Hello, little turtles¶
Not happy about this
I am unhappy about this session.
Instead:
- Start from a remote desktop environment
- Ignore X forwarding
Learning outcomes
- Practice using the documentation of your HPC cluster
- Practice using the Python book How to Think Like a Computer Scientist: Learning with Python 3
- Have a first 'Get stuff to work' experience
- Rehearse creating a script
- Experience when importing a Python package gives an error
- Search for a module that needs to be loaded
- Import a Python package successfully
For teachers
Teaching goals are:
- Learners have observed the error when importing a Python package without the needed module loaded
- Learners have searched through the modules of their HPC cluster
- Learners may find out that X-forwarding is important
- Learners have gotten 'stuff to work'
Other goals are:
- Verify that learners indeed have learned how to login with X-forwarding. Redirect to remote desktop environment as a solution
Lesson plan:
- 5 mins: prior knowledge
- 5 mins: presentation
- 25 mins: challenge
- 5 mins: feedback
Prior questions:
- What are features of the Python programming language?
- What are problems you may face when running someone else's Python code?
- Trick question: what is a module?
- Which problem do modules solve?
- What is a Python module/package?
- Which problem do Python modules/packages solve?
- What is X forwarding?
Overview¶
Sometimes you need to get 'stuff to work', for example, code written by someone else. In this session, we practice this, going through the problems and errors that occur when you 'just want to run the stupid code'.
flowchart TD
running_a_script[[Goal: Running a script]]
load_modules[Loaded modules?]
use_x_forwarding[Use X forwarding?]
success[Success: exercise 3]
failure_1[Failure: exercise 1]
failure_2[Failure: exercise 2]
running_a_script --> load_modules
load_modules --> |yes!| use_x_forwarding
load_modules --> |oops, forgot!| failure_1
use_x_forwarding --> |oops, forgot!| failure_2
use_x_forwarding --> |yes!| successExercises¶
Exercise 1: run without packages¶
Read the following sections of How to Think Like a Computer Scientist: Learning with Python 3:
- 3.1. Our first turtle program
Then:
- Log in to your favorite HPC cluster using SSH without X forwarding
Answer
| HPC Cluster | Example SSH login command |
|---|---|
| Alvis | ssh sven@alvis1.c3se.chalmers.se |
| Bianca | ssh sven@bianca.uppmax.uu.se |
| COSMOS | ssh sven@cosmos.lunarc.lu.se |
| Dardel | ssh -i ~/.ssh/id-ed25519-pdc svensv@dardel.pdc.kth.se |
| Kebnekaise | ssh sven@kebnekaise.hpc2n.umu.se |
| LUMI | ssh -i ~/.ssh/id_rsa_lumi svensson@lumi.csc.fi |
| Pelle | ssh pelle@rackham.uppmax.uu.se |
| Rackham | ssh sven@rackham.uppmax.uu.se |
| Tetralith | ssh x_svesv@tetralith.nsc.liu.se |
-
Do not load a Python module: it is the point of this exercise to see what happens if you forget to do so!
-
Copy-paste the first script in that section to a script called
my_turtle.pyon your favorite HPC cluster. Below is a copy of that script:
import turtle # Allows us to use turtles
wn = turtle.Screen() # Creates a playground for turtles
alex = turtle.Turtle() # Create a turtle, assign to alex
alex.forward(50) # Tell alex to move forward by 50 units
alex.left(90) # Tell alex to turn by 90 degrees
alex.forward(30) # Complete the second side of a rectangle
wn.mainloop() # Wait for user to close window
Do not call the script turtle.py
Do not call the script turtle.py.
Feel encouraged to do so anyways and observe the error message :-)
- Run the script on your HPC cluster using
pythonwithout loading any modules. Does your HPC cluster have theturtlePython package installed by default?
Answer
| HPC Cluster | Has turtle Python package installed by default? |
|---|---|
| Alvis | . |
| Bianca | Yes |
| COSMOS | Yes |
| Dardel | No |
| Kebnekaise | No |
| LUMI | No |
| Pelle | Yes |
| Rackham | Yes |
| Tetralith | Yes |
Here is the error:
[richel@sens2025560-bianca ~]$ python my_turtle.py
Traceback (most recent call last):
File "my_turtle.py", line 2, in <module>
wn = turtle.Screen() # Creates a playground for turtles
File "/usr/lib64/python2.7/lib-tk/turtle.py", line 3552, in Screen
Turtle._screen = _Screen()
File "/usr/lib64/python2.7/lib-tk/turtle.py", line 3568, in __init__
_Screen._root = self._root = _Root()
File "/usr/lib64/python2.7/lib-tk/turtle.py", line 458, in __init__
TK.Tk.__init__(self)
File "/usr/lib64/python2.7/lib-tk/Tkinter.py", line 1745, in __init__
self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use)
_tkinter.TclError: no display name and no $DISPLAY environment variable
[richel@cosmos2 ~]$ python my_turtle.py
Traceback (most recent call last):
File "/home/richel/my_turtle.py", line 2, in <module>
wn = turtle.Screen() # Creates a playground for turtles
File "/usr/lib64/python3.9/turtle.py", line 3664, in Screen
Turtle._screen = _Screen()
File "/usr/lib64/python3.9/turtle.py", line 3680, in __init__
_Screen._root = self._root = _Root()
File "/usr/lib64/python3.9/turtle.py", line 435, in __init__
TK.Tk.__init__(self)
File "/usr/lib64/python3.9/tkinter/__init__.py", line 2270, in __init__
self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use)
_tkinter.TclError: no display name and no $DISPLAY environment variable
b-an01 [~]$ python my_turtle.py
Traceback (most recent call last):
File "my_turtle.py", line 1, in <module>
import turtle # Allows us to use turtles
File "/usr/lib/python2.7/lib-tk/turtle.py", line 107, in <module>
import Tkinter as TK
File "/usr/lib/python2.7/lib-tk/Tkinter.py", line 42, in <module>
raise ImportError, str(msg) + ', please install the python-tk package'
ImportError: No module named _tkinter, please install the python-tk package
[richel@pelle2 ~]$ python my_turtle.py
Traceback (most recent call last):
File "/domus/h1/richel/my_turtle.py", line 2, in <module>
wn = turtle.Screen() # Creates a playground for turtles
File "/usr/lib64/python3.9/turtle.py", line 3664, in Screen
Turtle._screen = _Screen()
File "/usr/lib64/python3.9/turtle.py", line 3680, in __init__
_Screen._root = self._root = _Root()
File "/usr/lib64/python3.9/turtle.py", line 435, in __init__
TK.Tk.__init__(self)
File "/usr/lib64/python3.9/tkinter/__init__.py", line 2270, in __init__
self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use)
_tkinter.TclError: no display name and no $DISPLAY environment variable
[richel@rackham1 ~]$ python my_turtle.py
Traceback (most recent call last):
File "my_turtle.py", line 2, in <module>
wn = turtle.Screen() # Creates a playground for turtles
File "/usr/lib64/python2.7/lib-tk/turtle.py", line 3552, in Screen
Turtle._screen = _Screen()
File "/usr/lib64/python2.7/lib-tk/turtle.py", line 3568, in __init__
_Screen._root = self._root = _Root()
File "/usr/lib64/python2.7/lib-tk/turtle.py", line 458, in __init__
TK.Tk.__init__(self)
File "/usr/lib64/python2.7/lib-tk/Tkinter.py", line 1745, in __init__
self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use)
_tkinter.TclError: no display name and no $DISPLAY environment variable
[x_ricbi@tetralith3 ~]$ python my_turtle.py
Traceback (most recent call last):
File "/home/x_ricbi/my_turtle.py", line 2, in <module>
wn = turtle.Screen() # Creates a playground for turtles
File "/usr/lib64/python3.9/turtle.py", line 3664, in Screen
Turtle._screen = _Screen()
File "/usr/lib64/python3.9/turtle.py", line 3680, in __init__
_Screen._root = self._root = _Root()
File "/usr/lib64/python3.9/turtle.py", line 435, in __init__
TK.Tk.__init__(self)
File "/usr/lib64/python3.9/tkinter/__init__.py", line 2270, in __init__
self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use)
_tkinter.TclError: no display name and no $DISPLAY environment variable
For those that use MobaXterm that cannot get an error
It seems that for some MobaXterm users, the X-forwarding is always on, so you cannot get this error.
To get the error: create a new terminal
and login via ssh without the -X
- Load the Python software module of the correct version
| HPC Cluster | Python version |
|---|---|
| Alvis | 3.12.3 |
| Bianca | 3.11.4 |
| COSMOS | 3.11.5 |
| Dardel | 3.12.3 |
| Kebnekaise | 3.11.3 |
| LUMI | 3.11.7 |
| Pelle | 3.13.1 |
| Rackham | 3.12.7 |
| Tetralith | 3.10.4 |
Reminder
- Run the script on your HPC cluster using
python(now: with the modules loaded). What is the error message now?
Answer
| HPC Cluster | Will turtle work with modules loaded? |
|---|---|
| Alvis | ? |
| Bianca | Never |
| COSMOS | Yes |
| Dardel | TODO |
| Kebnekaise | ? |
| LUMI | ? |
| Pelle | Yes |
| Rackham | Yes |
| Tetralith | Yes |
Here is the error:
[richel@sens2025560-bianca ~]$ python my_turtle.py
Traceback (most recent call last):
File "my_turtle.py", line 2, in <module>
wn = turtle.Screen() # Creates a playground for turtles
File "/usr/lib64/python2.7/lib-tk/turtle.py", line 3552, in Screen
Turtle._screen = _Screen()
File "/usr/lib64/python2.7/lib-tk/turtle.py", line 3568, in __init__
_Screen._root = self._root = _Root()
File "/usr/lib64/python2.7/lib-tk/turtle.py", line 458, in __init__
TK.Tk.__init__(self)
File "/usr/lib64/python2.7/lib-tk/Tkinter.py", line 1745, in __init__
self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use)
_tkinter.TclError: no display name and no $DISPLAY environment variable
[richel@cosmos2 ~]$ python my_turtle.py
Traceback (most recent call last):
File "/home/richel/my_turtle.py", line 2, in <module>
wn = turtle.Screen() # Creates a playground for turtles
File "/usr/lib64/python3.9/turtle.py", line 3664, in Screen
Turtle._screen = _Screen()
File "/usr/lib64/python3.9/turtle.py", line 3680, in __init__
_Screen._root = self._root = _Root()
File "/usr/lib64/python3.9/turtle.py", line 435, in __init__
TK.Tk.__init__(self)
File "/usr/lib64/python3.9/tkinter/__init__.py", line 2270, in __init__
self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use)
_tkinter.TclError: no display name and no $DISPLAY environment variable
richelbi@login1:~> python my_turtle.py
Traceback (most recent call last):
File "my_turtle.py", line 1, in <module>
import turtle # Allows us to use turtles
ImportError: No module named turtle
To fix:
richelbi@login1:~> module load miniconda3
Lmod is automatically replacing "cpeGNU/24.11" with "PrgEnv-gnu/8.6.0".
Lmod is automatically replacing "cce/18.0.1" with "gcc-native/12.3".
Lmod is automatically replacing "PrgEnv-cray/8.6.0" with "cpeGNU/24.11".
Due to MODULEPATH changes, the following have been reloaded:
1) cray-libsci/24.11.0 2) cray-mpich/8.1.31
However, this still fails:
richelbi@login1:~> conda install turtle
EnvironmentNotWritableError: The current user does not have write permissions to the target environment.
environment location: /pdc/software/24.11/eb/software/miniconda3/25.3.1-1-cpeGNU-24.11
uid: 3222772
gid: 3222772
TODO
b-an01 [~]$ python my_turtle.py
Traceback (most recent call last):
File "my_turtle.py", line 1, in <module>
import turtle # Allows us to use turtles
File "/usr/lib/python2.7/lib-tk/turtle.py", line 107, in <module>
import Tkinter as TK
File "/usr/lib/python2.7/lib-tk/Tkinter.py", line 42, in <module>
raise ImportError, str(msg) + ', please install the python-tk package'
ImportError: No module named _tkinter, please install the python-tk package
[richel@pelle2 ~]$ python my_turtle.py
Traceback (most recent call last):
File "/domus/h1/richel/my_turtle.py", line 2, in <module>
wn = turtle.Screen() # Creates a playground for turtles
File "/usr/lib64/python3.9/turtle.py", line 3664, in Screen
Turtle._screen = _Screen()
File "/usr/lib64/python3.9/turtle.py", line 3680, in __init__
_Screen._root = self._root = _Root()
File "/usr/lib64/python3.9/turtle.py", line 435, in __init__
TK.Tk.__init__(self)
File "/usr/lib64/python3.9/tkinter/__init__.py", line 2270, in __init__
self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use)
_tkinter.TclError: no display name and no $DISPLAY environment variable
[richel@rackham2 ~]$ python my_little_turtle.py
Traceback (most recent call last):
File "/domus/h1/richel/my_little_turtle.py", line 2, in <module>
wn = turtle.Screen() # Creates a playground for turtles
File "/sw/comp/python/3.10.8/rackham/lib/python3.10/turtle.py", line 3664, in Screen
Turtle._screen = _Screen()
File "/sw/comp/python/3.10.8/rackham/lib/python3.10/turtle.py", line 3680, in __init__
_Screen._root = self._root = _Root()
File "/sw/comp/python/3.10.8/rackham/lib/python3.10/turtle.py", line 435, in __init__
TK.Tk.__init__(self)
File "/sw/comp/python/3.10.8/rackham/lib/python3.10/tkinter/__init__.py", line 2299, in __init__
self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use)
_tkinter.TclError: no display name and no $DISPLAY environment variable
[richel@rackham2 ~]$
[x_ricbi@tetralith3 ~]$ python my_turtle.py
Traceback (most recent call last):
File "/home/x_ricbi/my_turtle.py", line 2, in <module>
wn = turtle.Screen() # Creates a playground for turtles
File "/usr/lib64/python3.9/turtle.py", line 3664, in Screen
Turtle._screen = _Screen()
File "/usr/lib64/python3.9/turtle.py", line 3680, in __init__
_Screen._root = self._root = _Root()
File "/usr/lib64/python3.9/turtle.py", line 435, in __init__
TK.Tk.__init__(self)
File "/usr/lib64/python3.9/tkinter/__init__.py", line 2270, in __init__
self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use)
_tkinter.TclError: no display name and no $DISPLAY environment variable
The error is no display name and no $DISPLAY environment variable.
In simpler terms, this can be read as 'Nothing to show graphics with'.
The solution is to login to your HPC cluster with X forwarding enabled. For sensitive data HPC clusters, this means running a terminal within a remote desktop environment.
Exercise 3: Running a first program¶
Now we try to make this script work!
Read:
Now, try to get the script to work.
When running the code, there should be a visible pop-up window. If not, re-read the UPPMAX documentation page 'Login to Rackham' and enable X-forwarding. If X-forwarding does not work, use the Rackham remote desktop environment.
Need more hints?
The exercise is about practicing to search for an UPPMAX module, hence giving away the answer makes this session useless.
However, if you feel stuck too much, you can watch a video in which this exercise is done
- Log in to your HPC cluster using SSH with X forwarding. How does it look? For sensitive data HPC clusters, use a remote desktop environment, as X is disabled.
Answer
This is how to log in with X forwarding enabled:
| HPC Cluster | Python version |
|---|---|
| Alvis | ssh -X sven@alvis1.c3se.chalmers.se |
| Bianca | You cannot. Instead, start a terminal from a remote desktop |
| COSMOS | ssh -X sven@cosmos.lunarc.lu.se |
| Dardel | ssh -X -i ~/.ssh/id-ed25519-pdc svensv@dardel.pdc.kth.se |
| Kebnekaise | ssh -X sven@kebnekaise.hpc2n.umu.se |
| LUMI | ssh -X -i ~/.ssh/id_rsa_lumi svensson@lumi.csc.fi |
| Pelle | ssh -X pelle@rackham.uppmax.uu.se |
| Rackham | ssh -X sven@rackham.uppmax.uu.se |
| Tetralith | ssh -X x_svesv@tetralith.nsc.liu.se |
It looks like this:
