Amberjack Ubuntu GPU Machine Install

This is how a new machine, amberjack, was configured.

Machine

The machine was purchased from Mwave. I’ve purchased a few machines from them and always impressed with their service. Here is the configuration

AC16427	MSI B450I GAMING PLUS AC AM4 Mini-ITX Motherboard				1	1	$225.00	$225.00
AB83276	SilverStone Strider Essential ST60F-ES230 600W 80 Plus Power Supply		1	1	$75.00	$75.00
AC19487	Crucial P1 500GB NVMe M.2 PCIe 3D NAND SSD CT500P1SSD8				1	1	$89.00	$89.00
AC23360	Respawn Ninja x MWAVE Gaming Mouse Pad Small - Black				1	1	$1.00	$1.00
AB47402	Mwave Custom PC Assembly and Testing Service					1	1	$199.00	$199.00
AB52361	Advanced Transportation Packing Solution					1	1	$19.99	$19.99
AC26501	Kingston HyperX FURY RGB 32GB (2x 16GB) DDR4 3200MHz Memory			1	1	$209.00	$209.00
AC29726	ASUS GeForce RTX 2060 SUPER Turbo EVO 8GB Video Card				1	1	$649.00	$649.00
AC12989	Seagate ST8000DM004 8TB BarraCuda 3.5" SATA3 Desktop Hard Drive			1	1	$299.00	$299.00
AB64976	Windows 10 Professional 64-bit OEM DVD						1	1	$219.00	$219.00
AB59620	SilverStone Sugo Series SG13 Mini ITX Case - Mesh Front Panel			1	1	$69.00	$69.00
AC24744	AMD Ryzen 5 3600X 6 Core Socket AM4 3.8GHz CPU Processor + Wraith Spire Cooler	1	1	$369.00	$369.00

Total of Invoice Inc GST $2,490.33
Total GST $226.39

Here is the motherboard manual.

Step 1 Update BIOS to enable virtualisation

In the BIOS settings set

Overclocking -> OC Explore Mode -> Expert
Overclocking -> CPU Features -> SVM Mode -> Enable

then boot machine (into Windows 10).

Step 2 Install Ubuntu

Erase disk and install everything to /dev/nvme0n1. Select LVM.

Step 3 Move /opt /var /home to hard disk

sudo -i
mkdir /srv; mkdir /src/fs
mount /dev/sda1 /srv/fs
rsync -aXP /opt /var /home /srv/fs
cd /
mv opt opt.old
mv var var.old
mv home home.old

Add the mounts to /etc/fstab

# mount the local HD to /home, /var and /opt
/dev/disk/by-uuid/HARD_DISK /srv/fs auto nodev,nofail,x-gvfs-show 0 0
/srv/fs/home	/home	none	bind	0	0
/srv/fs/var	/var	none	bind	0	0
/srv/fs/opt	/opt	none	bind	0	0

and reboot. After it reboots successfully you can

sudo rm -rf /opt.old /home.old /var.old

Step 4 Install cuda

sudo apt update
sudo apt upgrade
sudo apt install openssh-server net-tools rclone

Then follow the Nvidia instructions using the Package Manager method and deb(network) installer type. This doesn’t quite work as you need to do a

sudo apt purge nvidia-*
sudo apt autoremove
sudo ubuntu-drivers autoinstall

before installing cuda

sudo apt install cuda=10.2.89-1

In ~/.profile add

export PATH=/usr/local/cuda/bin${PATH:+:${PATH}}
export LD_LIBRARY_PATH=/usr/local/cuda-10.2/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}

Step 5 Install anaconda/pytorch

Install anaconda

wget https://repo.anaconda.com/archive/Anaconda3-2020.07-Linux-x86_64.sh
sh Anaconda3-2020.07-Linux-x86_64.sh
conda install pytorch torchvision cudatoolkit=10.2 -c pytorch

Seems to work

(base) cruxml@amberjack:~$ cat /proc/driver/nvidia/version
NVRM version: NVIDIA UNIX x86_64 Kernel Module  450.51.06  Sun Jul 19 20:02:54 UTC 2020
GCC version:  gcc version 7.5.0 (Ubuntu 7.5.0-3ubuntu1~18.04) 
(base) cruxml@amberjack:~$ python
Python 3.8.3 (default, Jul  2 2020, 16:21:59) 
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import torch
>>> torch.cuda.current_device()
0
>>> torch.cuda.device(0)
<torch.cuda.device object at 0x7fa9a5fab310>
>>> torch.cuda.get_device_name(0)
'GeForce RTX 2060 SUPER'
>>> 

Step 6 Install docker

sudo apt update

sudo apt install docker.io
sudo systemctl start docker
sudo systemctl enable docker
sudo usermod -aG docker cruxml

You need to log out and log in again for the group change to work.

Step 7 Install other stuff

sudo apt install hddtemp lm-sensors nvme-cli
sudo sensors-detect --auto # unfortunately didn't find anything!
sudo add-apt-repository universe
sudo apt update
sudo apt install exfat-fuse exfat-utils

Step 8 Vivado

Installed Vitis

sudo sh Xilinx_Unified_2019.2_1106_2127_Lin64.bin
# installed to /opt instead of /tools

The following did not work:

sudo apt install ./xrt_201920.2.3.1301_18.04-xrt.deb

So I installed XRT from the instructions https://xilinx.github.io/XRT/master/html/build.html.

Following https://www.hackster.io/AlbertaBeef/vitis-ai-1-1-flow-for-avnet-vitis-platforms-part-1-007b0e:

HOME=$HOME
export VITIS_AI_HOME=$HOME/src/xilinx/Vitis-AI
export SDX_PLATFORM=$HOME/src/xilinx/ULTRA96V2/ULTRA96V2.xpfm
export TRD_HOME=$VITIS_AI_HOME/DPU-TRD-ULTRA96V2
cd /opt/Xilinx/Vitis/2019.2
source settings64.sh
cd /opt/xilinx/xrt
source setup.sh
cd $TRD_HOME/prj/Vitis
# make KERNEL=DPU DEVICE=ULTRA96V2

Step 9 Install Balena Etcher

Follow instructions at https://www.balena.io/etcher/

Step XX (Decided against running ubuntu under windows 10)

How to set up Ubuntu 18.04 under Hyper-V

Right click on the Windows button and select ‘Apps and Features’.
Select Programs and Features on the right under related settings.
Select Turn Windows Features on or off.
Select Hyper-V and click OK.

I then mounted my home samba shared disk:

In File explorer, right click on the PC -> Add a Network Location -> \machinename\back1

Then install Ubuntu.

In Hyper-V manager (Quick create).
I wanted the virtual hard disk to be on the E: drive. Edit the settings of the VM and edit the Virtual Hard Disk” to convert the image from C:\Users\Public\Public Documents\Hyper-V\Virtual Hard Disks to E:\srv\amberjack\hyperv\ubuntu-hd1.

Don’t upgrade to 20.04!

Update

9/4/2021 Bluetooth stopped working and I couldn’t turn it on any more. Fixed with:
```
$ sudo rmmod btusb
$ sudo modprobe btusb
```

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