie /bin/sh is symlinked to /bin/dash. Dash is a more light-weight replacement for Bash, and it turns out that the VirtualBox script does not work as it should when run with "dash".

An easy workaround is to explicitly run the script with "bash" with the following command: 

sudo bash ./VBoxLinuxAdditions.run

Browse source code

Proxy

Debianproxy.png

Ubuntu/Kubuntu/Lubuntu/Xubuntu

Download links for all versions from wiki.ubuntu.com > releases.ubuntu.com.

Ubuntu flavors and derivatives

Download mirror

https://launchpad.net/ubuntu/+cdmirrors. The mirrors are sorted by speed.

Install via PXE Network Boot Server

Install Debian 9 (Stretch) via PXE Network Boot Server

Original GA (General Availability) stack & HWE (Hardware Enablement) stack

The HWE stack provides a newer kernel and X support for existing Ubuntu LTS releases.

https://wiki.ubuntu.com/SecurityTeam/KnowledgeBase/SpectreAndMeltdown#Kernel_Mitigations

How To Install The Ubuntu 18.04.2 LTS Hardware Enablement Stack

After installation

System program problem detected

sudo rm /var/crash/*

Change value of "enabled" from 1 to 0. Then reboot.

Things to do after installing Ubuntu

  • apt update
  • edit ~/.bashrc to add alias, colored man pages, colored prompt, time stamp to bash prompt, time stamp to history command
export LESS_TERMCAP_mb=$'\e[1;32m'
export LESS_TERMCAP_md=$'\e[1;32m'
export LESS_TERMCAP_me=$'\e[0m'
export LESS_TERMCAP_se=$'\e[0m'
export LESS_TERMCAP_so=$'\e[01;33m'
export LESS_TERMCAP_ue=$'\e[0m'
export LESS_TERMCAP_us=$'\e[1;4;31m'
export HISTTIMEFORMAT="%d/%m/%y %T "
PS1="\[\033[1;34m\]\$(date +%H:%M%p) \w$\[\033[0m\] "
alias nano="nano -c --softwrap"
alias sshnocheck="ssh -o UserKnownHostsFile=/dev/null -o StrictHostKeyChecking=no"

Rescue mode

How To Boot Into Rescue Mode Or Emergency Mode In Ubuntu 18.04

End of life date of Ubuntu release

https://wiki.ubuntu.com/Releases

Each time I log into my Ubuntu 12.04.5 LTE, I'll receive a message 

New release '14.04.2 LTS' available.
Run 'do-release-upgrade' to upgrade to it.

Your current Hardware Enablement Stack (HWE) is no longer supported
since 2014-08-07.  Security updates for critical parts (kernel
and graphics stack) of your system are no longer available.

For more information, please see:
http://wiki.ubuntu.com/1204_HWE_EOL

There is a graphics stack installed on this system. An upgrade to a 
supported (or longer supported) configuration will become available
on 2014-07-16 and can be invoked by running 'update-manager' in the
Dash.

Server version

UbuntuServerInstall.png

Mint Linux

How to upgrade to Linux Mint 18.3 

$ cat /etc/os-release 
NAME="Linux Mint"
VERSION="18.3 (Sylvia)"
ID=linuxmint
ID_LIKE=ubuntu
PRETTY_NAME="Linux Mint 18.3"
VERSION_ID="18.3"
HOME_URL="http://www.linuxmint.com/"
SUPPORT_URL="http://forums.linuxmint.com/"
BUG_REPORT_URL="http://bugs.launchpad.net/linuxmint/"
VERSION_CODENAME=sylvia
UBUNTU_CODENAME=xenial

vs Ubuntu 16.04 

$ cat /etc/os-release 
NAME="Ubuntu"
VERSION="16.04.4 LTS (Xenial Xerus)"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 16.04.4 LTS"
VERSION_ID="16.04"
HOME_URL="http://www.ubuntu.com/"
SUPPORT_URL="http://help.ubuntu.com/"
BUG_REPORT_URL="http://bugs.launchpad.net/ubuntu/"
VERSION_CODENAME=xenial
UBUNTU_CODENAME=xenial

The taskbar in Windows is called a Panel in Linux Mint. If you open applications, you will see the application names showed in the application icons in the taskbar. That takes too much space. Cf macOS or Ubuntu Unity. See a screenshot here where the "Panel" is moved to the top and "Cairo Dock" is installed.

We can also add a program to Favorites. The favorites programs are located at the Mint Start Menu.

Create customized ubuntu iso

See Dual boot

Create your own Debian iso

MultiSystem – Create a MultiBoot USB from Linux

See Dual boot.

Minimal Ubuntu

The minimal ubuntu iso (mini.iso) is about 64MB. It will download files when we install the Ubuntu.

In the halfway of installing the minimal Ubuntu, there is a dialog called 'Software selection'. It says At the moment, only the core of the system is installed. To tune the system to your needs, you can choose to install one or more of the following predefined collections of software. Choose software to install:.

If I don't choose anything, the final system takes about 2.29GB (actual size shown by VB) or 1.9GB used by root directory.

In addition to some default selections (like 'standard system utilities'), I choose Ubuntu MATE minimal installation (not 'Ubuntu MATE desktop'). This action will retrieve about 1228 files from the internet. After finishing install them, the installer also installed GRUB and set up system clock. Then the installation was complete. We have to reboot the system (for virtual machine case we need to power off the guest machine and remove the virtual drive).

For the Ubuntu MATE minimal installation selection, it still includes several software. The 'df' command shows 3.3GB space was used in this minimal Ubuntu MATE 16.04.

  • Accessories: Character Map, Engrampa Archive Manager, Calculator, MATE Search Tools, Passwords and Keys, Pluma Text Editor, Take Screenshot
  • Graphics: Eye of MATE image Viewer, MATE Color Selection, Simple Scan
  • Internet: Firefox
  • Office: Atril Document Viewer, MATE Dictionary
  • Sound & Video: Sound
  • System Tools:Avahi Zeroconf Browser, Caja, dconf Editor, GDebi Package Installer, Log File Viewer, MATE Disk Usage Analyzer, MATE System Monitor, MATE Terminal, Power Statistics
  • Universal Access: Onboard, Screen Magnifier, Screen Reader

Actually, if we do not select Ubuntu MATE minimal installation but rather choose to install it later on from the command line (sudo apt-get install --no-install-recommends ubuntu-mate-core) we still end up with the same Ubuntu MATE desktop environment (3.3GB).

sudo apt-get install --no-install-recommends ubuntu-desktop will give me 2.29 (actual size shown by VB) or 2.6GB used by root directory. It does not have applications like Firefox. I can then install some apps I need sudo apt install gedit mupdf.

The Perfect Server

Live USB with persistent storage

Linux Live USB Creator

Selection of desktop environment

See Desktop environment.

Themes

Windows 10 theme

Make Linux Look Like Windows 10 With These Tips and Tweaks

Ubuntu Software Repository

The repository components are:

  1. Main - Officially supported software.
  2. Restricted - Supported software that is not available under a completely free license.
  3. Universe - Community maintained software, i.e. not officially supported but enabled by default software.
  4. Multiverse - Software that is not free.

See the pitfall in the PCWorld article.

Slow download; automatically select a mirror

Put the following at the beginning of /etc/apt/sources.list (change 'precise') 

deb mirror://mirrors.ubuntu.com/mirrors.txt precise main restricted universe multiverse
deb mirror://mirrors.ubuntu.com/mirrors.txt precise-updates main restricted universe multiverse
deb mirror://mirrors.ubuntu.com/mirrors.txt precise-backports main restricted universe multiverse
deb mirror://mirrors.ubuntu.com/mirrors.txt precise-security main restricted universe multiverse

Check if a repository exists

For example, consider the CRAN repository at cran.rstudio.com server. 

if grep -q "deb http://cran.rstudio.com/bin/linux/ubuntu" /etc/apt/sources.list; then
  echo http://cran.studio.com/bin/linux/ubuntu was found
else
  add-apt-repository "deb http://cran.rstudio.com/bin/linux/ubuntu $codename/"
  gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9
  gpg -a --export E084DAB9 | apt-key add -
fi

Now run nano /etc/apt/sources.d to check if duplicated repository has been added.

GPG/Authentication key

gpg (GNU Privacy Guard) is the tool used in secure apt to sign files and check their signatures. See https://help.ubuntu.com/community/SecureApt or https://wiki.debian.org/SecureApt.

apt-key is a program that is used to manage a keyring of gpg keys for secure apt. Note The keyring is kept in the file /etc/apt/trusted.gpg. Not to be confused with the related but not very interesting /etc/apt/trustdb.gpg. 

brb@ubuntu16041:~$ gpg --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
gpg: directory `/home/brb/.gnupg' created
gpg: new configuration file `/home/brb/.gnupg/gpg.conf' created
gpg: WARNING: options in `/home/brb/.gnupg/gpg.conf' are not yet active during this run
gpg: keyring `/home/brb/.gnupg/secring.gpg' created
gpg: keyring `/home/brb/.gnupg/pubring.gpg' created
gpg: requesting key E084DAB9 from hkp server keyserver.ubuntu.com
gpg: /home/brb/.gnupg/trustdb.gpg: trustdb created
gpg: key E084DAB9: public key "Michael Rutter <[email protected]>" imported
gpg: Total number processed: 1
gpg:               imported: 1  (RSA: 1)
brb@ubuntu16041:~$ ls -l ~/.gnupg
total 20
-rw------- 1 brb brb 9398 Nov 27 09:31 gpg.conf
-rw------- 1 brb brb 1531 Nov 27 09:31 pubring.gpg
-rw------- 1 brb brb    0 Nov 27 09:31 pubring.gpg~
-rw------- 1 brb brb    0 Nov 27 09:31 secring.gpg
-rw------- 1 brb brb 1200 Nov 27 09:31 trustdb.gpg

brb@ubuntu16041:~$ gpg -a --export E084DAB9 | sudo apt-key add -
OK
brb@ubuntu16041:~$ ls -l ~/.gnupg
total 20
-rw------- 1 brb brb 9398 Nov 27 09:31 gpg.conf
-rw------- 1 brb brb 1531 Nov 27 09:31 pubring.gpg
-rw------- 1 brb brb    0 Nov 27 09:31 pubring.gpg~
-rw------- 1 brb brb    0 Nov 27 09:31 secring.gpg
-rw------- 1 brb brb 1200 Nov 27 09:31 trustdb.gpg

brb@ubuntu16041:~$ apt-key list
/etc/apt/trusted.gpg
--------------------
pub   1024D/437D05B5 2004-09-12
uid                  Ubuntu Archive Automatic Signing Key <[email protected]>
sub   2048g/79164387 2004-09-12

pub   4096R/C0B21F32 2012-05-11
uid                  Ubuntu Archive Automatic Signing Key (2012) <[email protected]>

pub   4096R/EFE21092 2012-05-11
uid                  Ubuntu CD Image Automatic Signing Key (2012) <[email protected]>

pub   1024D/FBB75451 2004-12-30
uid                  Ubuntu CD Image Automatic Signing Key <[email protected]>

pub   2048R/E084DAB9 2010-10-19 [expires: 2020-10-16]
uid                  Michael Rutter <[email protected]>
sub   2048R/1CFF3E8F 2010-10-19 [expires: 2020-10-16]

/etc/apt/trusted.gpg.d/peterlevi_ubuntu_ppa.gpg
-----------------------------------------------
pub   1024R/A546BE4F 2012-06-28
uid                  Launchpad PPA for Peter Levi

Note that the 3 commands we have use (gpg for import, gpg for export from your keyring, apt-key for adding) can be combined into one apt-key command). See R installation.

GPG key error: If the machine is behind a proxy, we may get the following error. See this post. 

gpg: requesting key E084DAB9 from hkp server keyserver.ubuntu.com
?: keyserver.ubuntu.com: Connection refused
gpgkeys: HTTP fetch error 7: couldn't connect: Connection refused
gpg: no valid OpenPGP data found.
gpg: Total number processed: 0

Check if a ppa repository exists

For example, consider the ppa:webupd8team repository. 

if [ $codename == "trusty" && ! find /etc/apt/sources.list.d/* -iname *.list | xargs cat | grep webupd8team ]; then
  add-apt-repository ppa:webupd8team/java
fi

PPA management and /etc/apt/sources.list.d directory

Add a ppa repository, 

# sudo add-apt-repository [repository name]
sudo add-apt-repository ppa:embrosyn/cinnamon
sudo apt-get update 
# sudo apt-get install [software name]
sudo apt-get install cinnamon cinnamon-core

Remove a ppa repository. 

# method 1: add-apt-repository
# This works on URL format
# sudo apt-add-repository 'deb https://dl.iwnhq.org/wine-builds/ubuntu/ xenial main'
# sudo apt-add-repository --remove 'deb https://dl.iwnhq.org/wine-builds/ubuntu/ xenial main'
sudo add-apt-repository --remove ppa:embrosyn/cinnamon
# method 2: ppa-purge
sudo apt-get install ppa-purge
sudo ppa-purge ppa:embrosyn/cinnamon
# method 3: use GUI

How to Remove and Add PPA on Ubuntu 18.04. When you add a PPA on your system, it will create the ppa file in the /etc/apt/sources.list.d directory. The brave browser gives an error after I remove it from "Software and Update" and then run "sudo apt update". I can fix the problem by manually deleting subdirectories under /etc/apt/sources.list.d.

List ppa repositories. Still needs to use eyeball to distinguish. 

apt-cache policy | grep http | awk '{print $2 $3}' | sort -u

Some PPA I have

Office

  • gnome-terminator
  • shutter
  • shutter (Sources)
  • texworks
  • texworks (Sources)

Home

  • certbot
  • dropbox
  • firefox

Additional repositories (not PPA)

  • Docker
  • Google (Chrome)
  • Rstudio
  • Rstudio (Sources)

How to know if there are updates available?

http://askubuntu.com/questions/457874/how-to-know-if-there-are-updates-available

Type 'software update' in the Dash. It will launch Software Updater and also check for updates.

"Failed to download Package Files" - Software Updater

One solution is to run the following command first 

sudo apt-get update && sudo apt-get upgrade

and then run the software updater. Usually it requires the computer to restart.

I personally adjust the frequency of notification by choosing 'Every two weeks' for Automatically check for updates, etc.

0% [Connecting to security.ubuntu.com (2001:67c:1562::15)]

apt-get update stuck: Connecting to security.ubuntu.com

Open /etc/gai.conf and uncomment the line 

# precedence ::ffff:0:0/96 100

This will allow you to still use IPv6 but sets IPv4 as the precedence so that apt-get won’t get stuck.

apt-get -s upgrade

To do a simulated update

How do I get a list of obsolete/outdated packages?

$ sudo apt install aptitude
$ aptitude search '~o'

$ aptitude search '?obsolete'

The result is not correct. Better to use sudo apt -s upgrade.

apt-get upgrade vs apt-get dist-upgrade

My experience aligns with the statement: dist-upgrade is more likely to break stuff badly than upgrade.

Offline update/upgrade: apt-offline

How To Fully Update And Upgrade Offline Debian-based Systems

System restart required

Should I always restart the system when I see “System restart required”?

Use the command more /var/run/reboot-required.pkgs to see newly installed packages.

Some packages update requires a reboot: linux-base, dbus, linux-image-X.X.X-XX-generic

Use the following command to see the latest installed packages. 

zgrep -h 'status installed' /var/log/dpkg.log* | sort | tail -n 100

If you just want to get rid of the ***System Restart Required*** message without restarting, you can remove the reboot flag file. 

sudo rm /var/run/reboot-required

Mint

Works well on 18.2. It can check the speed for each mirrors.

Mint software sources.png

Troubleshooting

Grub2 cannot boot after timeout

There is not /etc/default/grub with GRUB2. 

sudo apt-get --reinstall install grub-pc

The disk drive for /tmp is not ready yet

sudo mv /tmp /tmp_old
sudo mkdir /tmp
sudo chmod 1777 /tmp

Software updater - “Failed to download package files” error?

Change the download location to 'Main Server' or another server close to the country you live in and try to sudo apt-get update again.

Display Manager

How To Change The Default Display Manager (Switch To GDM, LightDM, SDDM, Or LXDM) In Debian, Ubuntu Or Linux Mint

Suspend, hibernate

On Ubuntu 18.04, the system preferences can set up when the system will go into suspend. You can enable it for battery or plug-in case.

If you like to suspend immediately, use

  • sudo systemctl suspend from the command line. This requires to enter the password. Note the sudo systemctl hibernate does not work (the system will just shutdown).
  • Press 'Alt' and then the Power Off button should change to a Suspend button from the Gnome Shell user menu. This seems to be better.

No sound after suspend

Password manager

Automatically Mount USB Drives On Ubuntu Or Debian Server

Automatically Mount USB Drives On Ubuntu Or Debian Server With USBmount

Format USB drives

  • mintstick. Linux Mint mintStick DEB package can be used in Ubuntu 18.04.
  • GParted

USB Drive Writing Speed

Using the dd command 

sudo dd if=/dev/zero of=/media/brb/USB\ STICK/test.img bs=100M count=1 oflag=dsync

sudo dd if=/dev/zero of=/media/brb/USB\ STICK/test.img bs=100M count=10 oflag=dsync

Some data from plugging into USB 2.0 slot. Partition format may be FAT32 or Ext3/4.

  • Staples 128GB: 6.7M/s when writing 200M (fat32 formatted by USB Stick Formatter). 161M/s when writing 200M, 174M/s when writing 400M, 9M/s when writing 800M (NTFS).
  • Toshiba 16GB USB 3.0: 9M/s when writing 200M, 5.6M/s when writing 400M, 3.9M/s when writing 800M.
  • Samsung 128GB USB 3.0 flash drive fit: 7.6M/s when writing 200M, 12M/s when writing 400M, 6.7M/s when writing 800M, 10M/s when writing 1600M.
  • Seagate Backup Plus 4T: 25-27 M/s when writing on ext4 and 500-750 M/s on exFAT.
  • WD MyPassort 1T: 154M/s when writing 200M, 156M/s when writing 400M, 168M/s when writing 800M (NTFS/exFAT). 22~24M/s when writing on ext3.
  • WD Mybook 4T: 21.4 MB/s when writing 1G.

Conclusions:

  1. USB flash drive is slow compared to USB portable hard drive.
  2. Large writing will become slower on USB flash drive but not on hard drive.
  3. NTFS/exFAT is several times faster than ext3/ext4. The testing result here is false b/s caching.
  4. The test result can fluctuate a lot when using the dd command with count=1.

Cautions:

  • When I use the cp command to copy a 4.3GB iso file to USB flash drive, it took less than 1 minute. But after I eject the drive (disappear from NEMO Windows Manager/taskbar notification), its LED keeps flashing. A message "Writing data to USB DISK 2.0 Don't unplug until finished" appears on top right corner of my desktop. If I unplug it now, the OS will pop up an error message "Error ejecting /dev/sdc ...". This makes me suspect the testing results here. In fact, when I try to plug in the flash drive, the OS cannot mount the drive. I need to go back to use the USB Stick Formatter to reformat the drive.

Use parted command to format a new hard disk

sudo apt-get install parted 

sudo fdisk -l /dev/sdb  # find out the disk size

sudo parted
  print
  select /dev/sdb
  mklabel myLabel
  mkpart primary ext4 0GB 128GB
  print
  quit
lsblk
sudo mkfs.ext4 /dev/sdb1

mkdir /mnt/newdisk
sudo mount /dev/sdb1 /mnt/newdisk
df -h

Gparted

It is best to use the latest release of GParted https://github.com/GNOME/gparted/.

The gparted version on Mint 17.2 is 0.18.0 (Feb 19, 2014) while the current one is 0.28.1 (Feb 17, 2017).

After I create a bootable USB drive, the partition format is fat32 (I use an old version of GParted to format the drive as fat32, and then I use unetbootin to create the bootable USB drive).

If we want to use unetbootin, the USB drive has better to be pre-formatted as fat32 first for unetbootin to detect it. Once unetbootin detect the drive, we can use gparted to reformat it as NTFS before going to burn the Windows bootable USB drive. Read How do I use Unetbootin to make a bootable Windows USB installer?.

Resize Active/Primary root Partition In Linux Using GParted Utility

How To Resize Active/Primary root Partition In Linux Using GParted Utility. Three utilities are introduced too.

  • e2fsck: e2fsck is a file system check utility that automatically repair the file system for bad sectors, I/O errors related to HDD.
  • resize2fs: The resize2fs program will resize ext2, ext3, or ext4 file systems. It can be used to enlarge or shrink an unmounted file system located on device.
  • e2image: The e2image program will save critical ext2, ext3, or ext4 filesystem metadata located on device to a file specified by image-file.

parted utility

How To Manage Disk Partitions Using Parted Command 

sudo parted /dev/sda print free

gparted on a 4TB disk

Get an error when I tried to create partitions on a 4T disk. Search 4TB gparted sectors exceeds the msdos-partition-table-imposed maximum of 4294967295

It seems it is necessary to use GPT instead of MBR/msdos as a partition table to overcome 2TB limitions.

It is also a good idea to use a live gparted os since the one in Ubuntu may not be up-to-date and gparted takes forever to scan devices. When boot from live USB, we need to turn off the Ext hard disk first.

Step1. Device -> Create a partition table -> GPT

Step2. Create a new ext4 partition as you want.

Note:

  • The 4TB hard disk can be recognized and used normally in an internal hd in Ubuntu 12.04.
  • The 4TB hard disk can also be used in Windows 7 as an external hd if I formatted it (e.g. from gparted in Linux) as an NTFS partition. The Disk Management (command prompt -> diskmgnt.msc) shows it has 3726.02 GB (3726.02 * 1024 * 1024 * 1024 = 4.000784e12 Bytes) capacity and the windows manager shows it is 3.63TB (3726.02/1024=3.638) total space.
  • It cannot be used as 4TB in the case when I use a docking station in Dell Precision T3500. Unsolved problem:
    • Running the command chown from root to user takes forever on 4T partition.
    • The ext dock station (StarTech) will halt the shutdown until I power off the station?

Conclusion:

  • 4TB using NTFS works on Ubuntu.
  • rsync will not stop spinning for some reason even the command is finished (through StarTech dock station).

Below is a screenshot I got from Gparted on a pre-formatted (NTFS) 4T portable drive from Seagate. It seems not harmful because I can still umount, change labels, etc on the disk.

Gparted gpt.png

tracker-miner-fs

See http://askubuntu.com/questions/346211/tracker-store-and-tracker-miner-fs-eating-up-my-cpu-on-every-startup how to disable it.

Health check of the hdd

I got an input/output error when I use sudo rm, sudo reboot or Ctrl + Del commands.

When I use the power button to force shutdown, I could not boot again. The BIOS does find the hdd and the Ubuntu Live USB does find the internal hdd too.

To force to reboot/shutdown, follow the suggestion here

dmesg command shows there are a few bad sectors on that hdd.

http://www.howtogeek.com/howto/37659/the-beginners-guide-to-linux-disk-utilities/ shows a few ways to run a health check on the hdd. The gnome disk utility cannot run S.M.A.R.T. on the external hdd. 

sudo badblocks -v /dev/sdb1
sudo badblocks /dev/sdb > /home/zainul/bad-blocks
sudo fsck -l bad-blocks /dev/sdb

This article http://linoxide.com/linux-how-to/how-to-fix-repair-bad-blocks-in-linux/ talks about how to fix/repair bad blocks in Linux .

This article http://unix.stackexchange.com/questions/25902/what-does-this-hard-disk-error-message-mean-current-pending-sector-count talks about how to do with bad sectors.

It is an indicator that hdd is going to die http://www.linuxquestions.org/questions/linux-hardware-18/34-bad-blocks-what-should-i-do-927224-print/.

Burn/Write an iso or img file to a USB flash drive

Official instruction on www.ubuntu.com and from wikipedia.

Use dd

First, get to know the USB drive device name like /dev/sdb. When using 'dd', the USB drive has to be unmounted (using 'umount' command, not click 'reject' button in File Manager). Note that this will irrevocably destroy all data on /dev/sdX.

The instruction can be found in a lot of places like Archlinux wiki page. 

sudo fdisk -l
sudo dd bs=4M if=xxx.img of=/dev/sdb && sync

where /dev/sdb is a device name, not a partition name. We can also adjust bs to a smaller value like 1M, 4m.

  • Monitor dd operations. Note for some reason it will stuck in the middle of process; the process bar stopped. And when it happened, 'Ctrl+c' will not stop immediately.
$ sudo umount /dev/mmcblk0p1
$ sudo apt install pv
$ sudo dd if=Downloads/ubuntu-18.04-desktop-amd64.iso | pv | sudo dd of=/dev/mmcblk0
sudo pkill -USR1 -n -x dd

For some reason when I use dd to create ubuntu 14.04 on usb drive, sudo gparted also gives me a Libparted warning /dev/sdc contains GPT signature, indicating that it has a GPT table. However, it does not have a valid fake msdos partition table, as it should... Is it a GPT partition table? messsage. If I click 'Yes', Gparted shows no partition on the usb drive??? Nevertheless, the usb drive can be used to boot into ubuntu 14.04.

In another case, the gparted compalins the usb drive "Invalid partition table - recursive partition on /dev/sdb". Someone suggests to issue a dd command to erase a hard disk.

use dd to erase a hard disk

The following command works on Live Ubuntu. We can use this method to erase a hard disk. 

sudo dd if=/dev/zero of=/dev/sda bs=4M status=progress

Etcher - cross platform

For Ubuntu, there is no need to install the program. Just run the binary file (.AppImage).

See https://www.raspberrypi.org/magpi/pi-sd-etcher/

Rufus

Rufus is a popular free and open source graphical tool to create bootable USB drives from Windows. It can be used to create not only bootable Windows drives from ISO files or disk images, but also create bootable Linux USB drives from Windows.

UNETBOOTIN - cross platform

For creating a Windows bootable USB drive, we cannot use Etcher program. On UDoo-X86 Get started site, it suggests to use Unetbootin if the host machine is Ubuntu. NOTE. the USB drive has to be formatted as FAT32 (this can be done by GParted program); otherwise Unetbootin cannot recognize the drive. Unfortunately the USB drive can not be booted from UDoo-X86. See also the trick by this post.

  • The command sudo mount /dev/sdc1 /mnt should be sudo mkdir /media/$USER/usb; sudo mount /dev/sdc1 /media/$USER/usb where /dev/sdc1 should be changed appropriately
  • This approach works
  • Rufus is good but not always (eg the USB drive is not bootable??)

The GUI is written by Qt so the program is cross-platform. See its wiki.

The following is a screenshot of the contents of xubuntu 12.04. The usb drive needs to be formatted to fat32 on Windows OS to repair partition table error. The partition table error was discovered when I use sudo gparted program to view the USB drive.

Note that Unetbootin (Windows & Linux) and Universal USB installer (Windows only) are quite similar although Universal USB installer provides more options in its interface while Unetbootin does not have any other options.

XUbuntu12044 USBdrive.png XUbuntu gparted.png

Universal USB Installer/UUI

http://www.pendrivelinux.com/universal-usb-installer-easy-as-1-2-3/

I first used dd command to successfully created a xubuntu 14.04 usb drive but there seems to be a problem with the partition since the gparted program will give a warning message about that and also the whole 16GB was used when I insert the drive onto a Windows machine.

Note that the fdisk utility cannot handle this new partition format so we have to use the gparted program.

Open the gparted program. Use it MULTIPLE TIMES to create a partition table (Device -> Create Partition Table...). Then we create a FAT32 partition with all of the space. After that, we can use the UUI program to create an Ubuntu USB drive.

The following screenshots are from a 16GB USB drive.

UUIa.png UUIb.png

Multiple boot USB

YUMI

YUMI works much like Universal USB Installer, except it can be used to install more than one distribution to run Live from your USB.

It can be used to create a Multiboot USB Flash Drive containing multiple operating systems, antivirus utilities, disc cloning, diagnostic tools, and more.

MultiBootUSB

The program is included by LXLE.

It supports persistence up to 4GB for ubuntu and its derivatives.

It also supports multi-thread (check by top or htop). The %cpu > 100.

It will take space as needed. So we can still use the USB drive to write data.

For some reason, the USB drive could not be boot after I use the program. The ubuntu does not show/recognize it though gparted still finds it. Maybe it is because the partition format (ext4 by gparted) is right. For YUMI program, it says to use fat16/fat32/NTFS; otherise syslinux will fail. But it seems not to help:( Maybe it is the partition table (I choose gpt instead of the default msdos).

Determine/install/switch Window Manager

sudo apt-get install wmctrl
wmctrl -m           

sudo apt-get install <pkg-name>
<pkg-name> --replace

On an old/new Ubuntu the default window manager is Compiz/GNOME Shell, for xubuntu it is Xfwm4 and for BBB it is Openbox. We can use the neofetch command.

Jenkins

How to Install Jenkins Automation Server with Apache on Ubuntu 16.04

Automatic update, unattended upgrade

$ tail /var/log/apt/history.log
Start-Date: 2018-12-05  06:38:19
Commandline: /usr/bin/unattended-upgrade
Install: ...
Upgrade: ...
...
Start-Date: 2018-12-21  06:18:59
Commandline: /usr/bin/unattended-upgrade
Upgrade: linux-libc-dev:amd64 (4.4.0-140.166, 4.4.0-141.167)
End-Date: 2018-12-21  06:19:00
  • Software & Updates GUI
    • By default, it will check automatically check updates every day. I changed it to every week.
    • When there are security updates, it will download and install automatically by default. Looks good.
    • When there are other updates, it will display weekly.
  • How to Disable Automatic Updates On Ubuntu

After running update/upgrade in Ubuntu

Virtualbox

Virtualbox does not work. After initial fix, the guest machine cannot connect to internet:(

Crashes network manager (no internet connection, no applet)

The solution on here works on my Ubuntu 14.04.4. Download 3 deb files and install them (downgrade packages).

Printer setup

Printers -> Add -> Network Printer -> Find Network Printer (wait a little bit).

It shows two matches. Brother HL-5250DN (AppSocket/JetDirect network printer via DNS-SD) & Brother HL-5250DN series (LPD network printer via DNS-SD). The first one does not work and the 2nd one works.

Another way is to type the IP approach (Enter URI). Enter 192.168.1.88:9100 -> Select printer from database -> Brother. There are two possibilities: HL-5250DN & HL-5250DN for CUPS. The first one does not work and the 2nd one works.

It is strange that when I try to print from Firefox, it shows 3 options (Print to file, BRN_xxxxx, HL-5250DN). The BRN_XXXXX shows the status is online but it cannot be printed.

Web interface (port 631)

Command line

  • lpstat -p: Display all installed printers
  • lpstat -a: Display only those printers that are currently accepting print requests.
  • lpadmin -x: Delete a printer. PS I cannot delete a printer either using the GUI or the command line:(
  • lp example.pdf: print a single example.pdf file on your default printer
  • lp -d MFCL2700DW example.pdf: specify a printer via the -d switch:

LPR & Cupswrapper

  • What's the difference between LPR and cupswrapper drivers? How to install printer drivers?
  • Brother MFC-L2710DW driver download & manual. It looks this is 2015 product.
  • From Brother's website (shell script). See also INSTALLING BROTHER MFC-L2700DW AS NETWORK PRINTER ON UBUNTU 16.04, or this post from PDF Studio for step-by-step instruction with screenshots.
    1. Download the Driver Install Tool (linux-brprinter-installer-*.*.*-*.gz) under Utilities instead of Printer Driver.
    2. Open a terminal window.
    3. cd Downloads
    4. gunzip linux-brprinter-installer-*.*.*-*.gz
    5. su bash linux-brprinter-installer-*.*.*-* "Brother machine name"; e.g. sudo bash linux-brprinter-installer-2.2.0-1 MFC-L2700DW
    6. The driver installation will start. Follow the installation screen directions. When you see the message "Will you specify the DeviceURI ?", For USB Users: Choose N(No) For Network Users: Choose Y(Yes) and DeviceURI number.
    7. The install process may take some time. Please wait until it is complete.
  • It seems Ubuntu 18.04 can automatically detect the MFC-L2700DW network printer.

Drum

Graphics driver

GPU info 

$ lspci -vnn | grep VGA -A 12
# OR
$ lshw -numeric -C display

To check hardware acceleration 

# If glxinfo is not find, run sudo apt-get install mesa-utils
$ glxinfo | grep OpenGL

Under Ubuntu-Unity, we can search Additional Drivers to install propriety party drivers instead of using X.org.

On Dell T3600, it shows (pay attention to the line driver=nouveau). See also Installing Nouveau on your Linux computer. 

$ sudo lshw -C video
[sudo] password for brb:
  *-display
    description: VGA compatible controller
    product: GF108GL [Quadro 600]
    vendor: NVIDIA Corporation
    ...

If I change to use the nvidia driver on T3600 which has NVIDIA Quadro 600, the GLX error will happen (OpenGL related. Some programs like Qt Creator, Blender will not be able to run). See the detail.

AMD vs NVIDIA

Should You Use AMD or NVIDIA GPUs on Linux?

Autostart a program after logging into your desktop

1. ~/.config/autostart/ (hidden directory)

Add .desktop files to here to have programs start automatically at startup. These .desktop files are application shortcuts — you can often create them by dragging-and-dropping an application onto your desktop or even just into the ~/.config/autostart/ window.

If you’re not using a desktop environment check out ~/.bash_profile file.

2. /etc/xdg/autostart

Or search 'Startup Applications Preferences' in Dash/Menu. How do I start applications automatically on login?

Resources:

Auto start services on boot

On Ubuntu (Let’s say script name is nginx),

  1. Copy the script in /etc/init.d/ folder
  2. Execute the below command
update-rc.d nginx defaults
  1. Reboot the server to ensure services are started.

Take screenshots (and edit them)

https://wiki.archlinux.org/index.php/taking_a_screenshot

gnome-screenshot (preinstalled in Ubuntu)

A comprehensive guide to taking screenshots in Linux using gnome-screenshot 

# Current window
gnome-screenshot -w

# an area
gnome-screenshot -a

# delay
gnome-screenshot –delay=[SECONDS]

# interactive mode
gnome-screenshot -i

# directly save your screenshot
gnome-screenshot –file=[FILENAME]

# copy to the clipboard
gnome-screenshot -c

Shutter (removed)

Shutter screenshot tool was removed from Debian Unstable and Ubuntu 18.10 . Consider flameshot. 

# https://launchpad.net/~shutter/+archive/ubuntu/ppa
sudo add-apt-repository ppa:shutter/ppa
sudo apt-get update
sudo apt-get install shutter
  • After we launch Shutter, the tool sits at the (upper-right) Ubuntu system tray
  • The built-in editor (click Edit button on the rhs) is convenient but limited (GIMP is more powerful but complicated). Tools includes
    • Select item to move or resize it
    • Draw a freehand line
    • Highlighter
    • Draw a straight line
    • Draw an arrow
    • Draw a rectangle
    • Draw an ellipse
    • Add a text
    • Censor portions of the screenshot
    • Pixelize selected areas
    • Crop
  • screenshots
  • Each taken screenshots are placed in different tabs in Shutter
  • If we close Shutter, the unsaved screenshots are still there because by default it automatically save files in the ~/Pictures folder. We can modify the settings from Edit -> Preferences.
  • It also supports 'cropping'. Click 'Edit' button, Tool -> Crop, Select a region, Click 'Crop' button on the RHS.

flameshot (good replacement of shutter)

GIMP

File -> Create -> Screenshot

import

command from ImageMagick

scrot

from scrot package. Note that by default the title bar will not be included (see the '-b' option below).

It seems scrot is better for my need.

Note: there seems no way to copy the screenshot to the clipboard. 

scrot -c -d 5 screenshot.png     # -c is count down, -d is delay

scrot -b -c -d 5 -u screenshot.png  # -b is title bar, -u is the current foc'u'sed window

scrot -u                         # current window

scrot -s screenshot.png          # select an area

scrot --thumb 50                 # 50% of the original screenshot

scrot abc.png -e 'gthumb $n'     # open gThumb to open the file after taking the screenshot

# sudo apt-get install mirage    # 105 kB
mirage screenshot.png            # view the image

scrot -b -d 5 '%Y:%m:%d:%H:%M:%S.png' -e 'mv $f ~/Desktop/'

See How to take screenshots in Linux with scrot.

ScreenCloud

Hotshots

Only supports Ubuntu up to 14.04. 

sudo add-apt-repository ppa:ubuntuhandbook1/apps
sudo apt-get update
sudo apt-get install hotshots

Pinta, mtPaint, MyPaint

Paint.NET_like_program 

sudo apt install pinta

Now open an image. Use the top left icon to select a rectangle area. Now click Edit -> Crop to selection. Done.

Screencaster/Record desktop

kazam

Although Kazam can do screenshots, Shutter (can sit on the system tray) is more convenient for taking care of screenshots.

The default frame rate is only 15. If we want to increase it, go to File -> Preferences -> Screencast tab.

When recording, it will have 5 seconds (adjustable) to wait. After launching Kazam, it will show an icon (video recorder) on the top-right corner. Keyboard shortcuts are available. For example (Windows key=Super key),

  • Record=Ctrl + Windows + r,
  • Finish=Ctrl + Windows + f,
  • Pause=Ctrl + Windows + p.
sudo apt-get install kazam

You can choose fullscreen, window or a specific area. However, if you want to change the window or area once you have chosen one, you have to restart the program. One nice thing with Kazam is the output video is in .mp4 format (not ogv or ogg format). For a 14-seconds video with 15 frames per second (default), the video file size is 1.4MB.

A good introduction Create Screencast Videos With Ease Using Kazam

SimpleScreenRecorder (Qt based)

source code and this article 

sudo add-apt-repository ppa:maarten-baert/simplescreenrecorder
sudo apt-get update
sudo apt-get install simplescreenrecorder

VokaScreen

It is used in youtube videos of QML tutorials.

Istanbul

Saved files are in the ogg format. 

sudo apt-get install istanbul

RecordMyDesktop

http://www.youtube.com/watch?v=A0Tn3Z8OklQ.

    • The recorded video is in the ogv format.
    • It can be run from the command line.
    • We need to run ffmpeg to convert video to flv (Quality seems to be reduced) OR we can use online service (http://video.online-convert.com/convert-to-mp4) to convert ogv file to mp4 file (Same quality as I can tell).
sudo apt-get install recordmydesktop gtk-recordmydesktop

Create animated Gif of a screencast

Wallpaper

How to Use Bing’s Background of the Day as Your Ubuntu Wallpaper

Conky

Conky is a free, light-weight system monitor for X, that displays any information on your desktop.

Step 1. Install conky-all package

Step 2. create ~/.conkyrc file. This file can be downloaded from web.

Step 3. Run it: $ conky. If we want to run a specific configuration file, use conky -c CONKYRCFILE

Step 4. If you want to stop Conky: $ killall conky

Note that conky works automatically on Ubuntu's Unity.

For Lubuntu (tested on 14.04), the Conky's transparent function does not work at first. But This conkyrc works on Lubuntu desktop (mainly, tranparent function). To deal with the autostart, follow the suggestion from askubuntu.com. That is, go to ~/.config/autostart folder, create or copy+paste the file called conky.desktop with a content like 

[Desktop Entry]
Type=Application
Exec=sh "/home/brb/.conky/conky-startup.sh"
Hidden=false
NoDisplay=false
X-GNOME-Autostart-enabled=true
Name[en_IN]=Conky
Name=Conky
Comment[en_IN]=
Comment=

and 

brb@brb-VirtualBox:~$ cat .conky/conky-startup.sh 
conky &
exit 0
brb@brb-VirtualBox:~$ ls -l .conky/conky-startup.sh 
-rw-rw-r-- 1 brb brb 37 Aug 30 20:17 .conky/conky-startup.sh

Another way to configure conky is to install conky-manager. See this and project website page. But it seems it does not work well with desktop wallpaper.

What should I do when Ubuntu freezes?

Press Alt+Print and then type 'REISUB' (not work, it only does screenshot)

Customize the desktop

  • Install Cairo-Dock.

Show date in top bar of desktop

  • Ubuntu 18.04 dconf write /org/gnome/desktop/interface/clock-show-date 'true'

Remove overlay scroll bar

http://www.itworld.com/article/2698420/disable-overlay-scroll-bars-in-ubuntu-14-04.html

Change scroll bar color

See this post. Run sudo apt-get install gnome-color-chooser.

Go to Engines tab in gnome-color-chooser and choose clearlooks engine for scrollbars.

How to turn off/disable Compiz's “drag to maximize” behaviour?

http://askubuntu.com/questions/72452/how-to-turn-off-compizs-drag-to-maximize-behaviour

On Mint, go to Preferences -> Window Tiling -> Enable Window Tiling and snapping -> Off.

Snapping windows to left or right

  • Drag the window to left or right. I found when I drag the window to right, it just maximizes the window
  • Window key + Left/right key. It Works on Ubuntu 18.40.

Grub2

To show the grub2 screen, run 'sudo nano /etc/default/grub' and comment out the line GRUB_HIDDEN_TIMEOUT=0 and change the line GRUB_CMDLINE_LINUX_DEFAULT="quiet splash" to GRUB_CMDLINE_LINUX_DEFAULT="". Remember to run 'sudo update-grub' after any change to grub.

To add a splash image, follow the instruction at https://help.ubuntu.com/community/Grub2/Displays. Note that Grub2 will search the image based on some priority and there are also some minor requirements on the images. To test 

sudo apt-get install grub2-splashimages
sudo cp /usr/share/images/grub/Moraine_Lake_17092005.tga /boot/grub/
sudo update-grub

How do I set the grub timeout and the grub default boot entry?

https://askubuntu.com/questions/148095/how-do-i-set-the-grub-timeout-and-the-grub-default-boot-entry

  1. gksudo gedit /etc/default/grub
  2. Change as you like. Save and closed the file.
    • You can change the default from 0 to any number
    • You can change the "hidden timeout" (no menu)
    • You can force the grub menu to show by commenting out the two GRUB_HIDDEN lines with a # at the beginning of the line
    • set the grub menu timeout (default is 10 seconds)
  3. sudo update-grub
  4. Reboot

Boot into command line

http://www.linuxandubuntu.com/home/how-to-boot-into-linux-command-line

  1. Highlight the first item (default) and press 'e' in the GRUB menu
  2. Navigate to the line that starts with ‘linux’, change the runlevel to 3 (at the end of the line). Level 3 means multi-user, command-line only system
  3. Press Ctrl+x or F10 to boot into

To switch back to GUI, type sudo init 5. Level 5 is the default.

Grub Customizer - GUI program

How To Change The GRUB Boot Order Or Default Boot Entry In Ubuntu, Linux Mint, Debian, Or Fedora With Grub Customizer

Network Manager

Find Available Network Interfaces On Linux

Find Available Network Interfaces On Linux

  1. ifconfig -a
  2. ip link show # OR ip addr
  3. ls /sys/class/net
  4. cat /proc/net/dev
  5. netstat -i
  6. nmcli device status # OR nmcli connection show

Set up OpenDNS

Set up OpenDNS on Linux Mint or Set custom DNS servers on Linux with Network Manager or resolv.conf

Select the Method: Automatic (DHCP) addresses only and enter 208.67.220.220, 208.67.222.222 into the DNS field, then click Save.

But after the change (and reboot), I don't have internet anymore.

DNS problem and 127.0.1.1

(Ubuntu 16.04 on Odroid) For some reason, pinging my domain always goes to the wrong IP. If I go to System -> Administration -> Network to change DNS from 127.0.1.1 to 8.8.8.8, it fixes the problem. But if I reboot, the DNS entry goes back to 127.0.1.1 again.

When I follow this post nameserver 127.0.1.1 in resolv.conf won't go away, the DNS will be changed to local IP of my router and the problem is fixed (even I reboot the computer).

See also the next: How to flush the DNS cache

How to flush the DNS cache

sudo /etc/init.d/dns-clean

NM-applet

https://wiki.archlinux.org/index.php/NetworkManager

Turn on/off wifi adapter

The command-line equivalent of unchecking the nm-applet's 'Enable Wi-fi' should be 

nmcli nm wifi off
# OR
nmcli radio wifi off
# OR
sudo ifconfig wlan0 down

Proxy

Internet Shut Down

DHCP Server

How to Install a DHCP Server in Ubuntu and Debian

File Server

Network File System (NFS)

NFS allows a system to share directories and files with others over a network. By using NFS, users and programs can access files on remote systems almost as if they were local files.

Some of the most notable benefits that NFS can provide are:

  • Local workstations use less disk space.
  • There is no need for users to have separate home directories on every network machine. Home directories could be set up on the NFS server and made available throughout the network.

Server part: 

sudo apt-get install nfs-kernel-server

Configure the directories to be exported by adding them to the /etc/exports file. 

/home/USERNAME/SHAREFOLDER 192.168.1.0/24(rw,sync,no_subtree_check)
/ubuntu  *(ro,sync,no_root_squash)
/home    *(rw,sync,no_root_squash)
# replace * with one of the hostname formats.

where 'ro' means read only. See Linux Home Server Howto. The no_root_squash option will not prevent root on a client machine from writing files to the server as root; by default, NFS will map any requests from root on the client to the 'nobody' user on the server. See digitalocean.

To start the NFS server: 

sudo service nfs-kernel-server start

Client part:

PS.

  • There is no need to enter any password related to the NFS server.
  • See digitalocean for other ways to specify the arguments in </etc/fstab>.
sudo apt-get install nfs-common

sudo mount -t nfs example.hostname.com:/ubuntu /mnt/ubuntu
# The mount point directory /mnt/ubuntu must exist.
# or modify the /etc/fstab file 
# example.hostname.com:/ubuntu /mnt/ubuntu nfs rsize=8192,wsize=8192,timeo=14,intr
# localip:/sharedfolder /mnt/ubuntu nfs defaults 0 0

brb@brb-P45T-A:~$ ps -ef | grep nfs
root       675     2  0 11:16 ?        00:00:00 [nfsiod]
root     14783     2  0 16:51 ?        00:00:00 [nfsv4.0-svc]
brb      14960 13491  0 16:56 pts/0    00:00:00 grep --color=auto nfs

To make the mounting permanently, run sudo nano /etc/fstab and include a line like 

1.2.3.4:/home    /mnt/nfs/home   nfs auto,noatime,nolock,bg,nfsvers=4,intr,tcp,actimeo=1800 0 0

Some help:

Boot from an NFS server

With NFS booting, the core kernel and file systems are kept on a central server and then pushed out onto client systems to be booted on there. That means your files and desktop will always be available wherever you want to log in.

At the end, the client computer does not need any internal storage. Cool!

CIFS (Common Internet File System) and NTLMv2 (NT LAN Manager)

Note that this method is most suitable for transferring small files. Users transferring large amounts of data to and from Helix/Biowulf should continue to use scp or sftp. (nih.gov)

Samba - allows Linux to transfer files with Windows clients

sudo apt-get install -y samba samba-common python-glade2 system-config-samba
sudo cp -pf /etc/samba/smb.conf /etc/samba/smb.conf.bak
sudo sh -c 'cat /dev/null  > /etc/samba/smb.conf'
sudo nano /etc/samba/smb.conf
sudo service smbd restart
testparm
# password protected
sudo addgroup smbgrp
sudo useradd till -G smbgrp
sudo smbpasswd -a SOMEEXISTEDUSER
sudo mkdir -p /samba/secured
cd /samba
sudo chmod -R 0770 secured
sudo chown root:smbgrp secured
sudo nano /etc/samba/smb.conf
sudo service smbd restart 
testparm

sudo netstat -pant | grep smbd   # mine shows 139 & 445
  • I have trouble to connect to the samba server though connecting it itself from the samba server works fine.
$ smbclient -L //192.168.1.XX/sambashare -U SOMEEXISTEDUSER
WARNING: The "syslog" option is deprecated
Connection to 192.168.1.XX failed (Error NT_STATUS_IO_TIMEOUT)

# From server itself
$ smbclient -L //localhost 

# Solution: ufw
# https://askubuntu.com/a/184806
sudo ufw allow Samba

# From the client 
$ smbclient -L //192.168.1.XX/sambashare -U YYY
# No error. Return to the local prompt again.
# Now we can use Ubuntu's Files app to connect to the server
# smb://192.168.1.XX/
$ ps -ef | grep smbd    # see if the Samba daemon (smbd)
$ ps -ef | grep nmbd    # see if the NetBIOS name server daemon (nmbd) is running

$ sudo service smbd stop  # does not stop nmbd 
$ sudo service nmbd stop

$ sudo service smbd start
$ sudo service nmbd start
sudo apt-get install samba samba-common
sudo apt-get install python-glade2
sudo apt-get install system-config-samba

Use Dash and search for 'samba'. It will ask for the user's password first. The samba password can also be set by 

sudo smbpasswd -a USERNAME

A non-gui way to configuration samba is adding the following to the end of /etc/samba/smb.conf file, sudo nano -w /etc/samba/smb.conf (-w means no-wrap). Any line beginning with a semicolon (“;”) or a hash (“#”) character is ignored. 

[brb]
        path = /home/brb
;       writeable = no
;       browseable = yes
        guest ok = yes

On Windows PC, go to start and open 'Run' then enter ip with double backslash. Like this (\\192.168.1.XX).

Remove and re-install Samba

$ sudo apt-get remove --purge samba
$ sudo apt-get remove --purge smbclient libsmbclient

$ sudo apt-get install samba
$ sudo apt-get install smbclient libsmbclient

SambaCry vulnerability and check Samba version

http://pcworld.com/article/3199106/linux/the-sambacry-scare-gives-linux-users-a-taste-of-wannacry-petya-problems.html

To check your samba version 

$ smbd -V
Version 4.3.11-Ubuntu

Mounting a Samba Share using the cifs-utils package

Mounting a Samba Share

Change the default session when using auto login

See this post. We need to edit the file /etc/lightdm/lightdm.conf. Note that on my Ubuntu 12.04, I have the following desktop options. 

$ ls -lt /usr/share/xsessions/
total 16
-rw-r--r-- 1 root root 205 Apr 19  2012 gnome.desktop
-rw-r--r-- 1 root root 188 Apr 19  2012 gnome-shell.desktop
-rw-r--r-- 1 root root 208 Apr 19  2012 ubuntu-2d.desktop
-rw-r--r-- 1 root root 185 Apr 19  2012 ubuntu.desktop

sudo

How To Grant And Remove Sudo Privileges To Users On Ubuntu

Debian root user from remote access

When you login by SSH, then use the username you have chosen when you installed Debian as the root user is disabled for remote logins. Then run the command "su" to become root user. See howtoforget.com.

Terminal

Directory color on ssh

When I ssh to biowulf from Gnome/Terminal, the folder color became dark blue which is hard to read when the background color is black. A solution is https://serverfault.com/questions/137649/changing-terminal-colors-in-ubuntu-server.

1. append this to your ~/.bashrc 

    if [ "$TERM" != "dumb" ]; then
      [ -e "$HOME/.dir_colors" ] && 
      DIR_COLORS="$HOME/.dir_colors" [ -e "$DIR_COLORS" ] ||
      DIR_COLORS="" 
      eval "`dircolors -b $DIR_COLORS`" 
      alias ls='ls --color=auto'
    fi

2. create/edit your ~/.dir_colors, for example with 

  $ dircolors --print-database > .dir_colors

3. Then force a read of your .bashrc file with: 

  $ source ~/.bashrc

Everything should be pretty.

powerline

Remember terminal tabs

The trick on this post works for me on my GNOME Terminal 3.6.2 (gnome-terminal --version). 

# To save configuration into /home/$USER/terminal.cfg:
gnome-terminal --save-config=/home/$USER/terminal.cfg

# To load it back:
gnome-terminal --load-config=/home/$USER/terminal.cfg

To recall the titles, follow this simple hack. That is, add an entry Title=xxxx to each tab section.

Terminal tab color

If we open several tabs in the (GNOME) Terminal, the default color of the active tab is not quite different from the other tabs. We need a solution to change the tab colors.

http://askubuntu.com/questions/355297/gnome-terminal-tabs-no-contrast-between-active-and-inactive-tabs

Solution: edit ~/.config/gtk-3.0/gtk.css (you might have to create it) and add: 

TerminalWindow,
TerminalWindow.background {
        background-color: #6e6e6e;
        color: #000000;
}

TerminalWindow .notebook tab {
        padding: 2;
        background-color: #6e6e6e;
}

TerminalWindow .notebook tab:active {
        background-color: #d1d1d1;
}

Then close ALL terminal windows start and test.

How to practically use your Linux terminal for everything

Record terminal: script command

Font

Large text

This is useful on large screen displays or TVs.

Settings -> Universal Access on Ubuntu or Accessibility on Linux Mint. Turn on "Large text". Each application's name on the Linux Mint's taskbar, title on each application and texts in applications will be increased.

Install Microsoft Font in linux suite

PCWorld.com

Install language packs

sudo apt-get install language-pack-[cod] language-pack-gnome-[cod] language-pack-[cod]-base language-pack-gnome-[cod]-base

For example, [cod]=en or [cod]=zh.

Change locale language and character set

Display Chinese character (from vanilla Debian/Ubuntu system)

sudo apt-get install fonts-arphic-ukai fonts-arphic-uming

sudo apt-get install language-support-fonts-zh
# Or
sudo apt-get install ttf-arphic-uming ttf-wqy-zenhei

Chinese Input

Zhuyin-keyboard.gif

Ibus.png

  1. type 'language' in Dash search (Or click Power button on the top-right corner -> System Settings...) and click 'Language Support' (this may not be installed from (x)Ubuntu automatically. In such case, IBUS will be missing eg Chewing method). The 'Language Support' is under Settings menu in xUbuntu.
  2. Click 'Install' if a message popped up with the message 'The language support is not installed completely'. After the installation is done, the 'Language support' dialog comes back.
  3. Choose between ibus (ubuntu < 16.04) /fcitx (ubuntu 16.04).
    • Choose 'IBUS' for keyboard input method system (bottom of the dialog). IBUS is under 'System' menu in xUbuntu.
    • Choose 'fcitx'
  4. Click 'Install/Remove Languages'. Choose Chinese. Click 'Apply'. An 'Applying changes' dialog will appear.
  5. Click 'Close' button.
  6. Select Chinese
    • System Settings -> Text Entry -> '+' -> Chinese. Or Settings > Keyboard Input Method > Input method > Select an input method > Show only input methods for your region > Chinese 酷 Chewing. If we cannot find this dialog, we can launch it by ibus-setup command. If Chewing is not shown as one of Chinese input methods, we can log out and log in the desktop. If ibus does not have the chewing selection, we should try to install it sudo apt-get install ibus-chewing and/or run ibus restart.
    • Dash -> Fcitx Configuration. '+' -> Chewing. PS. On Ubuntu 16.04 it only shows a Chinese option without further options even I installed ibus-chewing.
  7. Make sure 'Show current input source in the menu bar' is checked.
  8. Click 'Close' button.

On Ubuntu 14.04, the super key is Windows.

On Ubuntu 16.04, ibus does not work. Use fcitx instead. Chewing(Fcitx) should be added to the "Text Entry" GUI. "fcitx" should be selected in the "Language Support" GUI (it's OK the language for menus and windows does not include 漢語 (臺灣). A linux or keyboard icon should appear in the taskbar.

On Ubuntu 18.04, I don't need to use fcitx (not available by default)

  1. I follow pingyinjoe to install Chinese from Language Support. Reboot (Log out seems to take forever).
  2. I follow this post to use sudo locale-gen zh_TW.UTF-8 to add chewing to the list (see next step).
  3. Type 'region' to search and click "Region and Language". Follow the GUI to add Chinese (Chewing).
  4. Test it by using Windows + Space to switch input methods.

Note that do not use 'Text Entry' application (shown as one options when we search 'language'). This application will conflict with ibus.

ibus

How To Setup Multilingual Input Method On Ubuntu 18.04

gcin

新注音 New Zhuyin

fcitx

https://daviwa.blogspot.com/2017_10_08_archive.html

  • On Linux Mint, it cannot show a list of candidate words. The trick of using killall fcitx-qimpanel works.
  • On Ubuntu Mate, the fcitx works fine. ps -ef | grep fcitx-qimpanel shows nothing.

/usr/lib/ibus/ibus-ui-gtk3 high memory usage

For some reason, the ubuntu 14.04 is not responsive. Htop shows ibus-ui-gtk3 is the culprit. The suggestion is to run 

killall ibus-daemon

After I run this command and wait a few seconds, the memory leak problem is solved.

Change time zone

http://wiki.debian.org/TimeZoneChanges 

$sudo dpkg-reconfigure tzdata

The command launches an ncurses based interface which allows arrow keys to be used to select the region specific time zone.

Make script run at boot time with init.d directory

http://www.debian-administration.org/articles/28

For example, see here from running a python script for raspberry pi.

  1. Create a script /etc/init.d/lcd
  2. Make the script executable
  3. Make the script known to the system by using the update-rc.d' command
sudo update-rc.d lcd defaults

/etc/rc.local file

Executing Commands and Scripts at Reboot & Startup in Linux

For CentOS, we use file ‘/etc/rc.d/rc.local’ instead of ‘/etc/rc.local’. We also need to make this file executable before adding any script or command to the file.

Note:- When executing a script at startup, make sure that the script ends with ‘exit 0’.

crontab

Executing Commands and Scripts at Reboot & Startup in Linux

wireless connection randomly drop off

My wireless adapter is TP-LINK, TL-WN722N.

http://askubuntu.com/questions/73607/wireless-connection-keeps-dropping-with-an-intel-3945abg-card 

sudo iwconfig wlan0 power off

5 Best Linux/Ubuntu compatible USB Wifi cards:

  • AirLink101 AWLL6075 Wireless N Mini USB Adapter
  • Medialink – Wireless N USB Adapter – 802.11n
  • ASUS (USB-N13) Wireless-N USB Adapter
  • Panda Mini Wifi (b/g/n) 150Mbps Card
  • TP-Link TL-WN722N 150Mbps High Gain Wireless USB Adapter

To show (USB) wireless adapter information 

sudo lshw -C network
sudo lsusb -v
iwconfig

To check wifi connection information (SSID, channel, address, frequency, qualiyt, signal level, ...) 

sudo iwlist wlan0 scan

My experience is quality should be at least 50/70 and signal level should be larger than -60dBm.

Back up DVDs

Top 5 Linux DVD RIP Software from cyberciti.biz.

dvdbackup command

It works and fast. It will create a new directory (no need to specify beforehand). 

sudo apt install dvdbackup
dvdbackup # get usage

dvdbackup -i /dev/dvd -o ~/Videos/ -M
# -M means to back up the whole DVD

We can further create an ISO file from a directory using 

genisoimage -o output_image.iso directory_name
# Or
mkisofs -lJR -o output_image.iso directory_name
# -l : Allow full 31 character filenames.
# -J : Generate Joliet directory records in addition to regular iso9660 file names.
# -R : Generate System Use Sharing Protocol (SUSP) and Rock Ridge (RR) records using the Rock Ridge protocol

Create an iso file from a CD/DVD or HD

See also

Method 1 (Better than Method 2). No need to umount the cdrom. 

mkisofs -o /tmp/DVD.iso /tmp/directory/

to make an ISO from files on your hard drive.

Method 2. Make sure the cdrom is NOT mounted. Type mount to confirm it. If cd was mouted automatically unmout it with umount command: like umount /dev/cdrom or umount /mnt/cdrom. Note that no extra forward slash after /dev/cdrom for the command below. 

dd if=/dev/cdrom of=~/DVD.iso status=progress
dd bs=4M if=/dev/sr0 of=~/DVD.iso status=progress 
# Works for me to back up some borrowed DVDs
# 
# Don't add the 'bs' parameter or you'll get an error reading '/dev/sr0': Input/output error
# or use VLC to watch a little bit of the DVD first to fix the problem (why it helps?)
# note that status=progress does not show the percentage. It shows how much is copied.
# OR
cat /dev/sr0 > ~/DVD.iso

For some reason I get an Input/output error. But after I use VLC to play the video, the Input/output error is gone when I try it again.

We can mount the iso file to a directory to check the iso file content is correct. 

mount -t iso9660 -o loop,ro DVD.iso /mnt

Method 3. Monitor the progress of percentage assume we know the disk size 

sudo apt-get install pv
dd if=/dev/urandom | pv -s 2G | dd of=/dev/null

Method 4. To see the progress of dd once it's running, open another terminal and enter: 

sudo kill -USR1 $(pgrep ^dd)

This will display dd progress in the dd terminal window without halting the process. If you're on BSD or OS X, use INFO instead of USR1. The USR1 signal will terminate dd.

If you would like to get regular updates of the dd progress, then enter: 

watch -n5 'sudo kill -USR1 $(pgrep ^dd)'

watch will probe the dd process every -n seconds (-n5 = 5 seconds) and report without halting it.

Note the proper single quotes in the commands above.

HandBrake

It works but it loses the menu page on DVD.

Have fun with /etc/hosts file

su -c "nano /etc/hosts" 

127.0.0.1	localhost
::1             localhost
74.125.67.100   DNS_NAME1 DNS_NAME2
  • If you want to add aliases for your machine that will lookup to the loopback address you can keep adding them as space separated values on that line.
  • "::1" is the ipv6 equivalent of 127.0.0.1 (which is for ipv4).

Block malware, adware

How to Use Your Computer’s Hosts File to Block Tons of Malware, Porn, and Other Types of Websites

Mount a remote file system over ssh

The trick is to use the sshfs tool.

On Ubuntu 

# Install the program
sudo apt-get install sshfs

# Mount the file system
sudo mkdir /mnt/droplet <--replace "droplet" whatever you prefer
sudo sshfs [email protected]:/ /mnt/droplet

# Unmount the file system
sudo umount /mnt/droplet

# Permanently Mounting the Remote File System
sudo nano /etc/fstab
sshfs#[email protected]:/ /mnt/droplet

Nautilus or Nemo (File Manager)

Bookmark the current directory to the sidebar

Ctrl + d. See also Files > Keyboard Shortcuts.

Ctrl + L

Change to a directory

Undo Ctrl+L

Press ESC.

Mount another Linux system in Nautilus

Very easy. Check out howtogeek.com

Create a desktop shortcut

Navigate to your application in Nautilus. Right-click, select "Make Link". Then drag shortcut to your desktop. Works in Ubuntu 12.04.

.desktop file format

Open a terminal

sudo apt-get install nautilus-open-terminal
nautilus -q

In Ubuntu 15.10, the functionality is already included in nautilus!

Mount and Unmount Storage Devices from the Linux Terminal

How to Mount and Unmount Storage Devices from the Linux Terminal

Mount iso file

$ sudo mkdir /mnt/iso
$ sudo mount -o loop /tmp/file.iso /mnt/iso
$ sudo umount /mnt/iso

Check ubuntu version from command line

http://www.howtogeek.com/206240/how-to-tell-what-distro-and-version-of-linux-you-are-running/ 

lsb_release -a     # command not found if we run it from a docker image

# OR
cat /etc/issue     # works on docker image

# OR
cat /etc/*release  # works on docker image

# check kernel version
uname -r           # docker will get this information from the host

# check 32/64 bit kernel
uname -a           # docker will get this information from the host

keyboard shortcuts

Go to keyboard app to change the settings. Note: Super key is also Windows key. Use 'Backspace' key to disable a shortcut.

  • List from ubuntu.com
  • Super: Open the Dash. Press and hold it to see a cheat sheet with a bunch of other nifty shortcuts.
  • Super + Number: Open the application that is at that position in the dock
  • Alt + Mouse: Move an application. Useful if an application's title bar is too high.
  • Alt + F2: Run an application by typing its name in the box which appears (same function as the Super key).
  • Alt + Space: Activate the window menu. Not useful so I assign this to "Show all applications" (Super + a). This will be consistent with macOS.
  • Ctrl + Super + D: To minimize all windows
  • Ctrl + Alt + Arrows: move to another workspace
  • Ctrl + Alt + Shift + Arrows: move current application to another workspace
  • Super + left/right: snap the window to left/right
  • Super + upper/down: maximize/resize the window

On Xubuntu,

  • Alt + F1 (Ctrl + ESC): Application menu.
  • Alt + F2 (Super + R): Application Finder.

Add a new keyboard shortcut

Let's say I want to assign Ctrl+Alt+s to bring the shutdown dialog.

  1. System Settings -> Keyboard -> Shortcuts -> Windows -> Toggle shaded state -> Backspace to disable it. For some reason, I cannot assign a new keybinding using the method of Custom Shortcuts' method.
  2. Open Ubuntu Software Center and install Compiz Config Setting Manager program. Open the program by search Compiz and then create a new command gnome-session-quit --power-off --force with a name like 'Shutdown' and the keyboard binding we want. CCSM -> General -> Commands.

With this approach, it will give a dialog with 4 options (lock suspend restart shutdown) but no one is pre-selected. If we want the shutdown icon being preselected, use this script where the zenity command was used to create a dialog. The zenity program was pre-installed in Ubuntu. See How to Make Simple Graphical Shell Scripts with Zenity on Linux.

Firefox

  • Space: page down
  • Shift + space: page up

BioLinux

See BioLinux.

Tomcat

Hardware/Device manager

How to List Your Computer’s Devices From the Linux Terminal mount , lsblk, df , fdisk , The /proc Files , lspci , lsusb , lsdev , lshw , lsscsi , dmidecode, hwinfo.

By default, ubuntu does not provide any graphical tool like device manager on Windows. A very close one is lshw (hardware lister). A GUI tool based on it is called lshw-gtk (seems not as informative as the command line one) and can be installed by sudo apt-get install lshw-gtk in Ubuntu/Debian or yum install lshw in Red Hat/Fedora/CentOS.

As you can see the line containing 'display' shows the motherboard (P45T-A), CPU (Intel Core 2 Duo E8400), graphical card (GeForce 9400 GT in this case), et al. 

brb@brb-P45T-A:~$ sudo lshw -short
H/W path         Device      Class       Description
====================================================
                             system      P45T-A (To Be Filled By O.E.M.)
/0                           bus         P45T-A
/0/0                         memory      64KiB BIOS
/0/4                         processor   Intel(R) Core(TM)2 Duo CPU     E8400  @
/0/4/5                       memory      64KiB L1 cache
/0/4/6                       memory      6MiB L2 cache
/0/f                         memory      8GiB System Memory
/0/f/0                       memory      2GiB DIMM DDR2 Synchronous 800 MHz (1.2
/0/f/1                       memory      2GiB DIMM DDR2 Synchronous 800 MHz (1.2
/0/f/2                       memory      2GiB DIMM DDR2 Synchronous 800 MHz (1.2
/0/f/3                       memory      2GiB DIMM DDR2 Synchronous 800 MHz (1.2
/0/100                       bridge      4 Series Chipset DRAM Controller
/0/100/1                     bridge      4 Series Chipset PCI Express Root Port
/0/100/1/0                   display     G96 [GeForce 9400 GT]
/0/100/1a                    bus         82801JI (ICH10 Family) USB UHCI Control
/0/100/1a.1                  bus         82801JI (ICH10 Family) USB UHCI Control
/0/100/1a.2                  bus         82801JI (ICH10 Family) USB UHCI Control
/0/100/1a.7                  bus         82801JI (ICH10 Family) USB2 EHCI Contro
/0/100/1b                    multimedia  82801JI (ICH10 Family) HD Audio Control
/0/100/1c                    bridge      82801JI (ICH10 Family) PCI Express Root
/0/100/1c/0      eth0        network     AR8121/AR8113/AR8114 Gigabit or Fast Et
/0/100/1c.3                  bridge      82801JI (ICH10 Family) PCI Express Root
/0/100/1c.3/0    wlan0       network     AR93xx Wireless Network Adapter
/0/100/1c.4                  bridge      82801JI (ICH10 Family) PCI Express Root
/0/100/1c.4/0                storage     JMB361 AHCI/IDE
/0/100/1c.4/0.1              storage     JMB361 AHCI/IDE
/0/100/1d                    bus         82801JI (ICH10 Family) USB UHCI Control
/0/100/1d.1                  bus         82801JI (ICH10 Family) USB UHCI Control
/0/100/1d.2                  bus         82801JI (ICH10 Family) USB UHCI Control
/0/100/1d.7                  bus         82801JI (ICH10 Family) USB2 EHCI Contro
/0/100/1e                    bridge      82801 PCI Bridge
/0/100/1f                    bridge      82801JIR (ICH10R) LPC Interface Control
/0/100/1f.2                  storage     82801JI (ICH10 Family) 4 port SATA IDE 
/0/100/1f.3                  bus         82801JI (ICH10 Family) SMBus Controller
/0/100/1f.5                  storage     82801JI (ICH10 Family) 2 port SATA IDE 
/0/1             scsi0       storage     
/0/1/0.0.0       /dev/sda    disk        250GB Samsung SSD 840
/0/1/0.0.0/1     /dev/sda1   volume      224GiB EXT4 volume
/0/1/0.0.0/2     /dev/sda2   volume      8190MiB Extended partition
/0/1/0.0.0/2/5   /dev/sda5   volume      8190MiB Linux swap / Solaris partition
/0/1/0.1.0       /dev/sdb    disk        2TB ST2000DM001-9YN1
/0/1/0.1.0/1     /dev/sdb1   volume      1863GiB EXT4 volume
/0/2             scsi2       storage     
/0/2/0.0.0       /dev/cdrom  disk        DVDRAM GH24NS90
/1                           power       Nikon Ultra Plus
/2                           power       To Be Filled By O.E.M.

For storage part, ubuntu provides a graphical tool. See "disk utility" on gnome based ubuntu or search for "disk" in launcher.

Set static IP - /etc/network/interfaces

root@debian:~# cat /etc/network/interfaces
auto lo eth0
iface lo inet loopback
iface eth0 inet dhcp

Now edit the file /etc/network/interfaces 

# The primary network interface
auto eth0
iface eth0 inet static
address 192.168.1.3
gateway 192.168.1.1
netmask 255.255.255.0
network 192.168.1.0                 # Optional
broadcast 192.168.1.255             # Optional
dns-nameservers 192.168.1.1 8.8.8.8 # Or skip 192.168.1.1

After it, restart the network by issuing 

/etc/init.d/networking restart

OR sudo reboot

Note: It does not work by editing /etc/resolv.conf since this file will be overwritten.

Change IP address from the command line

/sbin/ifconfig eth0 192.168.1.17 netmask 255.255.255.0 up
/sbin/ifconfig eth0

Windows OS.

ufw (uncomplicated firewall)

The default firewall configuration tool for Ubuntu is ufw. Developed to ease iptables firewall configuration, ufw provides a user friendly way to create an IPv4 or IPv6 host-based firewall. By default UFW is disabled.

Suppose I have a virtual machine running a web server at port 8888 (The vm may be initialized by the Vagrant command). I can access the webpage from my host machine using http://localhost:8888.

Now I want the web page to be accessible from other local machines. We can use the ufw command to enable the firewall wall and open ports for certain services. 

sudo ufw allow 8888/tcp
sudo ufw show added
sudo ufw enable
sudo ufw status
sudo ufw app list

nmap localhost

Now I can go to another machine, open a browser at http://hostip:8888/. I should be able to get the same result as I got from the host machine.

In one instance sshing to a server failed (connection time) for some reason. The solution is to run the following command on the server 

sudo ufw allow 22/tcp

A graphical interface program is called Gufw Firewall.

Other things ufw can do:

  • Allow/Deny by ports and (optional) protocols
  • Allow/Deny by service name
  • Disable ping requests.
  • Allow by specific IP
  • Allow by subnet
  • Allow by specific port and IP address
  • Deny by certain IP address
  • Deny by certain IP address and certain port

DNS tricks

5 DNS Servers Guaranteed to Improve Your Online Safety

http://www.makeuseof.com/tag/best-dns-providers-security/

5 Nifty Ways to Use DNS to Your Advantage

http://www.makeuseof.com/tag/nifty-ways-use-dns-advantage/

DNS Server

Protecting Your Privacy With Firefox on Linux

What is my DNS server /etc/resolv.conf or /etc/network/interfaces

Even I can change my DNS setting using the Network Manager (IPv4 -> disable Automatic -> Enter 8.8.8.8 -> Apply -> Toggle On/Off), the name solving does not work. Testing https://129.43.254.99 works but not https://brb.nci.nih.gov

Note: we are not supposed to edit /etc/resolv.conf file. See here on how to add DNS servers.

The real DNS servers IPs can be found by the network manager GUI or using the command line 

nmcli dev show | grep 'IP4.DNS'

On my home computer, it just shows one line nameserver 127.0.1.1. On work computer, it shows 

# Dynamic resolv.conf(5) file for glibc resolver(3) generated by resolvconf(8)
#     DO NOT EDIT THIS FILE BY HAND -- YOUR CHANGES WILL BE OVERWRITTEN
nameserver 127.0.1.1
search XXX.XXX.gov

On the VM of my work computer, it shows 

nameserver 127.0.0.53
search XXX.XXX.gov

It seems the /etc/resolv.conf file changes with the file on the host.

After any change, we can restart the network by using sudo service networking restart.

Note:

  • nameserver Name-server-IP-address: Point out to your your own nameserver or to ISP’s name server. Up to 3 name servers may be listed.
  • search domain.com: The search list is normally determined from the local domain name; by default, it contains only the local domain name. So when you type nslookup www, it will be matched to www.cyberciti.biz

You can also use Public Name Servers 

nameserver 8.8.8.8
nameserver 8.8.4.4

On Ubuntu 18.04, it uses netplan. See

dig Command Examples

dig (domain information groper) is a DNS lookup utility. 

$ dig google.com ANY
$ dig r-project.org  ANY
...
;r-project.org.                 IN      ANY

;; ANSWER SECTION:
r-project.org.          7199    IN      NS      ns2.urbanek.info.
r-project.org.          7199    IN      NS      ns1.urbanek.info.
r-project.org.          7199    IN      NS      ns2.wu-wien.ac.at.
r-project.org.          7199    IN      NS      ns3.urbanek.info.
r-project.org.          7199    IN      NS      ns4.urbanek.info.
r-project.org.          7199    IN      NS      ns1.wu-wien.ac.at.
r-project.org.          7199    IN      A       137.208.57.37
r-project.org.          7199    IN      MX      5 mc1.ethz.ch.
r-project.org.          7199    IN      MX      5 mc4.ethz.ch.
r-project.org.          7199    IN      MX      5 mc3.ethz.ch.
r-project.org.          7199    IN      MX      5 mc2.ethz.ch.
r-project.org.          7199    IN      TXT     "v=spf1 ip4:129.132.119.208/32 ~all"
r-project.org.          7199    IN      SOA     ns0.wu-wien.ac.at. postmaster.wu-wien.ac.at.

DNStracer

http://www.ubuntugeek.com/dnstracer-trace-dns-queries-to-the-source.html

Dyndns and ddclient

See

nano /etc/ddclient.conf 

protocol=namecheap
ssl=yes
use=web, web=dynamicdns.park-your-domain.com/getip
server=dynamicdns.park-your-domain.com
login=yourdomain.com
password=a9438540ba8a449fb0ed09c3737b9e32
@

Note that the specification should depend on the domain name registrar (eg namecheap). For namecheap, the login/password is NOT your actual credential from your domain name registrar. The password should be obtained from the domain name registrar website. The last line is about the host. If I am setting it up for a subdomain, I should enter the subdomain name (and skip the domain name part). The ssl=yes is to ensure the connection is made over https instead of http.

And run sudo ddclient -daemon=0 -debug -verbose -noquiet to verify ddclient is working. You shall get a long return with the last line looks like 

SUCCESS:  updating YOURSUBDOMAIN: good: IP address set to XX.XXX.XXX.XXX

No matter which method we use, we can go to our DNS account (in namecheap, go to Dashboard -> MANAGE button -> Domains -> Advanced DNS) and temporarily change the global IP address to another one, run the update script and then check if the global IP address has been updated to the correct one.

namecheap

Mail

no-ip

Similar to Dyndns. It has its own client program. Needs to build it yourself.

Also see the troubleshooting guide.

See http://ducky-pond.com/posts/12 for instruction of setting autostart on Debian system.

See http://www.coulterfamily.org.uk/pages/PCs/Linux/FAQ-LINUX-NO-IP-CLIENT.php for another approach.

Note: If noip2 cannot start automatically or noip2 does not update even it can be seen from ps -ef command, use sudo crontab -e command. For some reason, after I use sudo crontab, noip2 can update IP. So the only problem right now is it cannot update every 30 minutes even sudo noip2 -S says so. The problems may be 1. ps -ef shows the command runs from nobody user 2. sudo noip2 -S says it updates every 30 minutes via /dev/eth0 with NAT enabled.

Update: An alternative is to use ddclient. However, ddclient never updates the IP.

Mail

  • Allow only one MX record for each host for free no-ip account.
  • Click Host/Redirects > Manage Hosts > Modify.

webmin

See http://www.webmin.com/deb.html 

wget http://prdownloads.sourceforge.net/webadmin/webmin_1.600_all.deb
dpkg --install webmin_1.600_all.deb

The install will be done automatically to /usr/share/webmin, the administration username set to root and the password to your current root password. You should now be able to login to Webmin at the URL http://localhost:10000/. Or if accessing it remotely, replace localhost with your system's IP address.

Find out motherboard information

# No root
cat /sys/devices/virtual/dmi/id/board_{vendor,name,version}

# Root
sudo dmidecode  | grep -A4 '^Base Board Information'

Virtualize Linux

http://www.linuxuser.co.uk/features/how-to-virtualise-linux-part-1

CPU information

$ grep name /proc/cpuinfo | sort -u
model name	: AMD Phenom(tm) II X6 1055T Processor      # home

model name	: Intel(R) Xeon(R) CPU  X7560  @ 2.27GHz    # helix

model name	: Intel(R) Xeon(R) CPU E5-1650 0 @ 3.20GHz  # office

CPU usage

Find out if the OS is running in a virtual environment

Linux adds the hypervisor flag to /proc/cpuinfo if the kernel detects running on some sort of a hypervisor. See here. 

cat /proc/cpuinfo | grep hypervisor

Virtualbox

See here.

VBoxClient: the VirtualBox kernel service is not running

Got the above message on the upper right corner of the screen for every booting. Note I don't install VirtualBox. A solution is run 

gksudo gedit /etc/X11/Xsession.d/98vboxadd-xclient

find the line 

notify-send "VBoxClient: the VirtualBox kernel service is not running.  Exiting."

Now change notify-send to echo.

Thin client

https://help.ubuntu.com/community/ThinClients

UbuntuLTSP

LTSP

Raspberry Pi

Running Raspberry Pi’s as Thin Clients with Ubuntu 14.04 LTS

[https://help.ubuntu.com/community/UbuntuLTSP/RaspberryPi UbuntuLTSP/RaspberryPi ]

Remote desktop

Remote desktop using Chrome

Remote desktop connection from Windows 7

xtightvncserver may not play well in Unity.

Install xrdp on Ubuntu. That's it. See 

sudo apt-get install xrdp
sudo /etc/init.d/xrdp start

On Windows 7, open its Remote Desktop client utility mstsc.exe.

Remote desktop connection to Windows 7 from xubuntu

sudo apt-get update
sudo apt-get install rdesktop
rdesktop xxx.xxx.x.x -f -u USERNAME -p PASSWORD
rdesktop 192.168.1.4 -g 1280x720 -u USERNAME -p PASSWORD

where -f option means full screen and -g means geometry.

Remote desktop connection to NCI (outdated)

Note the information here is outdated now.

The version 1.7.1 of rdesktop program in Ubuntu 14 has a bug with mouse cursor (invisible). To fix the bug, download the version 1.8.3 and build it. See http://ubuntuforums.org/showthread.php?t=2266743 

sudo apt-get update
sudo apt-get install build-essential libx11-dev libssl-dev libgssglue-dev libpcsclite-dev
tar zxvf rdesktop-1.8.3.tar.gz 
cd rdesktop-1.8.3
./configure
make
sudo make install

After that the new rdesktop is located under /usr/local/bin folder. The old rdesktop installed through apt-get is not deleted.

ts.nci.nih.gov:1494

DOMAIN: NIH

resolution: 1024 x 768

Use remmina or rdesktop or freerdp (sudo apt-get install freerdp-x11) 

rdesktop ts.nci.nih.gov:1494 -d NIH -u XXXXX -g 1024x768

To share a folder from the local machine, use "-r" option 

rdesktop ts.nci.nih.gov:1494 -d NIH -u XXXXX -g 1280x1024 -r disk:remotedisk=/home/$USER/Downloads

The new secure connection relies on the SmartCard is using ncits-p111.nci.nih.gov.

RealVNC

The default vnc server included in Ubuntu is not quite compatible with other clients. For example I can connect to Ubuntu 14.04 from Ubuntu 16.04 but not from a Mac. The 3rd party software is better. See the following screenshot after I have installed RealVNC server.

Realvnc-server.png

Note that RealVNC Server is not free for commercial users but is free for home users up to 5 computers & 3 users; see https://manage.realvnc.com/. An email and a password can be used to sign in your account for activating the license in VNC Server.

To start VNC server, use (https://www.realvnc.com/docs/debian-install-remove.html) 

sudo /etc/init.d/vncserver-x11-serviced start

The RealVNC will have an icon sitting on the tray at the top-right corner.

Before using VNC viewer, we also need to create a VNC password in VNC Server.

On Mac, the viewer can be launched from Applications -> VNC Viewer (if we have drag and drop the app to the Applications folder).

On Chrome OS, there is an VNC Viewer for Google Chrome to use. The IP address is special. For example, 192.168.5.127:80 for port 5980. See https://www.realvnc.com/docs/faq/connect-fail.html. Unfortunately I cannot connect successfully:(

Remote desktop connection from Ubuntu to Ubuntu

  • https://help.ubuntu.com/16.04/ubuntu-help/sharing-desktop.html
  • How to connect to a remote desktop from Linux Remmina's minimal UI makes it easy to remotely access Linux PCs and Windows 10
  • How to Remote Access to Ubuntu 16.04 from Windows. The instruction is the same for older versions of Ubuntu.
    • On a Ubuntu server. Go to Dash, type 'desktop sharing' and select it. Check sharing. Close the dialog. Open a terminal and run ps -ef | grep vino to make sure the server is running.
    • Disable encryption. Run sudo apt install dconf-editor. Go to Dash and type 'dconf' and select 'dconf editor'. When it opens, navigate to org -> gnome -> desktop -> remote-access, and uncheck the value of 'require-encryption.' Another way is to run gsettings set org.gnome.Vino require-encryption false.
    • On a client machine (eg another Ubuntu), open a remote desktop client program (eg Remmina). Choose VNC as the protocol. Enter necessary information to connect to the server.
  • Install a VNC server on non-Unity desktop

Allow for remote desktop connection

  1. Go to System -> Preference -> Remote desktop. Allow other uses to view your desktop & uncheck you must confirm each access & require user to enter this password.
  2. Go to System -> Preference -> Monitor. Change monitor resolution to 1280 x 720.

Allow for remote desktop connection when vino failed

  • Teamviewer. It works fine. After launching it, the software automatically creates an ID and password. We can change the password so it is fixed. Then launch the software on the client. Use the partner's ID and password to connect to it.
  • NoMachine. I ran the service on my Ubuntu 12.04 server. I also tested the client on my Android 6.0 tablet and Odroid xu4 running Ubuntu 15.10. I am using the version 5.0.63. I need to use my server's user account info to connect.
odroid@odroid:~/Downloads$ ps -ef | grep nx
nx       12168     1  1 21:11 ?        00:00:20 /usr/NX/bin/nxserver.bin root 12151 --daemon
odroid   12199 12168  1 21:11 ?        00:00:12 /usr/NX/bin/nxnode.bin
nx       12225 12168  0 21:11 ?        00:00:00 /usr/NX/bin/nxd
odroid   12263 12199  1 21:11 ?        00:00:13 /usr/NX/bin/nxclient.bin --monitor --pid 1153
nx       15916 12225 24 21:28 ?        00:00:08 /usr/NX/bin/nxserver.bin -c /etc/NX/nxserver --login -H 5
odroid   15944 15916 33 21:29 ?        00:00:04 /usr/NX/bin/nxnode.bin -H 5
odroid   16130  8527  0 21:29 pts/1    00:00:00 grep --color=auto nx

odroid@odroid:~/Downloads$ ls /usr/NX/bin
drivers       nxd         nxkb        nxplayer      nxsh         nxusbd
nxagent       nxesd       nxkeygen    nxplayer.bin  nxspool
nxauth        nxexec      nxlocate    nxpost        nxssh
nxclient      nxfs        nxlpd       nxprint       nxssh-add
nxclient.bin  nxfsm       nxnode      nxserver      nxssh-agent
nxcodec.bin   nxfsserver  nxnode.bin  nxserver.bin  nxtunctl

If for some reason some nx programs disappeared, restart the service by 

sudo /usr/NX/bin/nxserver --restart

It is interesting that nomachine is faster than 'ssh -X' method when I tested running a Qt application launched from Qt Creator. For example, the progress bar is not moving when it is supposed to move forward and backward when the app is launched through 'ssh -X'.

NoMachine and Amazon cloud

https://www.nomachine.com/accessing-your-remote-linux-desktop-on-amazon-elastic-compute-cloud-via-NoMachine

It seems nomachine is using port 4000. 

odroid@odroid:~$ sudo nmap -sV localhost

Starting Nmap 7.01 ( https://nmap.org ) at 2016-11-16 20:10 EST
Nmap scan report for localhost (127.0.0.1)
Host is up (0.000051s latency).
Other addresses for localhost (not scanned): ::1
rDNS record for 127.0.0.1: odroid
Not shown: 997 closed ports
PORT     STATE SERVICE         VERSION
22/tcp   open  ssh             OpenSSH 7.2p2 Ubuntu 4ubuntu2.1 (Ubuntu Linux; protocol 2.0)
4000/tcp open  remoteanything?
7001/tcp open  X11             (access denied)
Service Info: OSs: Linux, Unix; CPE: cpe:/o:linux:linux_kernel

odroid@odroid:~$ sudo lsof -i :4000
COMMAND PID USER   FD   TYPE DEVICE SIZE/OFF NODE NAME
nxd     735   nx    3u  IPv4  19208      0t0  TCP *:4000 (LISTEN)
nxd     735   nx    4u  IPv6  21234      0t0  TCP *:4000 (LISTEN)

X2Go

used in Linux Data Science Virtual Machine by Microsoft.

Remote desktop connection through vmware workstation

We shall be able to remote desktop connect to a Windows guest machine if the guest machine has configured to use bridge connection and a static IP. If there is a problem, it is likely caused by Window's firewall. See the two screenshots. We can just turn off the firewall of home network but keep the firewall on for the public network.

We don't need to use port forward for the remote desktop connection.

ViewActiveNetwork.png Firewall.png

Install sshd

apt-get update
apt-get install openssh-server

sftp, vsftpd and virtual users

ProFTPd

How to install ProFTPd with TLS support on Ubuntu 16.04

Install LAMP

See the page [1] 

apt-get install apache2
a2enmod rewrite
apt-get install mysql-server   [I choose branch name as MYSQL root password]
apt-get install php5 php-pear php5-suhosin
apt-get install php5-mysql
/etc/init.d/apache2 restart

Another instruction including how to set up user directories for Apache web server http://wiki.debian.org/LaMp 

apt-get install mysql-server mysql-client
mysql_secure_installation
apt-get install apache2 apache2-doc
apt-get install php5 php5-mysql libapache2-mod-php5
apt-get install python libapache2-mod-python

The apache configuration file is in /etc/apache2/apache2.conf.

For PHP, it is also useful to install php for command line. 

sudo aptitude install php5-cli

Restarting apache before testing on web browser 

/etc/init.d/apache2 restart

Debian 8

https://www.digitalocean.com/community/tutorials/how-to-install-linux-apache-mysql-php-lamp-stack-on-debian-8 

sudo aptitude install apache2 apache2-doc
sudo aptitude install mysql-server php5-mysql
# optional
sudo mysql_secure_installation
sudo aptitude install php5-common libapache2-mod-php5 php5-cli
sudo service apache2 restart

AMPPS for a local server

http://www.howtogeek.com/219983/how-to-use-ampps-to-install-joomla-locally/

XAMPP is a free, open source cross platform web server solution stack package for Windows, Mac, and Linux. AMPPS is a software stack from Softaculous enabling Apache, MySQL, MongoDB, PHP, Perl, Python, and Softaculous auto-installer on a desktop.

Sandstorm: self-hostable web productivity suite

Content management systems

PageKit

How to Install PageKit CMS on Ubuntu 18.04 LTS

ProcessWire

How to Install ProcessWire CMS on CentOS 7

BookStack

How to Install BookStack on Ubuntu 16.04 LTS

A docker image is also available.

Mediawiki

aptitude install mediawiki php5 apache2 mediawiki-extensions libapache2-mod-php5

This will install latex. After the end, we can use Synaptic package manager to see what were installed. Now following the instruction in https://help.ubuntu.com/community/MediaWiki, we remove the '#' from the third line so that it reads 'Alias /mediawiki /var/lib/mediawiki': 

sudo nano /etc/mediawiki/apache.conf
sudo /etc/init.d/apache2 restart

Now we can start mediawiki by opening a browser and pointing it to http://localhost/mediawiki.

We need to enter 

Site config
  admin username: WikiSysop
  password:

Database config
  Database name: wikidb
  DB username: 
  DB password: 
  Superuser name: root
  Superuser password: [depend on how it was chosen when installing MYSQL]

Press the button of "Installing mediawiki". We will be welcomed to the wiki page. Following the instruction,

For security reason, I remove new account creation and anonymous editing. I also remove edit counters.

Backup and Restore mediawiki: The process involves 3 parts: mediawiki system, mysql and images. See docs.google.com note.

Install moinmoin

UpnP server

Jellyfin

Jellyfin: Free Software Emby Media Server Fork Is Announced After Emby Becomes Proprietary

PS3 Media Servver

https://github.com/ps3mediaserver/ps3mediaserver

minidlna

http://bbrks.me/rpi-minidlna-media-server/

It works even I use my phone to tether data (I don't need to turn on wifi on my phone). 

sudo apt-get update
sudo apt-get install minidlna
sudo nano /etc/minidlna.conf # the default location of media files is on /var/lib/minidlna

# rebuild the database. See the comments in <etc/minidlna.conf>
sudo service minidlna force-reload 
sudo service minidlna start
sudo update-rc.d minidlna defaults # ask minidlna to start up automatically upon boot.

Too bad is when I played certain videos the program crashed. The /var/log/syslog showed kernel: [96495.690373] minidlna[1627]: segfault at 0 ip 00007f4af2de9964 sp 00007fffa43014f8 error 4 in libc-2.15.so[7f4af2d54000+1b4000]. Also the minidlna process becomes 2 instead of 1 after the crash.

Kodi

Too bad the Kodi's upnp function is not stable. Kodi server disappeared so the client cannot find it.

Installing Kodi using Ubuntu based systems

Decrypt and Rip DVDs With Handbrake

PLEX

This seems to be the best from my test.

Subsonic media server

Airsonic media server

How to Install Airsonic Media Server on Ubuntu 18.04 LTS. OpenJDK, Nginx,

Icecast 2 music server

Sonerezh music server

How to install Sonerezh Music Streaming Server on Ubuntu 18.04 LTS

DockSTARTer

How to Set Up a Linux Media Server in Under One Hour

Storage server GlusterFS

https://www.howtoforge.com/tutorial/high-availability-storage-with-glusterfs-on-debian-8-with-two-nodes/

Security

Automatic security update

https connection

HTTPOXY

https://www.howtoforge.com/tutorial/httpoxy-protect-your-server/

Fail2Ban, Tinyhoneypot and IPv4 security

MYSQL security

Just execute mysql_secure_installation from the command line.

  • You can set a password for root accounts.
  • You can remove root accounts that are accessible from outside the local host.
  • You can remove anonymous-user accounts.
  • You can remove the test database, which by default can be accessed by anonymous users.

See http://www.mysql-optimization.com/mysql-secure-installation-program.html

Meltdown and Spectre

sudo apt-get update
sudo apt-get dist-upgrade

uname -a
# 4.4.0-109

HTTPS connection issue

An https connection problem with certificate. Error message comes from Google-chrome and Safari browsers.

Your connection is not private:

HttpsNotPrivateChrome.png, HttpsNotPrivateSafari.png

If we use wget or curl on a terminal, we will get an error message 

$ wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.7.0/sratoolkit.2.7.0-ubuntu64.tar.gz
--2017-04-14 09:40:01--  https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.7.0/sratoolkit.2.7.0-ubuntu64.tar.gz
Resolving ftp-trace.ncbi.nlm.nih.gov (ftp-trace.ncbi.nlm.nih.gov)... 130.14.250.7, 2607:f220:41e:250::13
Connecting to ftp-trace.ncbi.nlm.nih.gov (ftp-trace.ncbi.nlm.nih.gov)|130.14.250.7|:443... connected.
ERROR: cannot verify ftp-trace.ncbi.nlm.nih.gov's certificate, issued by ‘CN=DigiCert SHA2 High Assurance Server CA,OU=www.digicert.com,O=DigiCert Inc,C=US’:
  Unable to locally verify the issuer's authority.
To connect to ftp-trace.ncbi.nlm.nih.gov insecurely, use `--no-check-certificate'.

# curl -L https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.7.0/sratoolkit.2.7.0-ubuntu64.tar.gz -o sratoolkit.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
curl: (60) SSL certificate problem: Invalid certificate chain
More details here: https://curl.haxx.se/docs/sslcerts.html

curl performs SSL certificate verification by default, using a "bundle"
 of Certificate Authority (CA) public keys (CA certs). If the default
 bundle file isn't adequate, you can specify an alternate file
 using the --cacert option.
If this HTTPS server uses a certificate signed by a CA represented in
 the bundle, the certificate verification probably failed due to a
 problem with the certificate (it might be expired, or the name might
 not match the domain name in the URL).
If you'd like to turn off curl's verification of the certificate, use
 the -k (or --insecure) option.

It is interesting after a few tries, curl works again and wget works after adding the option --no-check-certificate 

$ wget --no-check-certificate https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.7.0/sratoolkit.2.7.0-ubuntu64.tar.gz
--2017-04-14 09:51:32--  https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.7.0/sratoolkit.2.7.0-ubuntu64.tar.gz
Resolving ftp-trace.ncbi.nlm.nih.gov (ftp-trace.ncbi.nlm.nih.gov)... 130.14.250.11, 2607:f220:41e:250::13
Connecting to ftp-trace.ncbi.nlm.nih.gov (ftp-trace.ncbi.nlm.nih.gov)|130.14.250.11|:443... connected.
WARNING: cannot verify ftp-trace.ncbi.nlm.nih.gov's certificate, issued by ‘CN=DigiCert SHA2 High Assurance Server CA,OU=www.digicert.com,O=DigiCert Inc,C=US’:
  Unable to locally verify the issuer's authority.
HTTP request sent, awaiting response... 200 OK
Length: 63707890 (61M) [application/x-gzip]
Saving to: ‘sratoolkit.2.7.0-ubuntu64.tar.gz’

sratoolkit.2.7.0-ubuntu64.tar. 100%[==================================================>]  60.76M  6.50MB/s    in 9.2s    

2017-04-14 09:51:42 (6.59 MB/s) - ‘sratoolkit.2.7.0-ubuntu64.tar.gz’ saved [63707890/63707890]

$ curl -L -O https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.7.0/sratoolkit.2.7.0-ubuntu64.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 60.7M  100 60.7M    0     0  6312k      0  0:00:09  0:00:09 --:--:-- 6820k

HTTPS at NCBI: Guidance for Users

https://www.ncbi.nlm.nih.gov/home/develop/https-guidance/

Compiling R

Use the following command to download required components before building any R packages. See also ubuntu package for R 

sudo apt-get build-dep r-base

AppImage file - new way of installing an application

What is an “AppImage”? How do I install it?

  • AppImages can be downloaded and run without installation or the need for root rights.
  • The key idea of the AppImage format is one app = one file. Every AppImage contains an app and all the files the app needs to run. In other words, each AppImage has no dependencies other than what is included in the targeted base operating system(s).

Some examples

Create .deb file

checkinstall command

dpkg-buildpackage command

Package maintenance

See Ubuntu package.

Software automation

Ansible

Ansible is a free and open source software that can be used to automate software provisioning, configuration management, and application deployment.

Terminal Assistant

Torrent

Top 6 Torrent Alternatives to The Pirate Bay (7/5/2017)

(old) Popular search sites

  • torrentz
  • thepiratebay
  • isohunt
  • kickass torrents

How to set up torrent scheduling on Linux

https://www.howtoforge.com/tutorial/how-to-set-up-torrent-scheduling-on-linux/. It covers 'Deluge', 'Transmission' and 'Rtorrent'.

This can be useful for people who want to take advantage of their computer while they are not using it, like during the nighttime for example. This way, large portions of huge files can be downloaded without delaying your work activities, or interrupting/undermining your media consumption.

Torrent client command line: aria2c

aria2 is a lightweight multi-protocol & multi-source command-line download utility. It supports HTTP/HTTPS, FTP, BitTorrent and Metalink. aria2 can be manipulated via built-in JSON-RPC and XML-RPC interfaces.

http://linuxconfig.org/aria2-all-in-one-command-line-download-tool 

sudo apt-get install aria2
aria2c magnet:?xt=urn:btih:1e99d95f1764644a86a8e99bfd80c ...

Torrent client: transmission-cli

https://wiki.archlinux.org/index.php/Transmission

Torrent client command line: rtorrent

We first need to create an .rtorrent.rc file under $HOME directory. Then run 

rtorrent XXX.torrent

In the simplest case, .rtorrent.rc looks like 

# On the terminal, mkdir ~/Downloads/rsession
download_rate = 0
upload_rate =50
directory = ~/Downloads
session = ~/Downloads/rsession
port_range = 55556-55560
scgi_port = 127.0.0.1:5000
use_udp_trackers = yes
encryption = allow_incoming,try_outgoing,enable_retry

As you can see here, I have created a sub-directory rsession under ~/Downloads/.

Keybinding:

  • ctrl + q = quit application
  • ctrl + d = stop an active download
  • ctrl + s = start downloading

glibc

Patch glibc 2.9

sudo apt-get update
sudo apt-get upgrade
sudo reboot

SSL

Install commercial SSL certificate

check openssl version

http://askubuntu.com/questions/504928/how-to-check-which-openssl-version-is-use-by-apache-on-ubuntu-12-04 

odroid@odroid:~$ apt-cache policy openssl
openssl:
  Installed: 1.0.2g-1ubuntu4.5
  Candidate: 1.0.2g-1ubuntu4.5
  Version table:
 *** 1.0.2g-1ubuntu4.5 500
        500 http://ports.ubuntu.com/ubuntu-ports xenial-updates/main armhf Packages
        500 http://ports.ubuntu.com/ubuntu-ports xenial-security/main armhf Packages
        100 /var/lib/dpkg/status
     1.0.2g-1ubuntu4 500
        500 http://ports.ubuntu.com/ubuntu-ports xenial/main armhf Packages

# Ubuntu 14.04
$ openssl version 
OpenSSL 1.0.1f 6 Jan 2014
# Macbook Pro 10.11
$ openssl version 
OpenSSL 0.9.8zh 14 Jan 2016

check openssl location

A more general way is to use openssl version -d 

# On Ubuntu 14.04
$ openssl version -d
OPENSSLDIR: "/usr/lib/ssl"
$ ls /usr/lib/ssl
certs  misc  openssl.cnf  private
$ ls -l /usr/lib/ssl
total 4
lrwxrwxrwx 1 root root   14 Oct  7 11:03 certs -> /etc/ssl/certs
drwxr-xr-x 2 root root 4096 Feb 11 09:12 misc
lrwxrwxrwx 1 root root   20 Jan 30 15:42 openssl.cnf -> /etc/ssl/openssl.cnf
lrwxrwxrwx 1 root root   16 Oct  7 11:03 private -> /etc/ssl/private
$ ls -l /etc/ssl/certs | head
total 912
lrwxrwxrwx 1 root root     26 Oct  7 11:03 00673b5b.0 -> thawte_Primary_Root_CA.pem
lrwxrwxrwx 1 root root     45 Oct  7 11:03 02265526.0 -> Entrust_Root_Certification_Authority_-_G2.pem
lrwxrwxrwx 1 root root     29 Oct  7 11:03 024dc131.0 -> Microsec_e-Szigno_Root_CA.pem
lrwxrwxrwx 1 root root     31 Oct  7 11:03 02b73561.0 -> Comodo_Secure_Services_root.pem
lrwxrwxrwx 1 root root     36 Oct  7 11:03 03179a64.0 -> Staat_der_Nederlanden_EV_Root_CA.pem
lrwxrwxrwx 1 root root     25 Oct  7 11:03 034868d6.0 -> Swisscom_Root_EV_CA_2.pem
lrwxrwxrwx 1 root root     16 Oct  7 11:03 03f2b8cf.0 -> WoSign_China.pem
lrwxrwxrwx 1 root root     41 Oct  7 11:03 04f60c28.0 -> USERTrust_ECC_Certification_Authority.pem
lrwxrwxrwx 1 root root     40 Oct  7 11:03 052e396b.0 -> AddTrust_Qualified_Certificates_Root.pem
$ ls -l /etc/ssl/certs | wc -l
533

# On Macbook Pro 10.11
$ openssl version -d
OPENSSLDIR: "/System/Library/OpenSSL"
$ ls -l /System/Library/OpenSSL
total 8
drwxr-xr-x  2 root  wheel    68 May 15  2016 certs
drwxr-xr-x  8 root  wheel   272 May 15  2016 misc
-rw-r--r--  1 root  wheel  9390 May 15  2016 openssl.cnf
drwxr-xr-x  2 root  wheel    68 May 15  2016 private
$ ls -l /System/Library/OpenSSL/certs/
$ # empty results

openssl & patch bug

brb@vm-1404:~$ sudo dpkg -l | grep  openssl
ii  libgnutls-openssl27:amd64   2.12.23-12ubuntu2.2   amd64        GNU TLS library - OpenSSL wrapper
ii  openssl                     1.0.1f-1ubuntu2.15    amd64        Secure Sockets Layer toolkit - cryptographic utility
ii  python-openssl              0.13-2ubuntu6         amd64        Python 2 wrapper around the OpenSSL library

brb@vm-1404:~$ lsb_release -a
No LSB modules are available.
Distributor ID:	Ubuntu
Description:	Ubuntu 14.04.1 LTS
Release:	14.04
Codename:	trusty

brb@vm-1404:~$ openssl version -a
OpenSSL 1.0.1f 6 Jan 2014
built on: Fri Jun 20 18:54:02 UTC 2014
platform: debian-amd64
options:  bn(64,64) rc4(16x,int) des(idx,cisc,16,int) blowfish(idx) 
compiler: cc -fPIC -DOPENSSL_PIC -DOPENSSL_THREADS -D_REENTRANT -DDSO_DLFCN -DHAVE_DLFCN_H -m64 
OPENSSLDIR: "/usr/lib/ssl"

brb@vm-1404:~$ sudo apt-get changelog openssl | grep CVE-2014-0224
    - debian/patches/CVE-2014-0224-regression2.patch: accept CCS after
    - debian/patches/CVE-2014-0224.patch: set the CCS_OK flag when using
    - debian/patches/CVE-2014-0224-1.patch: only accept change cipher spec
    - debian/patches/CVE-2014-0224-2.patch: don't accept zero length master
    - debian/patches/CVE-2014-0224-3.patch: allow CCS after resumption in
    - CVE-2014-0224

Let's Encrypt SSL

It takes less than 5 minutes for the whole process! 

sudo apt-get update
sudo apt-get install software-properties-common
sudo add-apt-repository ppa:certbot/certbot
sudo apt-get update
sudo apt-get install python-certbot-apache
sudo certbot --apache

Let’s Encrypt certificates are valid for 90 days, but it’s recommended that you renew the certificates every 60 days to allow a margin of error. The Let's Encrypt client has a renew command that automatically checks the currently installed certificates and tries to renew them if they are less than 30 days away from the expiration date.

So we can add the following line to the cron job that will execute the letsencrypt-auto renew command every Monday at 2:30 am. sudo crontab -e 

30 2 * * 1 certbot renew >> /var/log/le-renew.log

Note if you currently have already had a working SSL certificate (eg from a purchased one), then even you have removed the certificate from the relevant Apache files you still can't run through sudo certbot. But once your current working SSL certificate expires, sudo certbot will successfully go through even you don't manually remove the certificate from your system.

pem file

Install webmin

apt-get install perl libnet-ssleay-perl openssl libauthen-pam-perl libpam-runtime libio-pty-perl apt-show-versions python
wget http://prdownloads.sourceforge.net/webadmin/webmin_1.600_all.deb
dpkg --install webmin_1.600_all.deb

Webmin.png

File does not exist: /var/www/favicon.ico from /var/log/apache2/error.log

The reason? You have not created a favicon, also known as a website icon, for your website. It’s the icon that displays in the address bar of your web browser when you connect to a website. A web browser will request this icon file from every website.

If you choose to create one. Use a program such as Gimp and create a 16×16 pixel image and save it as a .ico filetype. Then upload that file to the DocumentRoot of your website. You will need one for each VirtualHost. If you don’t have Gimp, there are online resources such as favicon.cc where you can create a .ico file and download it for your own use.

As you know by now, not having a favicon.ico file, won’t stop web browsers from requesting it each time. But you can tell Apache not to log the event as an error message. You will still see the request in the access.log, but at least you will have a cleaner error.log file.

Add the following block of code to each VirtualHost, or at least the ones which don’t have a favicon file. 

Redirect 404 /favicon.ico
<Location /favicon.ico>
 ErrorDocument 404 "No favicon"
</Location>

Don’t forget to restart apache after making the change. If you want make a “global” change, which would apply to any and all VirtualHosts, you can create a file in Apache’s conf.d folder with a name such as nofavicon.conf and then add that block of code to the file. That would disable favicon across the board and save you from having to edit each VirtualHost.

Or, you create an empty file with the name “favicon.ico” in the directory root of Apache (for exemple /var/www/).

Show weather on the taskbar

http://www.noobslab.com/2012/10/important-thingstweaks-to-do-after.html

WebCam

https://help.ubuntu.com/community/Webcam

Install cheese or guvcview. An example of using computer vision on Raspberry Pi.

Watch TV

Freetuxtv

Running concrete5 On Nginx (LEMP)

http://www.howtoforge.com/running-concrete5-on-nginx-lemp-on-debian-squeeze-ubuntu-12.10

Open mms stream in google chrom in linux

http://www.thermetics.net/2011/12/07/how-to-open-mms-links-from-chrome-under-ubuntu/

Download mms stream (suitable if mms is an extension; for example, studioclassroom)

  • Use mimms (will NOT output to speaker at the same time; so is best in terms of performance)
sudo apt-get install mimms
mimms -t 60 mms://example.com/video

where -t option specifies number of minutes. See http://linuxers.org/howto/how-download-mms-streaming-videos-ubuntu The output will have the same extension as the input. But it is not always clear. For example 

$ mimms -t 3 mms://bcr.media.hinet.net/RA000073                                                                                                    
mms://bcr.media.hinet.net/RA000073 => RA000073.wmv
1.48 MB / ∞ B (8.79 kB/s, ∞ s remaining)           
Download stopped after user-specified timeout.


  • Use mplayer (will output to speaker at the same time, so suffer from performance, anyway do not get output)
mplayer mms:/link/something.xxx -dumpstream -dumpfile file.xxx

mms:/link/something.xxx - link to the stream you wish to download file.xxx - file to which you wish to download the stream, be careful to write the same extension xxx

Wait for the file to download and that's it. See http://ubuntuhowtos.com/howtos/download_mms_stream

Streaming

Stream Videos, Music And Pictures From Gnome To Chromecast With Cast To TV Extension (v6 And v7 Released)

Keep a linux process running after log out

# nohup command-with-options &

If we use ssh -X to connect to a remote computer, the command can launch a GUI application on my local computer (without strange messages shown on the terminal).

Open Firefox in cron job

The trick is to use export DISPLAY=:0 

export DISPLAY=:0
firefox http://www.google.com &

Close firefox gracefully

Use wmctrl command. 

sudo apt-get install wmctrl
wmctrl -c firefox

Audio

Change default audio player

Right-click an MP3 file, and from the menu select “Properties”. In the window that appears, go to the “Open With” tab and select VLC or whatever. Click the “Set As Default” button to set VLC as the default player.

You might also want to set the default player in the sound menu.

Audio editing

The Best Free Audio Editing Software

Audio recorder

Top 5 Audio Recorders for Ubuntu Recommendation 

sudo add-apt-repository ppa:audio-recorder/ppa
sudo apt update; sudo apt install audio-recorder

Record audio out from your browser using the command line

http://www.pantz.org/software/alsa/recording_sound_from_your_web_browser_using_linux.html

Step 1: Install required programs 

sudo apt-get install gnome-media pavucontrol lame

Step 2: Create a script file <recordfm.sh> 

#!/bin/bash
# Get pulseaudio monitor sink monitor device then pipe it to 
# sox to record wav, lame to encode to mp3, or flac to encode flac
FILENAME="$1"
STOPTIME="$2"
# Encoding options for lame and flac.
LAMEOPTIONS="--preset cbr 192 -s 44.1" 

if [ -z "$FILENAME" ]; then
    echo -e "
    Usage: $0 /path/to/output.mp3
    Usage: $0 /path/to/output.mp3 stopinseconds" >&2
    exit 1
fi

# Get sink monitor:
MONITOR=$(pactl list | egrep -A2 '^(\*\*\* )?Source #' | \
    grep 'Name: .*\.monitor$' | awk '{print $NF}' | tail -n1)
echo "set-source-mute ${MONITOR} false" | pacmd >/dev/null

# Record it raw, and pipe to lame for an mp3
echo "Recording to $FILENAME ..."

if [[ $FILENAME =~ .mp3$ ]]; then
  if [ -z $STOPTIME ]; then
    parec -d $MONITOR | lame $LAMEOPTIONS -r - $FILENAME 
  else
    echo -e "\nStopping in $STOPTIME seconds"
    parec -d $MONITOR | lame $LAMEOPTIONS -r - $FILENAME 2>&1 &
    SPID=$!
    sleep $STOPTIME
    kill -9 $SPID
  fi
fi

Step 3: play the music or launch a browser with a desired url.

Step 4: run the bash script 

chmod +x recordfm.sh
./recordfm.sh test.mp3 10

where <test.mp3> is the output filename and 10 is recording length (seconds). It works.

Note the script teaches us how to find out the ID for a process we just launched (cleaner than using ps -ef | grep commands). The command is 

SPID=$!
echo $SPID

Advanced audio control

https://www.howtoforge.com/tutorial/advanced-audio-control-on-linux/

  • Alsamixer
  • Pulse Audio Volume Control
  • Pulse Audio Equalizer

Podcast

Get started with gPodder, an open source podcast client

SMPlayer

MPV - terminal media player

sudo apt install mpv
mpv <URL_of_Video>

Listen to the radio at the Linux terminal

Listen to the radio at the Linux terminal

SMTube: search and watch youtube

  • https://www.smplayer.info/
  • http://www.smtube.org/. SMTube is an application that allows to browse, search and play YouTube videos. Videos are played back with a media player (by default SMPlayer) instead of a flash player, this allows better performance, particularly with HD content. No youtube ads.
sudo add-apt-repository ppa:rvm/smplayer
sudo apt-get update
sudo apt-get install smplayer smtube

Youtube command line tools

Play audio only

# play in background (prompt will return, a new vlc process will be launched)
cvlc --vout none https://www.youtube.com/watch?v=1O0W7jSd940
# or play in foreground (prompt will not return)
/usr/bin/vlc -I dummy --vout none https://www.youtube.com/watch?v=1O0W7jSd940

Using this approach to play audio only will save CPU power. Tested on Odroid.

However, it seems this approach does not work on a playlist, for example, https://www.youtube.com/playlist?list=PL6h94tLpXv3LabUa7B0tCz7K0pI5ZzZEi. See mpsyt for a solution!

Youtube-dl

https://rg3.github.io/youtube-dl/download.html 

# which youtube-dl
# sudo rm /usr/bin/youtube-dl

# Method 1.
sudo curl -L https://yt-dl.org/downloads/latest/youtube-dl -o /usr/local/bin/youtube-dl
sudo chmod a+rx /usr/local/bin/youtube-dl

# Method 2.
sudo pip install --upgrade youtube_dl

# Log out and log in
youtube-dl --version
# 2019.01.02

# Download a youtube playlist
youtube-dl -f mp4 --yes-playlist URL
  • For videos with 1080p resolution, youtube-dl will download 720p by default. To download 1080p, see this post
# show the available resolutions
youtube-dl -F XXX
# download the desired resolution
youtube-dl -f 137+141 XXXX 
# Note the two numbers 137, 141 is case dependent. They could be 137 & 140.
youtube-dl -f 22 XXX
# if the format 22 is mp4. If I do not specify the format, the mkv file will be downloaded
# But playing mkv file tends to be stuttering with VLC.

This assumes Ubuntu has installed avconv; otherwise video(mp4) and audio(m4a) files will be downloaded separately. To install avconv, install the libav-tools package. Note that libav-tools was replaced by ffmpeg in Ubuntu 18.04. 

sudo apt-get install ffmpeg
  • To download mp3 from a Youtube Video (assume libav-tools or ffmpeg has been installed). See more info here.
youtube-dl --extract-audio --audio-format mp3 URL
  • To convert the video to mp3 format, use soundconverter
sudo apt-get install soundconverter
mps-youtube

mpsyt: mps-youtube (mp3 + stream + youtube)

By default, mps-youtube is basically a YouTube audio player (and downloader), but you can enable external video playback (via mpv or MPlayer) from its options. Check out

  • An article on webupd8.
  • More keyboard controls can be found on the webpage of mps.

Installation on Linux (works on Odroid with low CPU usage for audio stream from youtube but Odroid gives dirty noise when I played the music). 

sudo apt-get install python3-pip
sudo pip3 install mps-youtube
sudo pip3 install youtube_dl

# On Ubuntu/Mint. Do not use mplayer. Use mpv instead.
# sudo add-apt-repository ppa:mc3man/mpv-tests
# sudo apt-get update && sudo apt-get install mpv

mpsyt   # launch
set player mpv
pl https://www.youtube.com/playlist?list=PL6h94tLpXv3LabUa7B0tCz7K0pI5ZzZEi   # a playlist
h       # help
Space   # pause
p       # play
q       # quit mpsyt

h search
url https://www.youtube.com/watch?v=hgIfZz8STLk   # retrieve specific youtube video by url or id

Installation on Windows

Some highlight

  • Search
  • Local playlist
  • support YouTube Playlists
  • Download
  • Music Album Matching

If something is wrong with using 'set' command, just run rm -rf ~/.config/mps-youtube/ and restart everything.

By default, it only streams audio. To watch the video, use set show_video true.

Below is what I got from the set command (as you can see the default player is mpv) 

  Key                 Value                                                  
  order             : relevance
  user_order        : 
  max_res           : 2160p
  player            : mpv
  playerargs        : 
  encoder           : 0 [None]
  notifier          : 
  checkupdate       : True
  show_mplayer_keys : True
  fullscreen        : False
  show_status       : True
  columns           : 
  ddir              : /home/odroid/Downloads/mps
  overwrite         : True
  show_video        : False
  search_music      : True
  window_pos        : 
  window_size       : 
  download_command  : 
  audio_format      : auto
  api_key           : AIzaSyCIM4EzNqi1in22f4Z3Ru3iYvLaY8tc3bo

The screenshot shows mpsyt contains basic playing keyboard shortcuts.

Mps-youtube.png

[Update 4-7-2017]: to fix an error Signature extraction failed: Traceback (most recent call last): 

sudo apt-get remove -y youtube-dl  # Removing youtube-dl (2014.02.17-1) ...
sudo pip3 install -U youtube-dl

$ youtube-dl --version
2017.04.11

Open Websites In A Floating, Borderless Window/Picture in picture

Open Websites In A Floating, Borderless Window With Pennywise

Bypass SSH password login (convenient for CVS, git etc)

http://www.howtogeek.com/tips/bypass-ssh-logins-by-adding-your-key-to-a-remote-server-in-a-single-command/

  1. ssh-keygen -t rsa
  2. (make sure the remote server has .ssh directory)
  3. cat ~/.ssh/id_rsa.pub | ssh user@hostname 'cat >> .ssh/authorized_keys'
  4. ssh user@hostname

It helps with CVS log in too when the CVS works by using ssh protocol. Note that step 3 allows to run a shell command at a remote machine.

See https://help.github.com/articles/generating-ssh-keys also for similar instruction when work on github.

The ssh key can be copied to another a machine (pay attention to mode). Or let the new machine to create its own key pair and use ssh-copy-id to append the identity file to remote machine's ~/.ssh/authorized_keys file. See http://superuser.com/questions/332510/how-to-transfer-my-linux-ssh-keys-to-another-machine.

We can even have multiple ssh key on local machine by using <.ssh/config> file. See http://www.karan.org/blog/index.php/2009/08/25/multiple-ssh-private-keys.

Install Ubuntu to a USB flash drive

The following approach assumes the boot loader will not be put on internal hard disk if you are careful enough. See also http://fernhilllinuxproject.com/guidesandhowtos/installubuntutousbdrive.html

  1. Boot from live CD in ubuntu.
  2. Insert the USB flash drive in USB Port.
  3. On desktop double click on icon 'install ubuntu 12.04'
  4. Click on continue and it will ask if you want to unmount the flash drive click on yes
  5. Choose some thing else when ask to where to install ubuntu.
  6. Next you will see your hard disk partitions and flash drive. Click on flash drive partition and then click on change. Change the partition type to ext4 and mount as to '/'. Click on ok to close the dialogue box.
  7. In last you will see a drop down menu on where to install the the boot loader. Initially it will be showing sdc,sdd but on drop down you must select sdc1 or sdd1. Failing this step you may render your computer unbootable.
  8. Then click on install and linux will be installed on your USB Flash drive.

Install a new hard drive

See also https://help.ubuntu.com/community/InstallingANewHardDrive and Mount drive

  1. Use sudo fdisk command to create partition table. Then 'n', 'p', '1', 'w' and several returns.
  2. Use sudo mkfs -t ext4 /dev/sdb1 to create a new partition
  3. Use sudo mkdir /mnt/ssd to create a new mount point
  4. Use sudo nano -Bw /etc/fstab to do auto mount on boot
  5. sudo chown -R USERNAME:USERNAME /mnt/ssd to give the ownership to the USERNAME.

Add second hard disk (3TB) to Ubuntu 16.04

How to install a Ceph Storage Cluster on Ubuntu

https://www.howtoforge.com/tutorial/how-to-install-a-ceph-cluster-on-ubuntu-16-04/

Building a simple Beowulf Like Cluster with Ubuntu

See also the Raspberry Pi page where a simple cluster was built.

MPICH2

Resource:

  1. http://byobu.info/article/Building_a_simple_Beowulf_cluster_with_Ubuntu/
  2. https://help.ubuntu.com/community/MpichCluster
  3. https://help.ubuntu.com/community/SettingUpNFSHowTo (NFS configure)

Here is my record for creating a cluster environment based on ubuntu 13.04. The master node is running on ubuntu 13.04 desktop with virtualBox 4.2. The virtualBox has added a host-only adapter (vboxnet0) with ip 192.168.56.1. This adapter will be added to the master node so I can use this ip to identify the master node in the host-only network. Creating cluster using VirtualBox is just for the education purpose, not for real practice.

  • (virtualBox) Create two virtual machines running on ubuntu 13.04 server. The ssh server was checked during installation. The host name for each of them is ubuntuNode1 and ubuntuNode2 respectively. The network adapter is left by default (NAT) during installation. But after the installation is done, I shutdown the system and add a host-only adapter (vboxnet0) to each of them. Then after the system is up again, I change the IP so it is static. Do sudo nano /etc/network/interfaces and append the following before running sudo /etc/init.d/networking restart to take the change in effect.
auto eth1
iface eth1 inet static
address 192.168.56.101 # use 192.168.56.102 for ubuntuNode2
netmask 255.255.255.0
network 192.168.56.0
broadcast 192.168.56.255

Note that it is better not to add host-only network before installation, or during installation it will ask what is the primary network (confusing). So at the end each new nodes should have both eth0 and eth1 adapters and they should not reside in same subset. ifconfig may not show all adapters so we should use ifconfig -a instead. Although host-only network is used for communication between guest and guest OR guest and host, since each guest node has NAT adapter by default so the guest machine can still access the internet.

  • (master node) Edit /etc/hosts so it like like
127.0.0.1 localhost
192.168.56.1 ubuntu1304
192.168.56.101 ubuntuNode1
192.168.56.102 ubuntuNode2

Note that the master node will be used to start jobs on the cluster although it is OK to let the master node as one of nodes to execute the jobs.

  • (all nodes) Run
sudo adduser mpiuser --uid 999

It is recommeneded to use the same password for the user. This will create a new directory /home/mpiuser. This is the home directory for user mpiuser and we will use it to execute jobs on the cluster.

  • (master node) Run
sudo apt-get install nfs-kernel-server
  • (other nodes) Run
sudo apt-get install nfs-client
  • (master node) Add the following to the file /etc/exports
/home/mpiuser *(rw,sync,no_subtree_check)

or something like 

/home/mpiuser 192.168.56.0/24(rw,sync,no_subtree_check)

Some people create a shared folder under /srv directory.

Now run 

sudo service nfs-kernel-server restart
  • (master node)
sudo ufw allow from 192.168.56.0/24
  • (other nodes)
sudo mount ubuntu1304:/home/mpiuser /home/mpiuser

And if we want to mount the NFS shared directory when the compute nodes are booted, edit /etc/fstab by adding 

ubuntu1304:/home/mpiuser /home/mpiuser nfs
  • (master node)
sudo apt-get install ssh
su mpiuser
ssh-keygen
ssh-copy-id localhost

We can test if the ssh works without passwords 

ssh ubuntuNode1
echo $HOSTNAME
  • (all nodes)
sudo apt-get install mpich2
which mpirun
which mpiexec
  • (master node, mpiuser)

Go to the home directory of mpiuser and create a new file hosts. Include host names for computing nodes (it is OK to include master node, ubuntu1304, as one of computing nodes) 

ubuntuNode1
ubuntuNode2
  • (all nodes)
sudo apt-get install build-essential
  • (master node, mpiuser). Creating a test file <mpi_hello.c>
#include <stdio.h>
#include <mpi.h>

int main(int argc, char** argv) {
    int myrank, nprocs;

    MPI_Init(&argc, &argv);
    MPI_Comm_size(MPI_COMM_WORLD, &nprocs);
    MPI_Comm_rank(MPI_COMM_WORLD, &myrank);

    printf("Hello from processor %d of %d\n", myrank, nprocs);

    MPI_Finalize();
    return 0;
}

And compile and run it by 

mpicc mpi_hello.c -o mpi_hello
mpiexec -n 3 -f hosts ./mpi_hello

We should see something like 

Hello from processor 0 of 2
Hello from processor 1 of 2

Successful! That's it.

OpenMPI

With R

File sharing in a local network - woof

Sharing internet

Simple Gui approach from GNOME desktop

When I tested the method with my rtl8187 wifi adapter by Rosewill (output by lsusb) on Odroid Xu4 running Ubuntu 14.04, I got an error on Step 3 (Create New Wi-Fi Network) ??? 

Failed to activate connection
(32) Access Point (AP) mode is not supported by this device

When I tried the wifi adapter RT2870/RT3070 802.11n by MediaLink (MWN-USB150N), there is no problem to create it. My android device can connect to it. However, there is no internet access:( ...... After some tweaks on command line (iptables; see Sharing internet via wifi: iptables below), it works!!!

And the output of nm-tool command also confirms the wifi device is connected. 

odroid@odroid:~/Downloads$ netstat -rn
Kernel IP routing table
Destination     Gateway         Genmask         Flags   MSS Window  irtt Iface
0.0.0.0         192.168.1.1     0.0.0.0         UG        0 0          0 eth2
10.42.0.0       0.0.0.0         255.255.255.0   U         0 0          0 wlan3
192.168.1.0     0.0.0.0         255.255.255.0   U         0 0          0 eth2

The ap hotspot from the wifi adapter has an IP 10.42.0.1 (ifconfig).

Sharing internet via wifi: ap-hotspot

I cannot make it to work to share the internet via wifi on my Xubuntu 13.04. However the solution in http://askubuntu.com/questions/287251/creating-an-infrastructure-hotspot-using-ubuntu-12-10 works for me. 

$ # Under rare situation, we need to run the following line to get 'add-apt-repository'
$ sudo apt-get install apt-get install software-properties-common
$ sudo su -
# add-apt-repository ppa:nilarimogard/webupd8
# aptitude update
# aptitude install ap-hotspot
# ap-hotspot configure
# ap-hotspot start

In the step of 'ap-hotspot configure' it will ask for Access Point name and WPA passphrase.

When I run the final line 'ap-hotspot start', it will ask me to disconnect my current wifi first.

At the end, I found my original configuration in ubuntu does not work even its setting is there. apt-hotspot create an infrastracture AP instead of adhoc.

Sharing internet via wifi: iptables

1. Assume the primary wired network connection, eth0 is connected to Internet.

2. Using your distro's network managment tool, create a new ad hoc wireless connection with the following settings: 

IP address: 10.99.66.55
Subnet mask: 255.255.0.0 (16)

3. Use the following shell script to share the internet connection 

#!/bin/bash
#filename: netsharing.sh
#Replace 10.99.0.0/16 by your network/netmask
#Usage: ./netsharing.sh input_interface output_interface
#Example: ./netsharing.sh eth0 wlan0

echo 1 > /proc/sys/net/ipv4/ip_forward
iptables -A FORWARD -i $1 -o $2 -s 10.99.0.0/16 -m conntrack --ctstate NEW -j ACCEPT
iptables -A FORWARD -m conntrack --ctstate ESTABLISHED,RELATED -j ACCEPT
iptables -A POSTROUTING -t nat -j MASQUERADE

4. Run the script as follows: 

sudo ./netsharing.sh eth0 wlan0

5. Connect your devices to the wireless network you just created with the following settings (Question: how about the SSID here?) 

IP address: 10.99.66.56 (and so on)
Subnet mask: 255.255.0.0

To make this more convenient, you might want to install a DHCP and DNS server on your machine, so it's not necessary to configure IPs on devices manually. A handy tool for this is dnsmasq which you can use for performing both DHCP and DNS operations.

Credit: Linux Shell Scripting Cookbook

A similar approach discussed on the Odroid forum.

iptables

~/.xsession-errors file is filling the hard disk

It is related to vino-server. See

Short solution is to use "kill -9 xxx" to kill the process and rm to remove ~/.xsession-errors file. The long time solution is to uninstall vino.

JRE and JDK

Install openjdk or Sun jdk. See http://www.maketecheasier.com/install-java-runtime-in-ubuntu/ (Ubuntu 12.04)

If we have multiple versions of JRE/JDK, we can use the following command to set the default version 

sudo update-alternatives --config java

This approach seems to be working in the case JAVA_HOME cannot be honored.

OpenJDK

How To Install Oracle Java 12 (JDK 12) In Ubuntu, Linux Mint Or Debian (Using PPA)

On my Ubuntu 12.04, I have two versions. 

$ whereis java
java: /usr/bin/java /usr/bin/X11/java /usr/share/java /usr/share/man/man1/java.1.gz
$ java -version
java version "1.6.0_38"

$ sudo apt-get -y install openjdk-7-jdk
$ ls -l /usr/lib/jvm
total 12
lrwxrwxrwx 1 root root   20 Nov 16  2013 java-1.6.0-openjdk-amd64 -> java-6-openjdk-amd64
lrwxrwxrwx 1 root root   20 Mar 24 06:20 java-1.7.0-openjdk-amd64 -> java-7-openjdk-amd64
drwxr-xr-x 7 root root 4096 Feb 20 08:43 java-6-openjdk-amd64
drwxr-xr-x 3 root root 4096 Jan 31  2014 java-6-openjdk-common
drwxr-xr-x 7 root root 4096 Mar 30 18:16 java-7-openjdk-amd64

$ ls -l /usr/bin/java
lrwxrwxrwx 1 root root 22 Jan 31  2014 /usr/bin/java -> /etc/alternatives/java

Question: how to switch to 1.6 or 1.7 version of java? (For example, snpEff requires java 1.7) 

$ update-java-alternatives -l
java-1.6.0-openjdk-amd64 1061 /usr/lib/jvm/java-1.6.0-openjdk-amd64
java-1.7.0-openjdk-amd64 1051 /usr/lib/jvm/java-1.7.0-openjdk-amd64
$ sudo apt-get install icedtea-7-plugin
$ sudo update-java-alternatives -s java-1.7.0-openjdk-amd64
update-java-alternatives: plugin alternative does not exist: /usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/IcedTeaPlugin.so
$ update-java-alternatives -l
java-1.6.0-openjdk-amd64 1061 /usr/lib/jvm/java-1.6.0-openjdk-amd64
java-1.7.0-openjdk-amd64 1051 /usr/lib/jvm/java-1.7.0-openjdk-amd64
$ java -version
java version "1.7.0_95"

Question: How to install OpenJDK 8 on 14.04 LTS? (for example, Picard 2 requires Java 1.8) 

$ sudo apt-get -y install openjdk-8-jdk   # works for Ubuntu 14.10 and later
# Unable to locate package openjdk-8-jdk on my Ubuntu 14.04

So the solution is to install Sun jdk.

Oracle JAVA

sudo apt-add-repository -y ppa:webupd8team/java
sudo apt-get update
echo debconf shared/accepted-oracle-license-v1-1 select true |  sudo debconf-set-selections
echo debconf shared/accepted-oracle-license-v1-1 seen true |   sudo debconf-set-selections
sudo apt-get install oracle-java8-installer

java -version

Notifications

Send email

It is useful to several occations:

Send emails through gmail: mail

Configuring sendmail with GMail relay on Ubuntu 16.04

Send emails through gmail: sSMTP

CPU/system load

Stacer - Linux System Optimizer and Monitoring

Stacer – The Linux System Optimizer You’ve Been Waiting For. Qt library.

Stacer.png

Grafana

I-Nex

A look at I-Nex – a CPU-Z like Application for GNU/Linux

CPU-G

See this instruction to install CPU-G program for viewing hardware information (process, mb, graphic, memory, system).

CoreFreq

http://www.tecmint.com/corefreq-linux-cpu-monitoring-tool/

System load indicator

System Load Indicator: it is used to view system information (cpu, memory, network) in real-time. 

sudo apt-get install indicator-multiload

sudo apt-get install indicator-cpufreq
indicator-cpufreq

Alert When Memory Gets Low

A Shell Script to Send Email Alert When Memory Gets Low

Monitor CPU Utilization And Send Email

Linux Shell Script To Monitor CPU Utilization And Send Email

Hard drive: hdparm and smartctl

Hard drive specification

http://www.cyberciti.biz/faq/find-hard-disk-hardware-specs-on-linux/ 

# hdparm command
sudo hdparm -I /dev/sda

# OR using lshw command
sudo apt-get install lshw
lshw -class disk -class storage

# Find Out Disks Name Only
lshw -short -C disk

# smartmontools package
sudo smartctl -i /dev/sda

Hard disk speed (3.0 or 6.0 Gb/s) & dd command

http://www.cyberciti.biz/faq/freebsd-command-to-find-sata-link-speed/ 

$ dmesg | grep -i SATA
[    0.311173] pci 0000:00:11.0: set SATA to AHCI mode
[    1.510881] ahci 0000:00:11.0: AHCI 0001.0200 32 slots 4 ports 6 Gbps 0xf impl SATA mode
[    1.512669] ata1: SATA max UDMA/133 abar m1024@0xfe02f000 port 0xfe02f100 irq 19
[    1.512672] ata2: SATA max UDMA/133 abar m1024@0xfe02f000 port 0xfe02f180 irq 19
[    1.512675] ata3: SATA max UDMA/133 abar m1024@0xfe02f000 port 0xfe02f200 irq 19
[    1.512677] ata4: SATA max UDMA/133 abar m1024@0xfe02f000 port 0xfe02f280 irq 19
[    1.832349] ata4: SATA link down (SStatus 0 SControl 300)
[    1.832418] ata2: SATA link down (SStatus 0 SControl 300)
[    2.004290] ata3: SATA link up 6.0 Gbps (SStatus 133 SControl 300)
[    2.004313] ata1: SATA link up 3.0 Gbps (SStatus 123 SControl 300)

To test the disk performance, follow cyberciti.biz. Note that the parameter oflag=dsync makes a difference.

Here I have a 7200rpm Seagate (ST2000DM001-1CH164) and a 5400rpm WD-blue (WD30EZRZ-00WN9B0) 

# Hard disk info https://en.wikipedia.org/wiki/Hdparm
sudo hdparm -I /dev/sda
sudo hdparm -I /dev/sdb

# Writing speed, where /tmp is a directory from the disk 
dd if=/dev/zero of=/tmp/test1.img bs=2G count=1; rm /tmp/test1.img
# 1.4 GB/s from either 5400 or 7200 rpm

dd if=/dev/zero of=/tmp/test1.img bs=2G count=1 oflag=dsync; rm /tmp/test1.img
# 115 MB/s from 5400 rpm
# 166 MB/s from 7200 rpm

# Latency
dd if=/dev/zero of=/tmp/test2.img bs=512 count=1000 oflag=dsync; rm /tmp/test2.img
# 27.7 kB/s from 5400 rpm  <==== This is interesting
# 12.5 kB/s from 7200 rpm

# Read speed
dd if=/dev/zero of=/tmp/test3.img bs=1G count=1 oflag=direct; rm /tmp/test3.img
# 122 MB/s from 5400 rpm
# 180 MB/s from 7200 rpm

Note

  • dd manual
  • oflag=dsync: Use synchronized I/O for data. Do not skip this option. This option get rid of caching and gives you good and accurate results

Hard disk directory size

See Display directory size with sorting and human readable by using the ncdu utility.

Monitor/run a short test on a hard disk health by command line/GUI

Using smartctl 

sudo apt-get install smartcontrol
sudo smartctl -a /dev/sda

# Run a short test
$ sudo smartctl -t short /dev/sda # It will start the test in the background
smartctl 6.2 2013-07-26 r3841 [x86_64-linux-4.4.0-101-generic] (local build)
Copyright (C) 2002-13, Bruce Allen, Christian Franke, www.smartmontools.org

= START OF OFFLINE IMMEDIATE AND SELF-TEST SECTION =
Sending command: "Execute SMART Short self-test routine immediately in off-line mode".
Drive command "Execute SMART Short self-test routine immediately in off-line mode" successful.
Testing has begun.
Please wait 1 minutes for test to complete.
Test will complete after Fri Dec  1 09:58:40 2017

Use smartctl -X to abort test.
$ sudo smartctl -l selftest /dev/sda
smartctl 6.2 2013-07-26 r3841 [x86_64-linux-4.4.0-101-generic] (local build)
Copyright (C) 2002-13, Bruce Allen, Christian Franke, www.smartmontools.org

= START OF READ SMART DATA SECTION =
SMART Self-test log structure revision number 1
Num  Test_Description    Status                  Remaining  LifeTime(hours)  LBA_of_first_error
# 1  Short offline       Self-test routine in progress 60%     11700         -
# 2  Short offline       Completed without error       00%     24992         -

or the GUI version 

sudo apt-get install gsmartcontrol
sudo gsmartcontrol

How to check Hard Drive Disk Health in GNU/Linux

Interpretation:

Email warnings for hd problems by smartd

Debian Linux

  1. Enable smart by editing /etc/default/smartmontools file.
  2. Smart Configuration file: /etc/smartd.conf
  3. Start/Stop smart: /etc/init.d/smartmontools start | stop

Hard disk temperature

http://www.cyberciti.biz/tips/howto-monitor-hard-drive-temperature.html

It seems the hddtemp command does not work on SSDs. 

sudo apt-get install hddtemp
sudo hddtemp /dev/sdb

/dev/sdb: ST2000DM001-9YN164: 40°C

For SSD, 

sudo apt-get install smartmontools
sudo smartctl -a /dev/sda

Hard disk power on time/hours

sudo smartctl --all /dev/sda | grep Power_On_Hours

Sample output: 

$ sudo smartctl -A /dev/sda | grep -i power
  9 Power_On_Hours          0x0032   034   034   000    Old_age   Always       -       58541
 12 Power_Cycle_Count       0x0032   100   100   020    Old_age   Always       -       164
$ sudo smartctl -A /dev/sdb | grep -i power
  9 Power_On_Hours          0x0032   100   100   000    Old_age   Always       -       585
 12 Power_Cycle_Count       0x0032   100   100   000    Old_age   Always       -       43
192 Power-Off_Retract_Count 0x0032   200   200   000    Old_age   Always       -       32

Free up disk space/clean up system space/remove or delete junk files

5 Easy Ways To Free Up Space (Remove Unwanted or Junk Files) on Ubuntu

system's hardware temperatures and voltages

https://www.howtoforge.com/tutorial/ubuntu-performance-monitoring/ 

sudo apt-get install lm-sensors
sensors

brb@brb-P45T-A:~$ sensors
acpitz-virtual-0
Adapter: Virtual device
temp1:        +30.0°C  (crit = +110.0°C)

coretemp-isa-0000
Adapter: ISA adapter
Core 0:       +41.0°C  (high = +78.0°C, crit = +100.0°C)
Core 1:       +36.0°C  (high = +78.0°C, crit = +100.0°C)

nouveau-pci-0100
Adapter: PCI adapter
temp1:        +68.0°C  (high = +95.0°C, hyst =  +3.0°C)
                       (crit = +125.0°C, hyst =  +3.0°C)
                       (emerg = +135.0°C, hyst = +10.0°C)

where nouveau is an open-source driver set for Nvidia cards. It is not clear about acpitz-virtual-0. Some suggested to use inxi which will produce human readable system info.

And on a Dell T3600 machine (running the samtools mpileup & bcftools programs), 

brb@T3600 ~ $ sensors
nouveau-pci-0300
Adapter: PCI adapter
fan1:        3510 RPM
temp1:        +52.0°C  (high = +95.0°C, hyst =  +3.0°C)
                       (crit = +105.0°C, hyst =  +5.0°C)
                       (emerg = +135.0°C, hyst =  +5.0°C)

coretemp-isa-0000
Adapter: ISA adapter
Physical id 0:  +70.0°C  (high = +81.0°C, crit = +91.0°C)
Core 0:         +60.0°C  (high = +81.0°C, crit = +91.0°C)
Core 1:         +60.0°C  (high = +81.0°C, crit = +91.0°C)
Core 2:         +56.0°C  (high = +81.0°C, crit = +91.0°C)
Core 3:         +60.0°C  (high = +81.0°C, crit = +91.0°C)
Core 4:         +70.0°C  (high = +81.0°C, crit = +91.0°C)
Core 5:         +60.0°C  (high = +81.0°C, crit = +91.0°C)

When all cores are 100% used (htop), the fan is getting noisy 

brb@T3600 ~ $ sensors
nouveau-pci-0300
Adapter: PCI adapter
fan1:        4560 RPM
temp1:        +61.0°C  (high = +95.0°C, hyst =  +3.0°C)
                       (crit = +105.0°C, hyst =  +5.0°C)
                       (emerg = +135.0°C, hyst =  +5.0°C)

coretemp-isa-0000
Adapter: ISA adapter
Physical id 0:  +82.0°C  (high = +81.0°C, crit = +91.0°C)
Core 0:         +78.0°C  (high = +81.0°C, crit = +91.0°C)
Core 1:         +81.0°C  (high = +81.0°C, crit = +91.0°C)
Core 2:         +78.0°C  (high = +81.0°C, crit = +91.0°C)
Core 3:         +80.0°C  (high = +81.0°C, crit = +91.0°C)
Core 4:         +81.0°C  (high = +81.0°C, crit = +91.0°C)
Core 5:         +77.0°C  (high = +81.0°C, crit = +91.0°C)

Unlock keyring

I got the prompt of unlocking keyring every time I open google chrome browser. 

google-chrome --password-store=basic

It is also helpful to remove ubuntu one from Ubuntu 12.04. See http://hex.ro/wp/blog/removing-ubuntuone-from-ubuntu-12-04/

netcat (nc) - arbitrary TCP and UDP connections and listens

Netcat or nc is a networking utility for debugging and investigating the network.

The nc (or netcat) utility is used for just about anything under the sun involving TCP, UDP, or UNIX-domain sockets. It can open TCP connections, send UDP packets, listen on arbitrary TCP and UDP ports, do port scanning, and deal with both IPv4 and IPv6.

For example, we can create simple network sockets and use them for text communication. We need two sockets: one listens for connections and the other connects to this one. 

# create a listening socket on the local machine
nc -l 1234

# connect to the socket from a 2nd computer 
nc IP_LocalMachine 1234

# send messages. 
# Type something and press Enter on the terminal from the 2nd computer.
# The message will appear on the terminal of the local machine.

To transfer files over the network (no any password is needed!!) 

# receiver machine
nc -l 1234 > destination_file

# sender machine
nc IP_Receiver 1234 < source_filename

List of all services/daemons

Run service --status-all to get a list off all the Upstart services and their status. See

  • man service
  • man initctl
service --status-all   # output format is clean

sudo initctl list      # show the process number too

where in the output "+" means started, "-" stopped, and "?" unknown.

systemd vs upstart

Cloud/online storage

Mounting

Mega

ownCloud

Use apt to install or go to the download page

One Drive

Google Drive

Caveats:

  • Unlike Windows or macOS, your Google Drive files are not downloaded and stored locally in Ubuntu. You must have an active internet connection to access your account.
  • The online account files are located under "/run/user/1000/gvfs/" directory.
  • PDF files can be opened by Document Viewer. When the file is loaded, it shows a random file name.
  • The doc files cannot be opened by LibreOffice. When I drag and drop the files to Terminal, they show random file names like /run/user/1000/gvfs/google-drive:host=gmail.com,user=XXXXXXX/1LOLKBssIIR0x7TWR7MHIEeSU0uPj9TwK_YuAGTzt'

Back up google photos

Office

Libre Office

Install

WPS Office 2016

https://www.wps.com/en-US/

ONLYOFFICE Desktop Editors

https://www.howtoforge.com/tutorial/how-to-install-onlyoffice-desktop-editors-51-on-ubuntu/

Microsoft Office

How to Install and Use Microsoft Office on Linux

Video rip/convert/transcoder

sudo add-apt-repository ppa:stebbins/handbrake-releases
sudo apt-get update
sudo apt-get install handbrake-gtk

sudo apt-get install handbrake-cli

To merge audio and video 

# naive: use the one with longer duration as the total length
avconv -i music.m4a -i input.mp4 -acodec aac -strict experimental output.mp4
# improved: specify the start time (-ss) and duration (-t)
# unfortunately the music at the specified end time may not be the end
# so a better way is to use a video editor (eg OpenShot) and specify fade out on the end of the audio!
avconv -i music.m4a -i input.mp4 -acodec aac -strict experimental -ss 00:00:00 -t 00:01:01 -codec copy output.mp4

To extract audio only: 

avconv -i INPUT.flv -codec copy -vn OUTPUT.mp4

PC build for video editing

Video Editing 4K PC Build: Creating Content for Under a Grand

Video editing in Linux

DaVinci Resolve

LosslessCut

Shotcut

It is a cross-platform open source software. See The best free video editing software: Great tools for YouTube stardom and more

I tested inserting a text in a video. Compared to Youtube video editor

  • The text is really a text. No pop-up shape to select
  • Not sure how to control the text so it only appears at a certain time interval

Not as intuitive to use.

Pitivi

Blender

Looks very professional too. Windows/Linux/OSX (binary files are provided). Worth to try.

Kdenlive

More complicated than OpenShot. Worth to try. Ubuntu 16.04.1 is needed.

Flowblade

Free Linux Video Editor Flowblade 2.0 Released With Configurable Timeline Editing Workflow, New Tools

Youtube Video Editor

Good

  • Annotation and Title (Video Manager -> Videos -> Edit -> End screens and annotations -> Annotations -> Add annotations (Speech bubble, Note, Title, Spotlight, Label). However, the annotations do not show up on mobile. See this post for a discussion.
  • Add photos

Bad

  • Music cannot have fade in/out

Notes

7 Things You Need to Build a Low-Cost YouTube Studio

http://www.makeuseof.com/tag/build-low-cost-youtube-studio/

Free or Open source Subtitle editor

Comparison of subtitle editors

For TV captions, use white color font with black color for borders and transparent background.

OpenShot-qt

sudo apt-get install openshot

When I needed to export the video (choose 'youtube' profile, 'youtube-HD' target, 'HD 270, 29 .97 bps', and 'high' quality), I found I need to install libx264 code. On Ubuntu, I open software center and seach 'libavformat'. I choose 'libavformat-extra-53'.

An introduction to video editing in Openshot 2.0 from howtoforge.

Don't use the version (1.4.3 date 2009) because it crashed too often.

The new version 2.0.7 (date 2016) looks a little different (theme is black. Cool!). Its icon and command (openshot-qt) are different too. The project saved from 1.4.3 cannot be opened in 2.0.7. The tools icons are different: Add track, Snapping tool, Add Marker, Previous Marker, Next Marker, Zoom in/out.

This version of OpenShot + (old) Core2Duo Ubuntu = Dynamic Heatmap Viewer video.

Audio library

You can download free music from Youtube Audio Library. If you use a copy righted music and upload your video to youtube, the video will show Ad eventually.

Take a snapshot

The keyboard shortcut Ctrl+d does not work.

One suggestion is to use VLC. VLC -> Video -> Take Snapshot. The snapshot will be automatically created in ~/Pictures/ directory (*.png format).

Procedure

  1. Put audio and video files in one folder
  2. Use openshot to create a new video. Also
    • Use the +/- sign for zoom in and zoom out
    • Right click video file and select Volume -> Entire clip -> level 0%
    • Right click audio and select Volume -> End of clip -> fade out (slow)
  3. openshot -> Save (arrow/download-like button)
  4. openshot -> Export (red circle button)
    • Modify the file name so it won't overwrite the original (openshot won't check it)
    • Select Profile = Web, Target=Youtube-HD, Video Profile=HD 1080p 25 fps, Quality=High.
  5. Check the exported video (play it first by VLC).
    • On one instance the audio is fuzzy until the middle of the video. So I have to change the audio
    • On another instance the video length is longer than I expected because the final annotation slide lasts too long. A solution is to change the setting (Profile=All Formats, Target=MP4 (h.264), Video Profile=HD 1080p 24 or 23.98 fps). If I use 25 fps, the file will be wrong.
  6. Upload to Youtube. Use Youtube video editor to include annotation.

VideoLAN Movie Creator

ffdiaporama

Create videos from images, movie clips and music.

Flowblade Movie Editor

It is written in Python. Only Linux version is available (no Windows nor OS X). Good for beginners. 

sudo apt-get install flowblade

Lightworks

Free and Pro versions are available. Windows/Linux/OSX.

Unity

Unity LauncherSwitcher

Ubuntugeek.com

Create Unity Launcher

Take RStudio for example,

  • Desktop icons are saved under /usr/share/icons/hicolor/16x16/apps/rstudio.png, where other than 16x16 there are also icons from 24x24, 32x32, 48x48 sizes (directories). Another place is ~/.local/share/icons/hicolor/16x16/ .
  • Unity launcher is created at /usr/share/applications/rstudio.desktop or ~/.local/share/applications/XXXX.desktop.
  • Desktop shortcut can be created by copy XXXX.desktop to ~/Desktop directory.

The icon size in the launcher can be adjusted by opening System Settings -> Apperance -> Launcher Icon Size (at the bottom).

k2pdfopt has an example how to do it for creating a desktop shortcut and be in the right click menu.

How to Convert the Unity Launcher into a Dock-Style Launcher

See an article from Howtogeek.com.

How to Get Unity’s Global App Menu in Linux Mint Cinnamon

http://www.makeuseof.com/tag/get-unitys-global-app-menu-linux-mint-cinnamon/

Remove floppy icon from Launcher

http://askubuntu.com/questions/457970/how-to-completely-disable-floppy-in-ubuntu-14-04 

echo "blacklist floppy" | sudo tee /etc/modprobe.d/blacklist-floppy.conf
sudo rmmod floppy
sudo update-initramfs -u

Application Launcher

The 9 Best Linux App Launchers to Help You Get Stuff Done Faster

Cerebro

Cerebro is an Open Source OS X Spotlight Equivalent for Linux

Ulauncher

Ulauncher is a Lightweight App Launcher for Linux Desktops

Synapse

Synapse or Albert — What’s Your Favourite App Launcher for Linux?

Gnome Do

Release June 2009

What date/when was the system installed

ls -l /var/log/installer

For other OSs, follow How To Find Exact Installation Date And Time Of Your Linux OS. For example on Debian (replace /dev/sda1 with /dev/mmcblk0p2 on Raspbian), 

$ sudo su
# dumpe2fs /dev/sda1 | grep 'Filesystem created:'
# OR
# tune2fs -l /dev/sda1 | grep 'Filesystem created:'

What is the last log in time for users

lastlog  # all users
last     # current user

System Logs

Read/view the system logs

How to View System Log Files on Ubuntu 18.04 LTS

'Show Application' -> 'Logs'.

What is the reboot time

The following method does not show the reboot history. 

last reboot

The above command only show the 'last' reboot time. If we want to see the boot history, see How to View System Log Files on Ubuntu 18.04 LTS. The GNOME Logs utility is best. At the top of the GUI, I can select the logs of the (boot) date. But it has a limit number of dates to choose from. The 2nd choice Log File Viewer utility is not useful since it does not provide a choice of the date. The command line approach is possible if we need to use grep to search of 'boot' in syslog or syslog.1 or syslog.X.gz files under /var/log/ directory. We may search for a very old boot log using this approach. For example, zcat /var/log/syslog6.log | grep boot.

Image/Photo

Crop an image

sudo apt-get install gthumb

Open an image. Click color palette icon on top-right corner (or use keyboard shortcut 'e'). Click 'crop'. There will be a rectangle on image where you can resize the rectangle.

Pinta and mtPaint can also take a screenshot of the desktop and crop the image.

Rename files in batch

GUI To Batch Rename Files On Linux With Exif And Music Tags Support: Inviska Rename

View exif information

gThumb works fine.

Mind-mapping

KeePass

Choice 1: KeePassXC, KeePass Cross-Platform Community Edition. I can open kdbx file in KeePassXC. It also has a browser integration (auto-fill) functionality. See Getting Started With KeePassXC 

sudo add-apt-repository ppa:phoerious/keepassxc
sudo apt-get update
sudo apt install keepassxc

Choice 2: KeePassX. Note that the kdbx file used in KeePass2 cannot be opened in KeePassX.

Choice 3: KeePass2 (this is what I am using now). There is no need to use ppa.launchpad.net to install from. You can install keepass2 by using sudo apt-get install keepass2 or install the latest version using Julian Taylor’s PPA. 

sudo add-apt-repository ppa:jtaylor/keepass
sudo apt-get update
sudo apt-get install keepass2

On Android: KeePassDroid

Chrome browser (not OS) integration: See the source code.

Chromebook: KeePass2 for Chromebook

Security:

KeePass with KeeAgent

http://code.mendhak.com/keepass-and-keeagent-setup/

KeeWeb: Free cross-platform password manager compatible with KeePass

KeeWeb – An Open Source, Cross Platform Password Manager

It can open from WebDAV, Dropbox (sync and offline access), Google Drive, OneDrive, ...

A Docker exists for the self hosting method.

Update Firefox

The following instruction is used to get security-testing packages. 

sudo add-apt-repository ppa:ubuntu-mozilla-security/ppa
sudo apt-get update
sudo apt-get install firefox

Or use the official PPA method. See How to install Firefox 57 “Quantum” on Linux Mint, Ubuntu, Debian, CentOS, Fedora… & How to Install Firefox Quantum in Ubuntu and other Linux Right Now 

sudo add-apt-repository ppa:mozillateam/firefox-next
sudo apt update && sudo apt upgrade

Bluetooth

* https://zach-adams.com/2014/07/bluetooth-audio-sink-stream-setup-failed/ Linux Mint 
sudo apt-get install bluetooth
sudo apt-get install bluetooth bluez-utils blueman

Then run lsusb | grep Bluetooth command which will shows the name of your bluetooth device. 

sudo apt-get install bluez

On my bluetooth adapter, the lsusb shows, 

$ lsusb
Cambridge Silicon Radio, Ltd Bluetooth Dongle (HCI mode)
...
$ sudo hcitool dev
Devices:
	hci0	00:1A:7D:DA:71:09

I can use Ubuntu's bluetooth setting dialog to connect my bluetooth keyboard without any problem (It will ask me to enter some code on pairing).

Note that the MAC address of my bluetooth keyboard shown above is the from the controller/adapter. It is NOT the same as my bluetooth keyboard one (90:7F:61:8F:D0:38) as shown from the bluetooth setting (GUI) dialog.

Bluetooth Audio Receiver

Remember to change the Mode from Telephony Duplex (HSP/HFP) to High Fidelity Playback (A2DP) from Sound Settings dialog (launched from Taskbar). See also Windows OS.

BluetoothAudioLinux.png

Open the default graphical applications using the command line (mime-types)

See /etc/gnome/defaults.list. 

# alias open='xdg-open'. Put this inside your ~/.bashrc or ~/.bash_aliases
xdg-open [name-of-PDF-file]

# If you want to use gnome-open, you need to install a package
sudo apt-get install libgnome2-bin
gnome-open [name-of-PDF-file]

gnome-open [dir-name-or-path] # To open a directory in Nautilus file manager

gnome-open https://www.howtoforge.com/ # To open a website in your system's default web browser

Unity display timeout

Go to Dash -> power setting -> Brightness Settings

Screensaver showing current time

xscreensaver + gltext

http://askubuntu.com/questions/64086/how-can-i-change-or-install-screensavers 

sudo apt-get install xscreensaver 
# sudo apt-get remove gnome-screensaver

Click Dash > xscreensaver or run the command line xscreensaver-demo. Mode = Only One Screen Saver & pick GLText. Click Setting & choose 'Display date and time' ,'Don't rotate'.

gluqlo

[Note that gluqlo uses too much cpu] I like gluqlo (flip clock) screensaver. However, it is not easy to make it to replace the gnome-screensaver. 

sudo apt-add-repository ppa:alexanderk23/ppa
sudo apt-get update
sudo apt-get install gluqlo
  • Follow the instruction to install it on Ubuntu machine.
  • Follow the instruction there to remove gnome-screensaver and install xscreensaver.
  • Configure xscreensaver to use only 1 screensaver. Edit ~/.xscreensaver file and add a line like
gluqlo -root                                \n\
  • Still follow the instruction to allow xscreensaver to start when the machine starts up. Don't try to edit ~/.xinitrc file as other sites suggested; start Dash and type 'startup' and follow the screen dialog to add xscreensaver -nosplash.
  • Still follow the instruction to add lock screen keyboard shortcut.

Note that the above steps work for Ubuntu 12.04 & 13.10 but not 14.04 (Ubuntu 14.04 changed to use LockScreen instead LightDM program to lock the screen). A solution on Ubuntu 14.04 is to disable screen lock.

  1. Still follow the above instruction to remove gnome-screensaver and install xscreensaver. Set gluqlo as the only one screensaver.
  2. Go to Brightness & Lock panel from the Unity Launcher. And set Turn screen off when inactive: to Never.
  3. Install "Unity Tweak Tool" with sudo apt-get install unity-tweak-tool. Run it from the Launcher and select System > Security > Enhance system security by disabling Desktop lock.
  4. To enable locking desktop (required a password to unlock the desktop), check 'Lock Screen After' option. I pick 1 minute.

For some reason, gluqlo suddenly uses all my cpu (6 cores) resource (Ubuntu 14.04). The computer thus makes some noise. I have to use 'kill' command to kill them.

Flash for browser

On Ubuntu 12.04, there is no way to directly install the pepperflashplugin-nonfree plugin. So we have to use ppa from other people. See this post 

sudo apt-get update
sudo apt-get install chromium-browser
sudo add-apt-repository ppa:skunk/pepper-flash
sudo apt-get update
sudo apt-get install pepflashplugin-installer
sudo update-pepperflashplugin-nonfree --install

The last step gives me an error: sudo: update-pepperflashplugin-nonfree: command not found

xed from Cinnamon Desktop

By default, recent open files are not shown (xed 1.6.3). See https://github.com/linuxmint/xed/issues/55.

Open Cinnamon Settings -> Privacy and enable 'remember recent files'.

Text file line ending in DOS and Unix

A DOS/Windows text file can be converted to Unix format by simply removing all ASCII CR characters with 

$ tr -d '\r' < inputfile > outputfile  # inputfile and outputfile cannot be the same

or, if the text has only CR newlines, by converting all CR newlines to LF with 

$ tr '\r' '\n' < inputfile > outputfile

SQL

MySQL Workbench

http://www.mysql.com/products/workbench/

sqliteman

https://sourceforge.net/projects/sqliteman/

User Interface Designer

Glade - RAD tool to enable quick & easy development of user interfaces for the GTK+ toolkit and the GNOME desktop environment

Devhelp - API documentation browser for GTK+ and GNOME

HTML editor

  • Atom
  • Bluefish
  • Brackets features
    • Inline Editors
    • Live Preview
    • Preprocessor Support
  • MonoDevelop
  • Kompozer and the installation instruction for Ubuntu.
  • BlueGriffon: a new WYSIWYG content editor. The interesting thing is the software BlueGriffon EPUB Edition: a cross-platform Wysiwyg editor able to natively create and edit EPUB2 and EPUB3 ebooks!

npm and Javascript

See npm package manager in Javascript.

chm reader

sudo apt-get install xchm

SCR3310 smart card

  • The usb device should be recognized by Ubuntu/Mint. Thus, the smart card can be used by Windows virtual machine (tested on Windows 10 VM).
brb@T3600 ~ $ lsusb
Bus 002 Device 003: ID 413c:2107 Dell Computer Corp.
Bus 002 Device 033: ID 09c3:0013 ActivCard, Inc.
Bus 002 Device 002: ID 8087:0024 Intel Corp. Integrated Rate Matching Hub
Bus 002 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
Bus 004 Device 001: ID 1d6b:0003 Linux Foundation 3.0 root hub
Bus 003 Device 003: ID 3938:1031
Bus 003 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
Bus 001 Device 003: ID 0b95:7720 ASIX Electronics Corp. AX88772
Bus 001 Device 002: ID 8087:0024 Intel Corp. Integrated Rate Matching Hub
Bus 001 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
sudo apt-get install libpcsclite1 pcscd pcsc-tools
lsusb 
# Bus 006 Device 002: ID 04e6:5116 SCM Microsystems, Inc. SCR331-LC1 / SCR3310 SmartCard Reader
dmesg | grep SCR3310
# [ 2005.300052] usb 6-1: Product: SCR3310 v2.0 USB SC Reader
  • Search "SCR3310 driver linux" on google.com.
# Download pcsc-lite-1.8.13.tar.bz2 from 
# https://alioth.debian.org/frs/?group_id=30105
sudo apt-get install libudev-dev
cd pcsc-lite-1.8.13
./configure
make
sudo make install

# Download libusb
http://libusb.info/
cd libusb-1.0.19
./configure
make
sudo make install

# Download scmccid_5.0.27_linux
# http://www.identive-infrastructure.com/index.php/products-solutions/smart-card-readers-a-terminals/smart-card-readers/scr3310

cd scmccid_5.0.27_l32r
sudo ./install.sh

Chroot

Note that we have to change the conf file a little bit. The 'location' word needs to be changed to 'directory'. Also at the last step when we are ready to test a 32-bit GUI app, we need to issue DISPLAY in a separate line; such as 

export DISPLAY=:0.0
su brb # brb is my root user in the host system that can invoke the schroot program
       # firefox does not allow to use root to start it
firefox

For a recap: 

1. Install the packages
sudo apt-get install debootstrap schroot -y
2. Create a schroot configuration file
sudo nano /etc/schroot/chroot.d/precise_i386.conf
3. Install 32-bit ubuntu with debootstrap
sudo mkdir -p /srv/chroot/precise_i386
sudo debootstrap --variant=buildd --arch=i386 precise /srv/chroot/precise_i386 http://archive.ubuntu.com/ubuntu/
4. Test the chroot environment
schroot -l
schroot -c precise_i386 -u root
uname -a
cat /etc/issue
5. Additional configuration
apt-get install ubuntu-minimal
# That's all.

The article also mentioned the home directories (Documents, Downloads, ...) of the users within the chroot are shared with the host. How to access them from the host?

Check/Diagnostic SD card, read-only file system

The above commands do not help in my case.

Snappy (package manager)

How Snappy packages are different from Deb

An article from PCWorld. Skype, Spotify, Minecraft, JetBrains Dev Suite, MySQL Workbench, Blender.

  • Applications are no longer installed system-wide. The base Ubuntu operating system is kept securely isolated from applications you install later. Both the base system and Snappy packages are kept as read-only images.
  • Snappy packages can include all the libraries and files they need, so they don’t depend on other packages.
  • An update can never fail, as a package installation could potentially fail and become incomplete with typical Linux packages.
  • Snappy also supports “delta” updates, which means only the changed bits of the package need to be downloaded and installed.
  • Snappy-based Ubuntu systems might be standard.

Snap commands

Some snap commands

  1. snap help
  2. snap version
  3. snap list: see a list of installed snap app
  4. snap find queryname: find a snap app. For example snap find browser, snap find media.
  5. snap install appname: install snap apps
  6. snap remove appname: remove snap apps
  7. snap info appname: see more information about a snap app
  8. sudo snap refresh: update a snap app. You actually don't need it since snapd runs in the background and handles updates automatically
  9. snap changes: see a history of the changes made to your system

How to run the Snap applications: you can run snap applications just like any other application installed on your system.

6 Essential Ubuntu Snap Commands You Should Know

How To Remove Old Snap Versions To Free Up Disk Space

https://www.linuxuprising.com/2019/04/how-to-remove-old-snap-versions-to-free.html 

$ du -sh /var/lib/snapd/snaps/
2.2G	/var/lib/snapd/snaps/
$ ls /var/lib/snapd/snaps/
anbox_167.snap             gnome-characters_206.snap
atom_222.snap              gnome-characters_254.snap
...
gnome-calculator_406.snap  sublime-text_58.snap
gnome-characters_139.snap
$ sudo snap set system refresh.retain=2   # Not useful
[sudo] password for brb: 
$ du -sh /var/lib/snapd/snaps/
2.2G	/var/lib/snapd/snaps/

$ nano remove-old-snaps
$ chmod +x remove-old-snaps
$ sudo ./remove-old-snaps
atom (revision 222) removed
atom (revision 223) removed
...
sublime-text (revision 51) removed
sublime-text (revision 44) removed
$ du -sh /var/lib/snapd/snaps/
1.1G	/var/lib/snapd/snaps/

Docker

I haven't found any tutorial yet!

Ova image

Sorry, I don't get the command line back. Booting stuck in the middle.

Beaglebone

http://beagleboard.org/snappy or http://www.ubuntu.com/things#try-beaglebone

Raspberry Pi 2

https://darrenjw2.wordpress.com/2015/02/07/getting-started-with-snappy-ubuntu-core-on-the-raspberry-pi-2/

Flatpak

Sublime, GIMP, Spotify, Visual Studio Code, Marker, Gradio, VLC, Android Studio, Audacity, Atom, FileZilla, draw.io desktop, Cozy and others.

Flatpak setup, Using flatpak

How To Use And Install FlatPak On Linux. Consider the Gradio app. 

$ flatpak install de.haeckerfelix.gradio.flatpakref
Installing: de.haeckerfelix.gradio/x86_64/stable
Required runtime for de.haeckerfelix.gradio/x86_64/stable (org.gnome.Platform/x86_64/3.26) is not installed, searching...
Found in remote flathub, do you want to install it? [y/n]: y
Installing: org.gnome.Platform/x86_64/3.26 from flathub
[####################] 10 delta parts, 79 loose fetched; 259556 KiB transferred 
Installing: org.freedesktop.Platform.ffmpeg/x86_64/1.6 from flathub
[####################] 1 delta parts, 2 loose fetched; 2649 KiB transferred in 0
Installing: org.gnome.Platform.Locale/x86_64/3.26 from flathub
[####################] 4 metadata, 1 content objects fetched; 14 KiB transferred
Installing: de.haeckerfelix.gradio/x86_64/stable from flathub
[####################] 1 delta parts, 1 loose fetched; 363 KiB transferred in 0 
Installing: de.haeckerfelix.gradio.Locale/x86_64/stable from flathub
[####################] 3 metadata, 1 content objects fetched; 1 KiB transferred 

$ flatpak uninstall de.haeckerfelix.gradio.flatpakref

Now we can launch the Gradio app from the Launch Menu.

Note: no 'sudo' is required.

Remove unused flatpak runtimes

How To Remove Unused Flatpak Runtimes To Free Up Disk Space

unable to open mtp device ubuntu 14.04

Use this tip. 

sudo apt-get install mtpfs

Install/upgrade google chrome browser

wget -N https://dl.google.com/linux/direct/google-chrome-stable_current_amd64.deb
sudo dpkg -i google-chrome-stable_current_amd64.deb

Note that '-N' option.

(Mar 7, 2016). We may experience an error "Failed to fetch http://dl.google.com/linux/chrome/deb/dists/stable/Release" when we run sudo apt-get update. It is because the 32-bit chrome has been discontinued. The solution is to modify the file </etc/apt/sources.list.d/google-chrome.list>. See reddit. 

$ sudo sed -i -e 's/deb http/deb [arch=amd64] http/' "/etc/apt/sources.list.d/google-chrome.list"
$ cat "/etc/apt/sources.list.d/google-chrome.list"
### THIS FILE IS AUTOMATICALLY CONFIGURED ###
# You may comment out this entry, but any other modifications may be lost.
deb [arch=amd64] http://dl.google.com/linux/chrome/deb/ stable main

Another suggestion to modify </opt/google/chrome/cron/google-chrome> (though the file exists) does not work .

How to Install Chrome on Linux and Easily Migrate Your Browsing From Windows 

sudo apt-get install libxss1 libappindicator1 libindicator7wget \
    https://dl.google.com/linux/direct/google-chrome-stable_current_amd64.deb

sudo dpkg -i google-chrome*.deb

Message Of The Day /etc/motd

.Trash-1000 folder

See this post. Ubuntu will create such folders when a file is deleted from a USB drive. Presumably this would allow a file to be restored if you accidentally deleted it.

Try to empty the paperbin or delete the folder with the terminal-command as root: sudo rm -rf /path/to/folder/.Trash-1000

Xbox wireless Gamepad

https://www.howtoforge.com/tutorial/how-to-configure-your-gamepad-on-ubuntu/

Games

Take to the virtual skies with FlightGear, FlightGear

Twitter client

Corebird

Birdie

Birdie vs Corebird

Elasticsearch & Kibana

Elasticsearch and Kibana : installation and basic usage on Ubuntu 16.04

TexLive

Recover files from Windows drives

sudo fdisk –l
sudo apt-get install ntfs-3g

sudo mount -t ntfs-3g /dev/sdaX /PARTITION/POINT

Best apps

100 Best Applications for Ubuntu 2018

Kernel

System Call

Other Flavors

Other tiny Linux

5 tiny Linux distros to try before you die

Arch linux, Manjaro Linux

7 Reasons Why I Use Manjaro Linux And You Should Too

How To Convert DEB Packages Into Arch Linux Packages

Pacman

pacman -Sy openssh

Manjaro Linux

Alpine Linux

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