From e646fe9206a3e9b1e44ca617b801d0aef856b2b3 Mon Sep 17 00:00:00 2001
From: patmjen <patmjen@dtu.dk>
Date: Thu, 3 Nov 2022 16:56:01 +0100
Subject: [PATCH] Add more formatting
This hopefully makes it easier to spot what's an actual step in the
and what is extra info.
---
HPC_Python_Guide.md | 76 ++++++++++++++++++++++-----------------------
1 file changed, 38 insertions(+), 38 deletions(-)
diff --git a/HPC_Python_Guide.md b/HPC_Python_Guide.md
index 09fa019..9e46750 100644
--- a/HPC_Python_Guide.md
+++ b/HPC_Python_Guide.md
@@ -48,11 +48,11 @@ a100sh
```
You should now be able to install packages with pip install <PACKAGE> as normal.
-If pip doesn't work, you may need to manually install it with:
-```
-easy_install pip
-```
-To run python, remember to use the `python3` command.
+
+> __Troubleshooting:__ If pip doesn't work, you may need to manually install it with:
+> ```
+> easy_install pip
+> ```
## III. Virtualenv activation
@@ -74,23 +74,23 @@ To run python, remember to use the `python3` command.
source <VENV_NAME>/bin/activate
```
-__Pro tip:__ To make life easy, put these commands in a bash script called `init.sh`:
-```
-#!/bin/bash
-module load python3/3.8.9
-module load numpy/1.19.5-python-3.8.9-openblas-0.3.13
-module load scipy/1.5.4-python-3.8.9
-module load cuda/11.0
-
-source <VENV_NAME>/bin/activate
-```
-
-which you can then run by entering:
-```
-source init.sh
-```
-
-and this will prepare everything
+> __Pro tip:__ To make life easy, put these commands in a bash script called `init.sh`:
+> ```
+> #!/bin/bash
+> module load python3/3.8.9
+> module load numpy/1.19.5-python-3.8.9-openblas-0.3.13
+> module load scipy/1.5.4-python-3.8.9
+> module load cuda/11.0
+>
+> source <VENV_NAME>/bin/activate
+> ```
+>
+> which you can then run by entering:
+> ```
+> source init.sh
+> ```
+>
+> and this will prepare everything
## IV. Jupyter notebooks on ThinLinc
@@ -122,12 +122,12 @@ and this will prepare everything
jupyter lab
```
This should open a browser with the Jupyter lab interface.
- Sometimes this has some issues and one then need to revert to Jupyter notebooks.
+ > __Troubleshooting:__ Sometimes Jupyter lab has some issues and you need to revert to Jupyter notebooks.
## V. Jupyter notebooks on the cluster in your own browser
-**WARNING:** This will be a bit involved...
-Credit goes to Niels Jeppesen who figured all this out.
+> __WARNING:__ This will be a bit involved...
+> Credit goes to Niels Jeppesen who figured all this out.
1. Open a terminal on the cluster, either through ThinLinc or ssh.
@@ -136,12 +136,12 @@ Credit goes to Niels Jeppesen who figured all this out.
```
tmux
```
- This way, _**if you lose your internet connection**_ your notebook will keep running.
- You can _**reconnect**_ to the tmux session by running:
- ```
- tmux attach
- ```
- in a terminal on the cluster.
+ > _**If you lose your internet connection**_ your notebook will keep running.
+ > You can _**reconnect**_ to the tmux session by running:
+ > ```
+ > tmux attach
+ > ```
+ > in a terminal on the cluster.
3. Take note of the node's hostname. You can see this by running:
```
@@ -176,14 +176,14 @@ Credit goes to Niels Jeppesen who figured all this out.
This should open the Jupyter interface. Any commands you run will be executed on the HPC
cluster.
- **NOTE:** If no URL beginning with `127.0.0.1` was printed in step 5, change the first part
- manually to `127.0.0.1` before entering it in your browser. In the example from step 5, you
- would change `n-62-20-9` to `12.0.0.1`.
+ > **NOTE:** If no URL beginning with `127.0.0.1` was printed in step 5, change the first part
+ > manually to `127.0.0.1` before entering it in your browser. In the example from step 5, you
+ > would change `n-62-20-9` to `12.0.0.1`.
If you close your browser, you can reconnnect by entering the URL again.
If you lose your internet connection, you can reconnect by repeating steps 5 and 6.
-**NOTE:** You can make inline plots in the notebook, but cannot open new windows for plotting.
-The closest you can get is by starting the server on a ThinLinc node with X11 forwarding.
-This will allow you to have the notebook in your own browser, but new windows will be opened
-in ThinLinc.
+> **NOTE:** You can make inline plots in the notebook, but cannot open new windows for plotting.
+> The closest you can get is by starting the server on a ThinLinc node with X11 forwarding.
+> This will allow you to have the notebook in your own browser, but new windows will be opened
+> in ThinLinc.
--
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