Jupyter notebooks are awesome. We should use them. Here are instructions for how to install in your local home directory on the UC Davis farm cluster.
Jupyter is a program written in Python. Anaconda is a package manager for Python. It’s straightforward to install and saves a lot of time.
Download it:
cd
curl -OL https://3230d63b5fc54e62148e-c95ac804525aac4b6dba79b00b39d1d3.ssl.cf1.rackcdn.com/Anaconda2-2.4.0-Linux-x86_64.sh
This will download a shell script which you can run to install Anaconda:
bash Anaconda2-2.4.0-Linux-x86_64.sh
(You will have to scroll through a policy document. Type yes, and yes again when prompted to add the default directory to your .bashrc).
Source and install Jupyter notebook:
source ~/.bashrc
conda install jupyter
Then install R kernel for Jupyter:
conda install -c r r-essentials
Source:
source ~/.bashrc
Start a notebook (change the port number to arbitrary 4 numbers, but remember it!):
jupyter notebook --port 8756
This will open a port 8756. Might take a little while depending on node traffic. Please be patient.
(Side Note: If you are logged on to another node, this will not work. Jupyter notebooks will need to access your home directory because OSError: [Errno 13] Permission denied: '/run/user/1126017'
Once it starts, you will see a screen , just type 'q' to quit out. It will give you this:
ljcohen@farm:~$ jupyter notebook --port 8756
[I 16:06:14.988 NotebookApp] Serving notebooks from local directory: /home/ljcohen
[I 16:06:14.989 NotebookApp] 0 active kernels
[I 16:06:14.989 NotebookApp] The Jupyter Notebook is running at: http://localhost:8888/
[I 16:06:14.990 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[I 16:08:09.444 NotebookApp] Creating new notebook in /msu_assemblies_finished/A_xenica
[I 16:08:26.245 NotebookApp] Kernel started: 1ef9327c-6cf6-4d30-a4cd-f0b1a987819a
[W 16:08:37.154 NotebookApp] Timeout waiting for kernel_info reply from 1ef9327c-6cf6-4d30-a4cd-f0b1a987819a
[1] "Got unhandled msg_type:" "comm_open"
[I 16:10:18.136 NotebookApp] Saving file at /msu_assemblies_finished/A_xenica/Untitled1.ipynb
[I 16:20:17.660 NotebookApp] Saving file at /msu_asse
On your local terminal, open another ssh connection to farm:
ssh -L 8888:localhost:8756 [email protected]
Now, you should be able to open a browser and type:
http://localhost:8888/tree/
This should give you a screen with your home directory on the farm cluster!
Now, you can make notebooks like this: https://github.com/ljcohen/MMETSP/blob/master/MMETSP_reverse_transrate.ipynb
Useful Links: