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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 |
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These two are definite necessities. In particular, need to install openssh-server before basically anything else because otherwise we can't get SSH access. | |
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openssh-server | sudo apt-get openssh-server |
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}}} 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. {{{ |
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'''VNC server configuration''' | '''Old VNC server configuration''' |
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# ! /bin/sh (no spaces: having trouble with Wiki editing!) | # ! /bin/sh [no spaces] |
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vncconfig -iconic & x-terminal-emulator -geometry 80x24+10+10 -ls -title "$VNCDESKTOP Desktop" & x-window-manager & gnome-panel & gnome-settings-daemon & metacity & nautilus |
vncconfig -iconic & x-terminal-emulator -geometry 80x24+10+10 -ls -title "$VNCDESKTOP Desktop" & x-window-manager & gnome-panel & gnome-settings-daemon & metacity & nautilus |
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{{{#!wiki xxx |
Install and run Anaconda: {{{ ls /opt/anaconda3 sudo bash [name of anaconda .sh file] pip install theano pip install keras apt-get install git |
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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 == {{{ vncserver -kill :yourvncnumber }}} |
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
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
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
vncserver -kill :yourvncnumber