Adventures of a self-learning data scientist - I built a PC, installed Pop!

Why need a new PC?

I have been using my company PC, a Panasonic note PC (Intel Core i5-7200U), to build and maintain this site. When I retire early next year, I have to return it to the company. I have to prepare a new one.

Why not buy?

At home, I am a long time Apple user (Mac SE, PowerBook 145B, iMac DV, iBook G4, iPad, iPad Retina, iPad Pro 12.9 inch). The natural choice is a Mac. However, no Mac is equipped with Nvidia GPU. I am planning to play with tensorflow for deep learning, and tensorflow practically requires Nvidia GPU. Mac is out.

I usually copy the codes in the book, run them and experiment to learn coding. I have found most books on data science assume the readers use Unix-like OS. When I use a Windows PC, I have to change some parts in the codes, and it is annoying. Shift-JIS character code of Japanese version of Windows is also annoying. Windows is out.

I considered to buy a used note PC with Nvidia GPU, and then to replace OS from Windows to Linux. I looked around used note PCs, but failed to find a resonably priced one. Used PCs tend to have less performance per cost than new PCs in Japan. Used PC is out.

Should I buy a new note PC with Nvidia GPU, like DELL XPS 15, and replace OS? I am afraid I will fail to install Linux on a new PC, as it usually takes some time for Linux to support new chips. New PC is out.

Eventually I decided to build a PC from parts which Linux is likely to have supported.

Build a PC

If I can transfer the work of maintaining this site from my company PC to my new home PC, it is a success. How probable is it? Will I successfully build a functional PC: prior probability 0.9. Will I successfully install a functional OS: probability 0.8. Will I run RStudio smoothly: probability 0.7. In total, as 0.9 x 0.8 x 0.7 equals 0.5, this project is a half/half bet. I can’t bet much money on this risky project. So I decided to go for a budget PC. But how much budget?

The Japanese government happens to be distributing one hundred thousand JPY to every resident. I just yesterday received an application form by mail. One hundred thousand JPY is 843 USD, if I exclude 10 percent consumption tax and exchange at 107.80 JPY/USD.

The parts I chose are below. I purchased all at Amazon. As I use my 49 inch Sony 4K TV, a monitor is not included. The total amounf of 829 USD is under the budget of 843 USD.

Table 1: Parts I purchased
#	Parts	Vendor	Price (USD)
1	CPU: Ryzen 5 1600 AF	AMD	94
2	Mother board: B450M Pro	Asrock	69
3	DRAM: 16GBx2	Skhynix	135
4	SSD: 500GB, M.2 NVMe	Micron	77
5	Graphic card: GeForce RTX 2060	Kuroutoshikou	307
6	Case: Q300L	Cooler Master	46
7	Funs: 120mmx3	Novonest	9
8	PSU: 80Plus Bronze, 550W	Kuroutoshikou	51
9	Wireless keyboard and mouse	Elecom	25
10	HDMI cable	Amazon	9
11	USB memory	Toshiba	4
12	Ball grip driver	Vessel	3
-	Total	-	829

Paul’s Hardware says Ryzen 5 1600 AF is a buy, if sold under 100 USD. Hardware Unboxed selects Asrock B450M Pro as the best B450 Micro ATX mother board. I followed their recommendations.

The hardest work in building a PC was to connect cables between the mother board and the PC case. I had to remove the graphic card to do so. That was the most dangerous moment. I nearly broke the mother board and/or the graphic card, as I didn’t know there is a lock mechanism in PCIe x16 slot. I should have connected cables, before I insert the graphic card into PCIe x16 slot, in the first place. Somehow I found how to unlock PCIe x16 slot, and could safely remove the graphic card. It took six hours for me to build a PC. When I restart and hit F2 button timely, I could enter UEFI settings. So far, so good.

Install Pop!_OS

Ubuntu 20.04 LTS is just released, and Ubuntu-based System 76 Pop!_OS 20.04 is now available. Which distro should I choose? Jay in LearnLinux.tv is a fan of Pop!_OS, reviews Pop!_OS 20.04 positively, but has not yet confirmed its stability. In the pre-reseach, I have found Pop!_OS 20.04 has more polished user interface, and is easier to install Nvidia driver. So I chose Pop!_OS 20.04.

Make a bootable USB memory

As connection to USB memory is disabled in my company PC for security reason, the only machine I can use is my old iBook G4, of which browser is TenFourFox. I downloaded an ISO file, Nvidia version, from System 76. Then, I followed the instructions in a seemingly promising page of how-to (Japanese).

Insert the USB memory to iBook G4
In the Terminal, type $ diskutil list, and confirm the USB memory is recognized as /dev/disk1
$ diskutil unmountDisk /dev/disk1
$ cd ~/Downloads
$ sudo dd if=pop-os_20.04_amd64_nvidia_6.iso of=/dev/disk1 bs=1m
When the writing is finished, pull out the USB memory

Boot from a USB memory

I inserted the USB memory to my new PC, restart, hit F2 button, and entered UEFI settings. In the Boot section, I selected the USB memory as Boot option priority. In the Exit section, I saved changes and exit. Reboot, and voila! Pop!_OS started.

Install Pop!_OS

It was pretty easy to install. I just followed the installer. Although I selected “Japanese” in keyboard layout, I selected “English” in language, as searching in English hits more helpful pages than in Japanese. Pop!_OS 20.04 is working. So far, so good.

Install Git, and set up SSH connection with GitHub

Looking at Linux Terminal Basics, I typed in the Terminal.

$ sudo apt update
$ sudo apt full-upgrade

Taking some advice in this page (Japanese), I installed git and curl.

$ sudo apt install git curl

And I generated a new SSH key, and added it to the ssh-agent and to my GitHub account, basically following the instructions in the GitHub help page.

Install R and RStudio

As I found “How to install RStudio on Ubuntu 20.04 Focal Fossa Linux” in linuxconfig.org, I followed the instructions.

But I failed to install “tidyverse”. I apt install nearly all modules in this shell script. Then I could install “tidyverse”.

RStudio Version 1.3.959 sometimes hangs in my environment. Nothing appears in the panels, and the menu does not respond. “How to force quit an hanging application in Pop OS” helped me. I pushed alt+f2, and xkill.

This is a known issue, and 1.3-patch will come, according to this page. I added the line below to .bashrc as a workaround. Now I type rstudio in the Terminal to start RStudio.

export RSTUDIO_CHROMIUM_ARGUMENTS="--disable-seccomp-filter-sandbox"

Still, “Failed to load module appmenu-gtk-module” message appeared in the Terminal. So I apt install modules below, following this page.

$ sudo apt install appmenu-gtk2-module appmenu-gtk3-module

There always is a small issue. After I installed maps library, I was asked to install mapproj library.

As a whole, it looks OK now.

Yesterday and today, I successfully updated my covid repository and my related shiny app from my new PC. And this is the first post from my new PC. So far, so good.

I hope this machine will serve me long and well.

PS I replaced Ryzen 5 1600 AF with Ryzen 5 5600 in May 2022.

--- title: I built a PC, installed Pop!_OS, and am running RStudio author: Mitsuo Shiota date: '2020-05-31' categories: - personal - R - Shiny --- ## Why need a new PC? I have been using my company PC, a Panasonic note PC (Intel Core i5-7200U), to build and maintain this site. When I retire early next year, I have to return it to the company. I have to prepare a new one. ## Why not buy? At home, I am a long time Apple user (Mac SE, PowerBook 145B, iMac DV, iBook G4, iPad, iPad Retina, iPad Pro 12.9 inch). The natural choice is a Mac. However, no Mac is equipped with Nvidia GPU. I am planning to play with tensorflow for deep learning, and tensorflow practically requires Nvidia GPU. Mac is out. I usually copy the codes in the book, run them and experiment to learn coding. I have found most books on data science assume the readers use Unix-like OS. When I use a Windows PC, I have to change some parts in the codes, and it is annoying. Shift-JIS character code of Japanese version of Windows is also annoying. Windows is out. I considered to buy a used note PC with Nvidia GPU, and then to replace OS from Windows to Linux. I looked around used note PCs, but failed to find a resonably priced one. Used PCs tend to have less performance per cost than new PCs in Japan. Used PC is out. Should I buy a new note PC with Nvidia GPU, like DELL XPS 15, and replace OS? I am afraid I will fail to install Linux on a new PC, as it usually takes some time for Linux to support new chips. New PC is out. Eventually I decided to build a PC from parts which Linux is likely to have supported. ## Build a PC If I can transfer the work of maintaining this site from my company PC to my new home PC, it is a success. How probable is it? Will I successfully build a functional PC: prior probability 0.9. Will I successfully install a functional OS: probability 0.8. Will I run RStudio smoothly: probability 0.7. In total, as 0.9 x 0.8 x 0.7 equals 0.5, this project is a half/half bet. I can't bet much money on this risky project. So I decided to go for a budget PC. But how much budget? The Japanese government happens to be distributing one hundred thousand JPY to every resident. I just yesterday received an application form by mail. One hundred thousand JPY is 843 USD, if I exclude 10 percent consumption tax and exchange at 107.80 JPY/USD. The parts I chose are below. I purchased all at Amazon. As I use my 49 inch Sony 4K TV, a monitor is not included. The total amounf of 829 USD is under the budget of 843 USD. |#|Parts|Vendor|Price (USD)| | ---: | :--- | :--- | ---: | |1|CPU: Ryzen 5 1600 AF|AMD|94| |2|Mother board: B450M Pro|Asrock|69| |3|DRAM: 16GBx2|Skhynix|135| |4|SSD: 500GB, M.2 NVMe|Micron|77| |5|Graphic card: GeForce RTX 2060|Kuroutoshikou|307| |6|Case: Q300L|Cooler Master|46| |7|Funs: 120mmx3|Novonest|9| |8|PSU: 80Plus Bronze, 550W|Kuroutoshikou|51| |9|Wireless keyboard and mouse|Elecom|25| |10|HDMI cable|Amazon|9| |11|USB memory|Toshiba|4| |12|Ball grip driver|Vessel|3| |-|Total|-|829| : Parts I purchased {#tbl-parts} [Paul's Hardware](https://www.youtube.com/channel/UCvWWf-LYjaujE50iYai8WgQ) says Ryzen 5 1600 AF is a buy, if sold under 100 USD. [Hardware Unboxed](https://www.youtube.com/channel/UCI8iQa1hv7oV_Z8D35vVuSg) selects Asrock B450M Pro as the best B450 Micro ATX mother board. I followed their recommendations. The hardest work in building a PC was to connect cables between the mother board and the PC case. I had to remove the graphic card to do so. That was the most dangerous moment. I nearly broke the mother board and/or the graphic card, as I didn't know there is a lock mechanism in PCIe x16 slot. I should have connected cables, before I insert the graphic card into PCIe x16 slot, in the first place. Somehow I found how to unlock PCIe x16 slot, and could safely remove the graphic card. It took six hours for me to build a PC. When I restart and hit F2 button timely, I could enter UEFI settings. So far, so good. ## Install Pop!_OS Ubuntu 20.04 LTS is just released, and Ubuntu-based System 76 Pop!_OS 20.04 is now available. Which distro should I choose? Jay in [LearnLinux.tv](https://www.learnlinux.tv/) is a fan of Pop!_OS, reviews Pop!_OS 20.04 positively, but has not yet confirmed its stability. In the pre-reseach, I have found Pop!_OS 20.04 has more polished user interface, and is easier to install Nvidia driver. So I chose Pop!_OS 20.04. ### Make a bootable USB memory As connection to USB memory is disabled in my company PC for security reason, the only machine I can use is my old iBook G4, of which browser is TenFourFox. I downloaded an ISO file, Nvidia version, from [System 76](https://pop.system76.com/). Then, I followed the instructions in [a seemingly promising page of how-to](https://genjiapp.com/blog/2014/10/13/booting-and-installing-lubuntu-14.04-from-usb-flash-drive-on-ibook-g4.html) (Japanese). - Insert the USB memory to iBook G4 - In the Terminal, type `$ diskutil list`, and confirm the USB memory is recognized as `/dev/disk1` - `$ diskutil unmountDisk /dev/disk1` - `$ cd ~/Downloads` - `$ sudo dd if=pop-os_20.04_amd64_nvidia_6.iso of=/dev/disk1 bs=1m` - When the writing is finished, pull out the USB memory ### Boot from a USB memory I inserted the USB memory to my new PC, restart, hit F2 button, and entered UEFI settings. In the Boot section, I selected the USB memory as Boot option priority. In the Exit section, I saved changes and exit. Reboot, and voila! Pop!_OS started. ### Install Pop!_OS It was pretty easy to install. I just followed the installer. Although I selected "Japanese" in keyboard layout, I selected "English" in language, as searching in English hits more helpful pages than in Japanese. Pop!_OS 20.04 is working. So far, so good. ## Install Git, and set up SSH connection with GitHub Looking at [Linux Terminal Basics](https://support.system76.com/articles/terminal-basics/), I typed in the Terminal. ``` $ sudo apt update $ sudo apt full-upgrade ``` Taking some advice in [this page](https://qiita.com/kenji-miyake/items/06b8c3807bef0ba5c451) (Japanese), I installed git and curl. ``` $ sudo apt install git curl ``` And I generated a new SSH key, and added it to the ssh-agent and to my GitHub account, basically following the instructions in the [GitHub help page](https://help.github.com/en/github/authenticating-to-github/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent#adding-your-ssh-key-to-the-ssh-agent). ## Install R and RStudio As I found ["How to install RStudio on Ubuntu 20.04 Focal Fossa Linux "](https://linuxconfig.org/how-to-install-rstudio-on-ubuntu-20-04-focal-fossa-linux) in linuxconfig.org, I followed the instructions. But I failed to install "tidyverse". I apt install nearly all modules in [this shell script](https://gist.github.com/luispuerto/a247301bc4337cccb04d9e4abd24fba8). Then I could install "tidyverse". RStudio Version 1.3.959 sometimes hangs in my environment. Nothing appears in the panels, and the menu does not respond. ["How to force quit an hanging application in Pop OS"](https://www.reddit.com/r/pop_os/comments/adhqs4/how_to_force_quit_an_hanging_application_in_pop_os/) helped me. I pushed alt+f2, and xkill. This is a known issue, and 1.3-patch will come, according to [this page](https://github.com/rstudio/rstudio/issues/6782). I added the line below to .bashrc as a workaround. Now I type `rstudio` in the Terminal to start RStudio. ``` export RSTUDIO_CHROMIUM_ARGUMENTS="--disable-seccomp-filter-sandbox" ``` Still, "Failed to load module appmenu-gtk-module" message appeared in the Terminal. So I apt install modules below, following [this page](https://askubuntu.com/questions/1074926/failed-to-load-module-appmenu-gtk-module-canberra-gtk-module). ``` $ sudo apt install appmenu-gtk2-module appmenu-gtk3-module ``` There always is a small issue. After I installed maps library, I was asked to install mapproj library. As a whole, it looks OK now. Yesterday and today, I successfully updated [my covid repository](https://github.com/mitsuoxv/covid) and [my related shiny app](https://mitsuoxv.shinyapps.io/covid/) from my new PC. And this is the first post from my new PC. So far, so good. I hope this machine will serve me long and well. PS [I replaced Ryzen 5 1600 AF with Ryzen 5 5600 in May 2022.](https://mitsuoxv.rbind.io/2022/05/15/i-updated-bios-and-installed-a-new-cpu-in-my-pc/)