I installed Anaconda on a CentOS VM on an Ubuntu server. I then created a conda environment for all of my python data science libraries on this VM. I have a matching conda environment on my laptop.
I then followed this guide to allow me to perform data analytics on the server using a Jupyter notebook remotely on my laptop: https://amber-md.github.io/pytraj/latest/tutorials/remote_jupyter_notebook
I am able to successfully load my Jupyter notebook on my laptop and perform analytics on the server. I can also mark my completed app as .servable() in the notebook and then use panel serve --show ... on ther VM terminal to serve the completed interactive app to LAN users via a web browser.
My issue is that when I instead mark my app with .show() to allow me to view the app/report that I am currently working on in the notebook, I get the following message outputted: <bokeh.server.server.Server at 0x7faa92ef5590> but the app does not load in a new browser tab as expected.
How can I make app.show() work when using a Jupyter notebook remotely instead of locally?
I know that I need to specify the port to .show() and make sure the user can access that port on the remote server:
For the illustration of this question(not actuals), say my server VM is address 192.168.0.1 and my laptop is 192.168.0.2 and the port that I want to use with app.show() is 3333 .
- Setup the port:
On the server ( 192.168.0.1 ):
- Check that port 3333 is not being used:
sudo lsof -i:3333 - Check that iptables aren’t showing the port as open:
sudo iptables-save | grep 3333 - Add the port to /etc/services file:
sudo nano /etc/services - I added the following line to the top of the file and saved:
# service-name port/protocol [aliases ...] [# comment]
bokeh-server 3333/tcp # Open port to allow app.show() to work on a remotely executed Jupyter Notebook
-
Enable the firewall:
sudo systemctl enable firewalld -
Start the firewall:
sudo systemctl start firewalld -
Check the status of the firewall:
sudo systemctl status firewalld -
Confirm that this port is now open:
sudo iptables-save | grep 3333
Output:
-A IN_public_allow -p tcp -m tcp --dport 3333 -m conntrack --ctstate NEW -j ACCEPT
- Test that the user can access the port on the server:
I installed ncat on the server ( 192.168.0.1 ):
sudo yum install nmap-ncat -y
Then I set up messaging between the server and my laptop:
- On server:
nc -l 3333 - On laptop:
nc 192.168.0.1 3333
and also between the laptop and the server:
- On laptop:
nc -l 3333 - On server:
nc 192.168.0.2 3333 - Messages successfully make it from server to laptop and vice versa.
- Confirmation of these two connections:
sudo lsof -i:3333
which outputted:
COMMAND PID USER FD TYPE DEVICE SIZE/OFF NODE NAME
nc 1776 XXX 5u IPv4 23627 0t0 TCP vmserver:bokeh-server->192.168.0.2:55358 (ESTABLISHED)
nc 1846 XXX 3u IPv4 22895 0t0 TCP vmserver:33658->192.168.0.2:bokeh-server (ESTABLISHED)
showing that the server on port 3333 can communicate with the laptop on a different port and the laptop on port 3333 can communicate with the server on a different port.
I’m not sure how to make them connect on the same port though? ie both on port 3333? Is this the source of my issue?
- Then in my jupyter notebook, I replaced
app.show()with
app.show(port=3333, websocket_origin=None, threaded=False)
However I am still experiencing the same behaviour as previously in that the app does not load in a new browser tab as expected.
I then experimented with parameters websocket_origin (tried “192.168.0.1”,“192.168.0.2” and “*”) and threaded (True/False) but changing these didn’t give my desired result of the app loading in a new browser tab.
A couple of interesting points :
- If I run my notebook which executes
app.show(port=3333, websocket_origin=None, threaded=False)
and then on the server run:
sudo lsof -i:3333
then the following is returned:
COMMAND PID USER FD TYPE DEVICE SIZE/OFF NODE NAME
ZMQbg/1 19328 xxx 45u IPv4 83214 0t0 TCP *:bokeh-server (LISTEN)
ZMQbg/1 19328 xxx 54u IPv6 83215 0t0 TCP *:bokeh-server (LISTEN)
It seems like the server is waiting for something to happen on port 3333? ie LISTEN ? Unlike when I was messaging between the server and my laptop (and vice versa) there doesn’t actually seem to be an ESTABLISHED connection though.
Please note that those 2 lines above only appear after I run the notebook.
- After I have executed my notebook (and the app in the new tab hasn’t opened), if I try to execute the notebook again then I get this warning in my jupyter notebook:
OSError: [Errno 98] Address already in use
So it does seem like the connection between the server and laptop has been ESTABLISHED or at very least reserved? To fix this, I then have to close the connection to my server and then on my laptop run the command: lsof -ti:8888 | xargs kill -1 before then reestablishing my connection between the server and my laptop as per https://amber-md.github.io/pytraj/latest/tutorials/remote_jupyter_notebook
As is probably obvious, I am no sysadmin and I’m really at the limits of my knowledge here!
If anyone has any advice or pointers as to how to get this working then I would be massively grateful.
Edit:
The more I look at this the more I think it may be down to my ssh settings rather than Panel itself - I’ll have a play with some different ssh settings tomorrow and will report back if I have any luck getting it working.
Software versions on the conda environment on the VM:
# Name Version Build Channel
_anaconda_depends 2019.03 py37_0
_libgcc_mutex 0.1 main
alabaster 0.7.12 py37_0
anaconda custom py37_1
anaconda-client 1.7.2 py37_0
anaconda-project 0.8.4 py_0
arrow-cpp 0.11.1 py37h0e61e49_1004 conda-forge
asn1crypto 1.3.0 py37_0
astroid 2.3.3 py37_0
astropy 4.0 py37h7b6447c_0
atomicwrites 1.3.0 py37_1
attrs 19.3.0 py_0
babel 2.8.0 py_0
backcall 0.1.0 py37_0
backports 1.0 py_2
backports.os 0.1.1 py37_0
backports.shutil_get_terminal_size 1.0.0 py37_2
beautifulsoup4 4.8.2 py37_0
bitarray 1.2.0 py37h7b6447c_0
bkcharts 0.2 py37_0
blas 1.0 mkl
bleach 3.1.0 py37_0
blosc 1.16.3 hd408876_0
bokeh 1.4.0 py37_0
boost-cpp 1.68.0 h11c811c_1000 conda-forge
boto 2.49.0 py37_0
bottleneck 1.3.1 py37hdd07704_0
bzip2 1.0.8 h7b6447c_0
ca-certificates 2019.11.28 hecc5488_0 conda-forge
cairo 1.14.12 h8948797_3
cartopy 0.17.0 py37hbb7e04d_1
certifi 2019.11.28 py37_0
cffi 1.13.2 py37h2e261b9_0
cftime 1.0.4.2 py37hdd07704_0