First, check if jupyter is installed
$ which jupyter
/usr/bin/which: no jupyter in (/opt/ibm/platform_mpi/bin:/shared/apps/lsf/9.1/linux2.6-glibc2.3-x86_64/etc:/shared/apps/lsf/9.1/linux2.6-glibc2.3-x86_64/bin:/shared/apps/python/Python-3.5.2/Python-3.5.2/INSTALL/bin:/shared/apps/slurm/slurm-14.11.8/INSTALL/sbin:/shared/apps/slurm/slurm-14.11.8/INSTALL/bin:/shared/apps/perl/perl-5.20.0/INSTALL/bin:/shared/apps/fftw/fftw-3.3.3/INSTALL/bin:/shared/apps/gnu-compilers/usr/bin:/usr/lib64/qt-3.3/bin:/opt/ibm/platform_mpi/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/r.west/.local/bin:/home/r.west/bin:/home/r.west/.local/bin)
Now use pip to install it in your $HOME userspace:
$ which pip
/shared/apps/python/Python-3.5.2/Python-3.5.2/INSTALL/bin/pip
$ pip install --user jupyter
And check you can find it (you should have put .local/bin at the end of your $PATH in your .bashrc file during chapter 4)
$ which jupyter
~/.local/bin/jupyter
Now, request allocation for an interactive job, as we learned in chapter 6:
First check which partitions have some idle nodes using sinfo, then request allocation on one using salloc, wait a moment, then find out which node you were given using squeue, then ssh to it.
$ sinfo | grep idle
$ salloc -N 1 --exclusive -p ht-10g-4
$ squeue -u r.west
$ ssh -X compute-3-041
Last login: Tue Dec 6 08:46:01 2016 from discovery2
Then try running jupyter notebook and read the output carefully.
[r.west@compute-3-041 ~]$ jupyter notebook
[I 08:54:25.409 NotebookApp] Serving notebooks from local directory: /home/r.west
[I 08:54:25.409 NotebookApp] 0 active kernels
[I 08:54:25.409 NotebookApp] The Jupyter Notebook is running at: http://localhost:8888/
[I 08:54:25.409 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[W 08:54:25.412 NotebookApp] No web browser found: could not locate runnable browser.
Jupyter runs a mini webserver which you access through your web browser.
It normally opens this browser for you, pointing to the correct URL, so
you don't usually need to worry about how it works.
The last line in the output above is telling you that it couldn't find a web browser on the compute node.
One option would be to ask the system administrators to install one;
but they will look at you funny (the compute nodes can't access the web, and don't have a screen, so what would you browse and how?). But if there was a browser, you could ssh with the -X (or -Y) option, and hope the browser windows appear on your own screen. But it would be very laggy and annoying, especially if you weren't on a super-fast connection to Holyoke.
Better plan is to use our own web browser, and connect to Jupyter's web server. A few lines before that in the output, Jupyter tells you what the address is - importantly, which port it is serving on: The Jupyter Notebook is running at: http://localhost:8888/.
If port 8888 was busy when you started the notebook, it'll use 8889, etc. The trouble is, that port is only being served locally, from the compute node to itself! (hence the web address localhost). We can't connect to it from anywhere else.
The solution is to tunnel to it, through a new ssh connection.
The following instructions are for a Mac, Linux, Windows using a bash shell, where you type
sshin a terminal to connect via ssh. Ubuntu is a good way to use bash shell with Windows. If you are on Windows and using Putty for your ssh connections, the options for port forwarding are somewhere in the GUI menus. Read this or ask google if you can't figure it out, then update this tutorial with a few pointers!
Leaving the existing ssh connection running, open a new terminal window (or tab) on your local computer (eg. New Tab from the Shell menu on OS X), and use it to open a new ssh connection, this time with port forwarding:
$ ssh -L 8888:compute-0-115:8888 r.west@discovery2.neu.edu
This new option requests that port 8888 on my local computer is forwarded (through the ssh tunnel to discovery2) to port 8888 on the remote computer compute-0-115. You will have to change the compute node name, possibly the port number, and your username. When I try this it logged in OK and looks like it worked, but read the first few lines of output carefully:
$ ssh -L 8888:compute-0-115:8888 r.west@discovery2.neu.edu
bind: Address already in use
channel_setup_fwd_listener_tcpip: cannot listen to port: 8888
Could not request local forwarding.
Last login: Tue Dec 6 08:34:10 2016 from c-65-96-167-0.hsd1.ma.comcast.net
+---------------------------------------------------------------------------+
| Northeastern University Research Computing Cluster (discovery.neu.edu) |
| Login Node |
+---------------------------------------------------------------------------+
| Usage of this cluster assumes you have read and agree to usage guidelines |
| at http://www.northeastern.edu/rc. |
| |
| Please do not run interactive jobs or GUIs on this node, it is against |
| usage policy that you agreed to when applying for the cluster account. |
| |
| See "Submitting Jobs on Discovery Cluster" page at |
| http://www.northeastern.edu/rc or contact researchcomputing@neu.edu. |
| |
| If you have reached this node in error please logout now and send an |
| email with your login id to researchcomputing@neu.edu. |
| |
| All other requests should be directed to researchcomputing@neu.edu. |
| |
| Thank you, |
| NU Research Computing Team (researchcomputing@neu.edu) |
+---------------------------------------------------------------------------+
[r.west@discovery2 ~]$
It "cannot listen to port: 8888" because it is "already in use". That's because I already have a local jupyter notebook running on my local port 8888!
So I disconnect ($ logout) and try again, forwarding my local port 9999 (arbitrary choice, you can use anything that's greater than 1024 and not already in use) to the compute node's port 8888:
$ ssh -L 9999:compute-0-115:8888 r.west@discovery2.neu.edu
This time it connects without any warning or error lines.
I should be able to point my browser at http://localhost:9999/ and it'll forward to port 8888 on compute-0-115.
However, any attempt to connect to the server in my browser fails and the ssh window says open failed: connect failed: Connection refused, because for security reasons Jupyter is configured to only accept connections from localhost (see here) and not from other computers.
You could try following the instructions to generate a configuration file and change this setting, but (a) it would make it less secure, and (b) I couldn't get it to work anyway!
My final approach, which works (or it wouldn't have been my final approach!), is to tunnel all the way through to the compute node using SSH, so the jupyter notebook thinks the connection is coming from itself (localhost). Leave your notebook serving on port 8888, but in the other window disconnect your existing ssh tunnels ($ logout) and then connect first to discovery2 forwarding your local 9999 to discovery's 8888, and then to the compute node, forwarding port 8888 to localhost:
RichardsMacBookPro13:DiscoverFunTimes rwest$ ssh -L 9999:localhost:8888 r.west@discovery2.neu.edu
[r.west@discovery2 ~]$ ssh -L 8888:localhost:8888 compute-0-115
[r.west@compute-0-115 ~]$
Now open a web browser and point it to http://localhost:9999/ !
To test it works as well as we can hope, make a new notebook and enter this in a cell and execute it:
import matplotlib
matplotlib.use('Agg')
%matplotlib inline
from matplotlib import pyplot as plt
plt.plot(range(5))When done, be sure to shut down and disconnect all your sessions (lazy way: press Ctrl-C and Ctrl-D a lot in each window!), to release the resources back to the Slurm queues.
Sometimes another Discovery user is doing this (now that another 14 of you know about it, the probability just increased) and you can end up both trying to use the same ports. For that reason, try different random numbers (greater than 1024 and unlikely to be in use) for the middle port in the chain (i.e the 9145 in the following example):
RichardsMacBookPro13:DiscoverFunTimes rwest$ ssh -L 9999:localhost:9145 r.west@discovery2.neu.edu
[r.west@discovery2 ~]$ ssh -L 9145:localhost:8888 compute-0-115
[r.west@compute-0-115 ~]$ jupyter
Why would it be helpful to run Jupyter on Discovery instead of on your own computer? One example was the sensitivity analysis in chapter 7b: we had to copy files back and forth to the server a bunch, especially when debugging. If we did the analysis in a notebook on Discovery, the data would be right there!
Also helpful if you are analyzing very large data files - Discovery has many terabytes of fast storage available. (Although not in your default $HOME directory - so be sure to ask research-computing for help and advice if you have "big data" to deal with).
Remember: Although Jupyter Notebooks are a great way to try things out and do one-off bits of analysis, and good for presenting your results, as your simulations get more complicated you probably want to be writing Python scripts and modules, and using an IDE like PyCharm to help you. Develop your code locally, once it's running and debugged, upload to Discovery and run it as a script. The other drawback of Jupyter Notebooks is collaboration with peers on git: it's much harder to merge simultaneous changes in a notebook than in a python script.