Category Archives: Tutorials

Tutorials

How to install Ubuntu Linux alongside Windows 10 (dual boot)

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You can kind of think of the Linux operating system (which is actually called GNU/Linux, look into it) as a loose definition, which describes a bunch of operating systems that are very similar. As most of them in general are pretty much free and open source, anyone can make a copy of one and modify it a little to become their own version of Linux, and that's exactly what everyone have done. That said, there are some more famous and common, perhaps the most famous one being Ubuntu. I personally prefer to use Fedora, which isn't really that much more complicated to use than Ubuntu, but if you're a total noob I think it's best you just go through with Ubuntu initially first, one reason being that there have been more people asking questions online about it, so you're more likely to find the exact instructions for any kind of problem that you may end up having. Don't let that scare you though, because Ubuntu works really quite well straight out of the box these days, so get ready!

Step 1: Resize windows partition

Critical: Make a backup of important files

You'll probably be fine if you follow these instructions, but resizing a partition can corrupt your file systems so make sure you make a backup of your most important files before continuing.

You need to make space for the linux partition on your hard drive, where Windows probably is taking up most of the space. Windows partitions are usually not encrypted, in which case you'll be fine just resizing the existing partition to make room for another one on your drive. If you have more than one drive, consider having your linux installation on the fastest (SSD) drive if one of them is significantly slower.

Move the end of the partition, not the beginning.
Leave space for linux installation (50GB or more recommended)
use the Windows 10 built in partition manager or download a program like partition wizard from the internet.

You might run into problems resizing your partition as it is more than likely mounted, and you are using files on the partition if this is your first time formatting your hard drive manually, in which case you could use GParted by booting from the Linux boot stick made in the following sections and trying the Live version of the Operating System before installing. GParted is a very good disk partitioning tool that comes standard in GNU/Linux.

Step 2: Make a linux boot stick

2.1 Download program to make usb stick

Rufus:

https://rufus.akeo.ie/

2.2 Prepare your usb stick

Make sure you have a 4GB usb stick. If you only have a smaller one see section (get alternative ubuntu)

2.3 Download ubuntu

https://ubuntu.org

Get the recommended Long Term Support (LTS) version (18.04). You should most likely use the 64-bit version unless your computer is older than 2005.

(Optional) Alternative ubuntu installation:

If you have a smaller usb stick available, you can try to download an alternative iso (Xubuntu: https://xubuntu.org/download/)

2.4 Install ubuntu on USB with Rufus

The program is very straight forward, so just use it an select the usb stick and the downloaded iso or other image type file.

Step 3: Boot from linux stick

Turn your computer completely off with the shut down option in Windows, and start it again while the usb stick is plugged in. This is important for some computers to reveal the option to show BIOS settings or other startup options to choose to boot from the usb stick.

When your computer is starting keep pressing the DEL key or F12 or F2 repeatedly to get startup options. There might be a hint suggesting which key to press.

Change bios boot order to removable drive first
If you don't want to change BIOS settings you can check if you have boot options in the startup sequence menu.
If you can't get it to boot check for safe boot in the BIOS settings and disable.

Step 4: Install ubuntu

Follow the instruction wizard, and choose the option "Something else" i.e any variation of custom when it asks where to install ubuntu (e.g Replace Windows 10, alongside Windows 10 etc.).

Create one partition for swap with approximately the same amount of ram your computer has or less (minimum around 1GB), and the rest of the free space as ext4 and mount point /. You will want to install your GNU/Linux distribution on this partition.

After the installation is done restart your computer and you will have the option through GRUB bootloader to boot into either Ubuntu or Windows 10. Congratulations and good job on completing the tutorial!

(Optional) Step 5: Install different desktop environments

Ubuntu comes with its default desktop environment which in 18.04 is a custom configured Gnome 3. You can install many different ones that you then select at login like XFCE4, KDE, LXDE for more customization. KDE is the most popular one for having the most options.

Beware that it may take up a lot of disk space, and install KDE with

sudo apt-get install kubuntu-desktop

For a clean GNOME you can install

sudo apt-get install ubuntu-gnome-desktop

And for XFCE4 (light weight, comes with Xubuntu)

sudo apt-get install xfce4

Tutorials

How to use PyMOL free libre, or | How to compile PyMOL from source on Ubuntu 18.04

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This will allow you to run PyMOL without an aqcuired license which you certainly would need if you were to use the compiled binaries provided from the PyMOL website. This is just a very simple guide providing a list of the packages you need to install, and showing how to run the scripts you need to download the source code and compile the program.
The version of the program will be a little stripped of menus and such, so you will need to rely more on command line interface arguments to use it.

From what I can gather the program used to be totally free, but the original developer passed away unexpectedly in 2009, after which it was acquired by Schrödinger, Inc. While the company does keep some of their updates closed source, requiring users to pay for a license, most of the functionality is still there in the Open Source version. There are also some rumors of provided binaries out there, but if you compile it yourself like this here, you will be sure to have the latest updates (last update 21 days ago at the time of writing), and you don't have to trust a third party not to put a virus in the program they give you for free for no reason.

If you're interested to see when the project was last updated, or just inspect the code, visit the project on github:
https://github.com/schrodinger/pymol-open-source

Now, just run these commands in your terminal and you should end up with a pymol executable on your computer in just a few minutes!

Install the required dependencies for compiling:

sudo apt-get install freeglut3-dev libglew-dev mesa-utils mesa-common-dev binutils libxml2-dev libmsgpack-dev python3-pip libglm-dev libpng-dev libfreetype6-dev git

Install the python Qt5 library, which is a python library, so it has to be installed with the python package manager pip that you just installed:

pip3 install PyQt5

Download the source code (i.e. clone the git repository)

git clone https://github.com/schrodinger/pymol-open-source.git

Enter the pymol source code directory that was just downloaded by git:

cd pymol-open-source

Run the install script, placing the compiled binaries in $HOME/programs/PyMOL or wherever you like

python setup.py install --prefix=~/programs/PyMOL/ --use-msgpackc=no

(Optional) Add the location of the compiled executable to your PATH, so you can run the program from anywhere in the terminal:

put the following in ~/.bashrc

export PYMOL_HOME=$HOME/programs/PyMOL
export PATH=$PATH:$PYMOL_HOME/bin

Now close your terminal and open a new one to reload the PATH variables.

And finally run

pymol

Or, if you didn't do the optional PATH step, cd into the directory you specified when running the script, and run ./pymol

You can also make a menu short cut entry by copying one of the .desktop files in /usr/share/applications/ and changing it to point to the location of your pymol executable.

Tutorials

Flashing Stock or Custom Firmware with Heimdall (on linux)

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I had a bit of a learning curve when learning how to use Heimdall to flash images onto my phone (i9506, aka ks01lte) so hopefully this can help others with what I learned.

First of all, Heimdall is a flashing software for putting firmware into the different partitions of Samsung Android phones. It's cross platform, and supposedly equivalent in functionality to that of Odin, although I've never tried Odin. Heimdall is also cross platform so you can follow this guide if you're on mac or windows I think.

Heimdall basics
There are two executable programs:
1. heimdall
2. heimdall-frontend

I recommend using heimdall-frontend, but you need both because heimdall-frontend depends on heimdall.

Heimdall version
At the time of this post, the newest version was 1.4.2. I had to compile that myself from source though, but it was relatively easy if you just follow the build instructions inside the readme. I had to use 1.4.2 to get it to work with my phone so if you have issues you should try getting the newest one. There were binaries of 1.4.0 on the official website, and 1.4.1 in the ubuntu repo.

Installing Heimdall
At the time, I could also install heimdall from ubuntu repos with apt-get install, however the packages were called heimdall-flash and heimdall-flash-frontend. Idk why, but they're the same. Also they were 1.4.1 so they unfortunately didn't work for me, so I had to install them myself after compiling.

So briefly how to install it, although I'm not gonna give the whole command specific walk through as it is in the readme:
It's located at the github page:
https://github.com/Benjamin-Dobell/Heimdall

clone the directory:
git clone https://github.com/Benjamin-Dobell/Heimdall.git

Enter the directory and follow the build instructions as detailed (the last time I checked) at the very bottom of the readme file, specific for Linux, so it was inside the Linux folder.

Now after building you'll have two executable files:
heimdall
heimdall-frontend

The problem now is that you need to run these as root to connect to your phone, and heimdall-frontend uses heimdall, so you need to add them to your PATH.
However, by running sudo the PATH gets reset, so if you just export PATH=$PATH:$HOME/heimdalldirectory its not gonna find it so what I did (which you shouldn't really do because it should be reserved for system applications but whatever, it works, and you can just delete the heimdall files after you finished to keep a clean system) was to put both files in /bin/
sudo mv ./heimdall /bin/
sudo mv ./heimdall-frontend /bin/
Now you can sudo heimdall-frontend

Other problems with heimdall
If you get libusb errors when trying to export pid or anything else, try a different USB cable, and try different ports on your computer. That actually worked for me.

Flashing of firmware
First of all, your phone needs to be in Download mode, so google how you do that. For me I had to power off the phone, and then hold Power+Vol Up+Home. Or Vol Down I can't remember.

Then sudo heimdall-frontend and go to Utilities, and try to detect device. It should show a little messages saying it was detected.

Download and save .pit file
Next you'll want to Download the pit file from your device. This is also a good way to check if heimdall is working correctly, by just trying to print the pit. But you should really download the pit file and store it because you'll need it for flashing. It works as a sort of partition map (Partition Information Table).

So go ahead and download that and save it.

Now that you have that, you've done a very good job so pat yourself on the back. You're a really advanced hacker person aren't you? Wow. Good job. Now the real shit begins though so get ready. This is where you might brick your device so beware.

Really. Be careful. If you flash the wrong thing you're fucked so. Yeah.

Also, the warranty of your phone will be void after you flash anything onto it like this, so this is a kind of point of no return, although you might be able to flash it back to warranty condition if you have the stock recovery img. Not sure if phones can recognize that or not.

Flash custom recovery first
The first thing you might want to do is install a custom recovery like TWRP. TWRP lets you backup all your partitions, which can be nice in case you flash the wrong thing and want to get back to square one. You can also save your partitions with dd but I'm not gonna get into that here.
Like I said, this might void your warranty, and after doing this, I could not update through the stock phone update mechanism anymore (I mean, as a regular person going into Settings->about->Check for updates on your phone, it said something like "Your phone has been changed, no updates for you".

So to flash TWRP, open up heimdall-frontend again, go to the Flash tab, browse for your .pit file. Then Add a partition file, and select RECOVERY as the name, and find your recovery.img file: See figure 1.

Figure 1 -- heimdall-frontend with RECOVERY flashing

Now, start, and it will reboot when it finishes probably so be ready, and make it reboot straight into recovery right away. If not the custom recovery will be wiped. For me, booting into recovery was the same as to boot into download, just the opposite direction volume.

Now go into BACKUP and backup everything, and store that somewhere on your computer. In case something goes wrong. TWRP backs up to a directory on your phone located in /TWRP/Backups/.....

Flashing the rest of the firmware
Next, we'll be flashing some more interesting things. Like the full firmware, with modem and everything.

In my case I wanted to flash the newest stock rom update, because I needed the updated bootloader and modem firmware to install LineageOS 15.1 (Android 8.1), which I could later simply install from within TWRP.
So I downloaded the newest stock rom update from sammobile.
You can get the newest firmware from there for free if you sign up, but have to pay for older ones it seemed.
It might also be important that you get the right ROM for the right region or country, I don't know if that affects the ability for the phone to boot or not, but I'd try to get the right one if I were you.
For me it was a large file of about 1.5 GB. A .zip file to be exact, which upon extraction revealed two files, one of them being a .tar.md5 file.
If I just renamed the .tar.md5 file to a .tar file (removing the .md5 part of the name) I could extract it, and it revealed the files that can be flashed by heimdall.

In my case the files were:
aboot.mbn
boot.img
cache.img.ext4
hidden.img.ext4
modem.bin
NON-HLOS.bin
recovery.img
rpm.bin
sbl1.mbn
sdi.mbn
system.img.ext4
tz.mbn

Which made me very anxious and insecure, and I felt that this was perhaps a bit much, but then I figured it out.
Just like that recovery file from before, all these files correspond to a Partition name in Heimdall Frontend, from the .pit file. So what we'll actually do here with heimdall is just put the contents of these files/images into the partitions of our devices, and then they'll replace whatever was there from before. So it's all quite simple really if you think about it.
The name of the partition isn't always the same as the file, but there is a file name hint below the name so look at that. For example the APNHLOS partition name corresponds to NON-HLOS.bin. See figure 2.

Figure 2: APNHLOS file name hint

Now just keep adding all these until they're all in heimdall (figure 3). This should be a pointer also to whether or not you're using the right firmware. All files should fit into a partition. However, you might want to not flash the RECOVERY to preserve the custom recovery previously installed. You might have to boot directly into recovery again after flashing this time too to avoid reseting to the stock recovery, but I'm not sure. Just in case.

Figure 3: Heimdall Frontend with all firmware files added, except for the recovery image.

Now, if you dare, hit the Start button, and wait in excitement. Remember that your phone should be in Download mode right now. Also be sure to boot into recovery right away! And then just reboot, but your recovery might ask you if you want to remove the "Read only" permissioning, which I think you should do.

Great! That's it! Hopefully you didn't brick your phone. If you did, then hopefully you backed up with TWRP like I said before, and then you can restore it in TWRP. I think though that's just if you "soft bricked" and not "hard bricked", which is worse probably.

Good riddance! Thanks for reading. I hope it helped.