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--- playground:playground [2021/02/23 16:32]
msovara [Security]
+++ playground:playground [2025/04/29 16:06] (current)
nmfuphi [Starting a notebook inside a job]
@@ Line 1: / Line 1: @@
-====== **Playground Test edits by MSovara** ======
+====== **Edits by MSovara** ======
 ===== Jupyter / Ipython Notebook =====
@@ Line 66: / Line 66: @@
 </code>
-**Remember to uncomment it, and don't just copy and paste my hash in**.
+**Remember to uncomment it, don't just copy and paste my hash in**.
+==== Starting a notebook inside a job ====
+There might be a cleaner way of doing this... Please let us know if you have one!
+**VERY IMPORTANT:**  Do not add the lines below to your .ssh/config file on the cluster, you //WILL// break any attempt at parallel processing!
+Open a terminal on your local machine and create a ''.ssh/config'' file.
+<code>
+touch .ssh/config
+</code>
+If your desktop system runs Windows, a simple way to deal with this is to run a unix-like environment inside Windows.  You can either use[[http://cygwin.com|Cygwin]] Cygwin directly, or start a "Local Terminal" in [[https://mobaxterm.mobatek.net/|MobaXterm]].  From this terminal you can edit the local ''~/.ssh/config'' file as if you were working on a Linux computer.
+Continue to edit the ''~/.ssh/config'' file on your local machine by adding in these lines:
+<code>
+Host cnode*
+    Hostname %h
+    User YOURUSERNAME
+    ProxyCommand ssh YOURUSERNAME@lengau.chpc.ac.za nc %h 22
+    LocalForward 8838 localhost:8838
+</code>
+**Note**
+  -//Each session will be assigned a different compute node (cnode* changes everytime you request for an interactive compute node session)//
+  -//Use localForward and localhost port number provided for each different session.//
+Ultimately, what this will do is allow you to ''ssh'' directly to a compute node (note you can only do this to nodes where you currently have a job running).
+<code>
+ssh cnode*
+</code>
+You should be prompted for your password, twice. This is because the ''ssh'' logs in to Lengau first and then from Lengau it logs into the the compute node.
+You are now ready to roll...
+In your browser go to: http://localhost:8838
+The jobscript will look something like:
+<file bash jupyter.qsub>
+#!/bin/bash
+#PBS -P SHORTNAME
+#PBS -q serial
+#PBS -l select=1:ncpus=8:mpiprocs=1
+#PBS -l walltime=08:00:00
+#PBS -N Jupyter
+#PBS -m abe
+#PBS -M YOUR@EMAIL.ADDRESS
+module add chpc/python/3.6.0_gcc-6.3.0
+JUPYTERPORT=8838  # you could change this too, if you wanted to.
+hostname > ~/jupyter.host
+jupyter-notebook --port=${JUPYTERPORT} --no-browser
+</file>
+If you submit that job and wait for it to start running then you can check which host the session is running on with:
+<code bash>
+cat ~/jupyter.host
+</code>
+Then, again on your local machine, you need to connect to the compute node, i.e. ''ssh cnode0101''.  If you are working in Windows, do this from your Cygwin or MobaXterm terminal command line.  You will be prompted for your Lengau login password.

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