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| | =On VDI= | | =On VDI= |
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| − | Currently, the easiest way to run IPython Notebook is on NCI's [http://nci.org.au/services/vdi/ | Virtual Desktop Infrastructure (VDI)]. For a guide to set up and use VDI, click [https://opus.nci.org.au/display/Help/VDI+User+Guide | here]. | + | Currently, the easiest way to run IPython Notebook is on NCI's [[VDI|Virtual Desktop Infrastructure (VDI)]]. For a guide to set up and use VDI, click [https://opus.nci.org.au/display/Help/VDI+User+Guide | here]. |
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| | Within VDI, open a Linux terminal ('''Applications menu''' -> '''System Tools''' -> '''Terminal'''). | | Within VDI, open a Linux terminal ('''Applications menu''' -> '''System Tools''' -> '''Terminal'''). |
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| | jupyter notebook | | jupyter notebook |
| | </syntaxhighlight> | | </syntaxhighlight> |
| − | <span style="background-color: #ffffff; color: #333333; display: block; font-family: "Helvetica Neue",Helvetica,Arial,sans-serif; font-size: 14px;">
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| − | ----
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| − | </span><span style="background-color: #ffffff; display: block; font-family: Arial,Helvetica,sans-serif;">
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| − | =On Raijin=
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| − | If you don't have access to VDI, you can still run IPython Notebook from Raijin in a browser on your local computer. Currently these instructions show how to run the notebook from the login node - '''which is not recommended''' - and, as such, are just a demonstration of what is possible. Ideally the notebook should be run from an interactive session.
| + | =On Gadi= |
| − | </span>
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| − | Log in to raijin using SSH, forwarding your ports as you go (you might have to sudo this)
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| − | <syntaxhighlight lang=bash>
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| − | ssh -L 8889:localhost:8889 [USERNAME]@raijin.nci.org.au
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| − | </syntaxhighlight>
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| − | Load the conda environment
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| − | <syntaxhighlight lang=bash>
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| − | module use /g/data3/hh5/public/modules
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| − | module load conda
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| − | </syntaxhighlight>
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| − | Set up an ipython profile that serves your notebooks (adapted from [[https://ipython.org/ipython-doc/dev/notebook/public_server.html]])
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| − | <syntaxhighlight lang=bash>
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| − | ipython profile create nbserver
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| − | </syntaxhighlight>
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| − | Then modify the Notebook config file in ~/.ipython/profile_nbserver/ipython_config.py (or create that file if it wasn't generated) so that it reads:
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| − | <syntaxhighlight lang=python>
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| − | c = get_config()
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| − | c.NotebookApp.open_browser = False
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| − | # It is a good idea to put it on a known, fixed port - must match port used to ssh in.
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| − | c.NotebookApp.port = 8889
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| − | c.NotebookApp.base_project_url = 'ipython'
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| − | # The following can be used to set up a password,
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| − | # from here: https://ipython.org/ipython-doc/dev/notebook/public_server.html
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| − | # c.NotebookApp.certfile = u'/absolute/path/to/your/certificate/mycert.pem'
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| − | # c.NotebookApp.ip = '*'
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| − | # c.NotebookApp.password = u'sha1:bcd259ccf...[your hashed password here]'
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| − | | |
| − | </syntaxhighlight>
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| − | The dependencies required for ipython have been installed and should load automatically when the ipython module is loaded.
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| − | You should be able to start the notebook with
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| − | <syntaxhighlight lang=bash>
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| − | ipython notebook --profile=nbserver
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| − | </syntaxhighlight>
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| − | On your local computer, direct your browser to [[http://127.0.0.1:8889/ipython/]] and you should have access to the notebook.
| + | You can also run a notebook from Gadi's compute nodes using the [https://github.com/COSIMA/cosima-cookbook/blob/master/scripts/jupyter_gadi.sh jupyter_gadi.sh] script. Note that unlike VDI this does cost SU allocation, as it is running on the supercomputer nodes. You also won't have access to the internet to download data. |
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| − | If another user is already running an ipython session using the port number above, the ipython process will tell you with a message like this:
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| − | <syntaxhighlight>
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| − | [I 11:06:03.545 NotebookApp] The port 8899 is already in use, trying another random port.
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| − | </syntaxhighlight>
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| − | and it will tell you which port it has chosen instead:
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| − | <syntaxhighlight>
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| − | [I 11:06:03.552 NotebookApp] The IPython Notebook is running at: http://localhost:8900/ipython/
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| − | </syntaxhighlight>
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| − | Unfortunately the ssh connection will only forward the port you specified when you logged in. You should edit the ~/.ipython/profile_nbserver/ipython_config.py file, change the port number to the one ipython chose (or another higher number less than 65535), log out and log back in, using the new port number.
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| − | <syntaxhighlight lang=bash>
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| − | ssh -L 8889:localhost:8890 [USERNAME]@raijin.nci.org.au
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| − | </syntaxhighlight>
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| − | The first port number is the one you connect to on your local computer, and can remain unchanged.
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| | [[Category:Python]] | | [[Category:Python]] |
On VDI
Currently, the easiest way to run IPython Notebook is on NCI's Virtual Desktop Infrastructure (VDI). For a guide to set up and use VDI, click | here.
Within VDI, open a Linux terminal (Applications menu -> System Tools -> Terminal).
Inside the Terminal, load the conda environment
module use /g/data3/hh5/public/modules
module load conda
You should then be able to start the notebook with
On Gadi
You can also run a notebook from Gadi's compute nodes using the jupyter_gadi.sh script. Note that unlike VDI this does cost SU allocation, as it is running on the supercomputer nodes. You also won't have access to the internet to download data.
