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wiki:documentation:computing

Computing resources

Lab email address

scholzlabcaesar@gmail.com Password is our standard lab password. Ask me if you don't know it.

remote computing on nif3004 via vnc

nif3004 is a decent work station loated in Monika's office. It can be used for behavior analysis and other simple tasks.

  • Ask Monika for an account. Your account will be FirstInitialLastname
  • on windows: install tightvnc
  • you need to be on the caesar ethernet or vpn, otherwise this won't work.

Log in to nif3004 using ssh

  • open the windows console
  • ssh username@nif3004
  • enter your password when prompted. You should see that your console changes and now says username@nif3004$
  • start a new vnc session by typing vncserver (if you have an old session, you can see a list of your old sessions by typing vncserver -list)
  • make a note of the display number eg. :4. Let's call it x
  • type exit to leave the ssh session

create an ssh tunnel and start vnc on windows

  • in your windows console type ssh -L <5900+x>:localhost:<5900+x> username@nif3004
  • type your password and again, your console should change to username@nif3004$
  • open tightvnc Viewer
  • type 'localhost:x' in the text field and connect
  • type your vnc password (you will get prompted to set that password the first time you start vncserver)
  • you should see a GUI. Start computing!

Installing PharaGlow on nif3004 (Ask Monika for help)

  • Obtain the environment file for the correct pumping environment environmentpumping.yml
  • log in to your nif3004 account via ssh/vnc and open a terminal (remote computing on nif3004 via vnc)
  • in a terminal on nif3004 type: conda env create -f ~/environmentpumping.yml
  • activate the environment: source activate pumping. You should see (pumping) appear at the start of the terminals prompt. Your are now in a so-called python environment that is standardized for running pharaglow.
  • clone pharaglow from the lab github:git clone https://github.com/scholz-lab/PharaGlow.git enter your github username and password when prompted.
  • enter the directory of pharaglow: cd PharaGlow
  • type python setup.py install –user. Look at the text output. There shouldn't be any errors.
  • test your installation by opening a python prompt in ther terminal: python
  • import pharaglow
  • exit the prompt by typing exit()

Running PharaGlow on nif3004

If everything is installed as per the following section, follow these steps to open a jupyter notebook to analyze movies:

  • open a terminal and type source activate pumping to activate the environment
  • open a jupyter notebook server by typing jupyter notebook
  • in the new browser window, navigate to your jupyter notebook and start analyzing!
wiki/documentation/computing.txt · Last modified: 2020/04/01 09:44 by mscholz

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