Setup for deep learning workstation

This page covers the steps for setting up a machine primarily intended for deep learning analyses. This is assuming Ubuntu has already been installed.

Ubuntu installation notes:

Should probably tweak the BIOS to match that of Agnew/Calculon/Lrrr/Ndnd if we set up any more of these. Just see one of those guys for the good options.
Can/should tick on the options for auto-installing updates and installing third-party software while installing Ubuntu
For some reason, on the rack-mount machines, when it tells you to hit enter to restart after installing, hitting enter doesn't do anything. You just have to power off the machine.
Another weird thing: On the rack-mount machines with two graphics cards, you have to switch back and forth between the two graphics cards during Ubuntu installation vs running vs using the BIOS or whatnot. It's weird. Just keep going back and forth... one or the other will work for any given scenario.

Other tips/notes on running analyses: KerasTips

Initial setup

Early on, presumably right after installation of OS, remember to update all packages:

sudo apt-get update
sudo apt-get upgrade

Package installation

These two are definite necessities. In particular, need to install openssh-server before basically anything else because otherwise we can't get SSH access.

sudo apt-get openssh-server
sudo apt-get install tightvncserver

The following may not be necessary anymore -- it was for our old VNC setup. But it shouldn't hurt to install these packages anyway, just in case we want to use something like the old setup again.

sudo apt-get install ubuntu-desktop gnome-panel gnome-settings-daemon metacity nautilus gnome-terminal

OLD VNC server configuration

# ! /bin/sh [no spaces]
[-x /etc/vnc/startup] && exec /etc/vnc/startup
[ -r $HOME/.Xresources ] && xrdb $HOME/.Xresources
xsetroot -solid grey
vncconfig -iconic & x-terminal-emulator -geometry 80x24+10+10 -ls -title "$VNCDESKTOP Desktop" & x-window-manager & gnome-panel & gnome-settings-daemon & metacity & nautilus

NEW VNC server configuration

Steps roughly follow https://www.digitalocean.com/community/tutorials/how-to-install-and-configure-vnc-on-ubuntu-16-04. Exact instructions below:

Install the following packages:

sudo apt-get install xfce4 xfce4-goodies
sudo apt-get install autocutsel

Next, start up VNC:

vncserver:yourvncnumber

It will prompt you to set and confirm a password; do so. Then end the session:

vncserver -kill :yourvncnumber

This creates ~/.vnc/xstartup.

Either edit ~/.vnc/xstartup , or delete it and make a new file. IF MAKING A NEW FILE, enter this command as well:

chmod 755 ~/.vnc/xstartup

The new contents of ~/.vnc/xstartup should be:

 #!/bin/bash
xrdb $HOME/.Xresources
startxfce4 &

Adding users

sudo adduser newusername
sudo usermod -aG sudo newusername

Keras setup

Install and run Anaconda:

ls /opt/anaconda3
sudo bash [name of anaconda .sh file]

pip install theano
pip install keras
apt-get install git

Edit keras.json (in home folder)

Change backend: from tensorflow -> theano

Change image_dim_ordering: from tf -> th

Install CUDA 8 and CUDNN:

http://askubuntu.com/questions/788323/change-runlevel-on-16-04

http://askubuntu.com/questions/481414/install-nvidia-driver-instead-nouveau (top solution)

Add CUDA directory cuda/bin to path

Copy cudnn.h to cuda include directory

Copy shared libraries to cuda library

Make .theanorc in home directory

Set CUDA/root environment variable

Change ldconfig in cuda lib directory: sudo ldconfig /usr/local/cuda/lib64 (unclear how often we have to do this -- each restart? Per user?)

Mount Farnsworth

Only needs to be done once. Will only unmount if we do so explicitly or if Agnew/Calculon/Lrrr/Ndnd gets rebooted (or if their network connection dies)

Install cifs-utils package: sudo apt-get install cifs-utils sudo mkdir /mnt/eeg_data_analysis (or whatever the share is named)

sudo mount -t cifs -o username=matt //farnsworth/eeg_data/analysis /mnt/eeg_data_analysis/ (replace username with your Farnsworth username)

Start VNC session

Enter in Terminal:

ssh yourusername@agnew/calculon.local
vncserver :yourvncnumber -geometry  (whatever, e.g.) 1280x800

Enter in VNC:

agnew/calculon.local :yourvncnumber

End VNC session