---
# System prepended metadata

title: PDC Intro Fall 2024

---

### PDC Introduction fall 2024
----------------------------

**Date:** 27th September 2024.
**Time:** 9:00 to 12:00 Local Time in Stockholm (CET).
**Place:** Online via Zoom. https://kth-se.zoom.us/j/66240368629


## Schedule

| General introductions                                  | Time          | Presentations                                 | Presenter  |
|--------------------------------------------------------------|---------------|-----------------------------------------------|------------|
| Welcome     | 9:00 - 9:05   |       | Juan de Gracia     |
| First presentation: Introduction to PDC environment.     | 9:05 - 9:45   | - How to login and module environment.       | Henric Zazzi     |
|                                                              |               | - Best practices.                            |            |
|                                                              |               | - Intro to slurm.                            |            |
|                                                              |               | - ThinLinc.                                  |            |
| 15 min break                                                 |               |                                               |            |
| Second presentation: Using python in Dardel.                 | 10:05 - 10:45 | - Using python in Dardel                    | Juan de Gracia        |
|                                                              |               | - Jupyter notebooks and conda environments.  | Juan de Gracia      |
| 15 min break                                                 |               |                                               |            |
| Third presentation: Singularity                              | 11:00 - 11:45 | - Singularity                                | Henric Zazzi     |
| Wrap-up                                                      | 11:45 - 12:00 | - Q and A.                                   | All        |


## Important links

Repository for presentations and labs: 
https://github.com/PDC-support/pdc-intro

### Course material

#### PDC Introduction lecture
https://drive.google.com/file/d/103l91XsHZ0QUNfU3-gBWGsLTMvqjx8mx/view?usp=sharing

#### Python virtual environments
https://drive.google.com/file/d/1K5w1pe0YllwbYHTOrhRwDFCvjmrGpeMJ/view?usp=share_link

#### Introduction to singularity lecture
https://drive.google.com/file/d/1Pi-hy5evDM5H-FBl01_PE9yHDOMMgLqc/view?usp=sharing

### Evaluation form
[Click here](https://forms.gle/hUgTecPkkmPnNjx8A)


## Support information

### PDC web portal
https://www.pdc.kth.se/

### Client software for kerberos installation

https://www.pdc.kth.se/support/documents/login/login.html#step-by-step-login-tutorial

### NAISS rules for applying to allocations

https://www.naiss.se/allocations/

### SUPR portal to submit proposals

https://supr.naiss.se/

## Questions

### Day 1: 
#### How to login and module environment
**Post your questions here:**
Example:
Q: *How do I log in with SSH?*
A: *We will answer here*

Q: I have a Windows computer, I managed to install dardel on WSL but not on Windows. Any tips (I tried to follow the PDC help page but I didn't succeed)?
A: what method did you try to access to Dardel, ssh keys or kerberos system?
Q: Kerberos
A: what error did you get? Did you install NIM (Network Identity Manager) ?
Q:Yes I installed NIM. I don't remember the error, I can try again during a break. I tried the ssh keys as well, but it didn't work either way.
https://www.pdc.kth.se/support/documents/login/windows_login.html#install-and-configure-kerberos-and-ssh-for-windows
A: OK, we can use a break room during the break if you want
Q: great, thank you!

Q:Is it possible to use Dardel in Visual Studio Code? (like creating a tunnel?)
A: yes, it is possible with creating ssh-tunnel
Q: Is there any resource to learn how to create ssh tunnel with VSC?
A: you need to check the website of VS code as the settings are mostly done on local computer, e.g.
https://code.visualstudio.com/docs/remote/tunnels
If you encouter any issues, you can send in support tickets to support@pdc.kth.se

Q: I have recently got a Dardel account. I would like to login to Dardel account in Ubuntu termial and I am using the command as suggested to login: ssh <username-at-pdc>@dardel.pdc.kth.se. I get an error after this command:  Permission denied (publickey,gssapi-keyex,gssapi-with-mic). I have key already registered. What can I do ?
A: The error is too general to figure the issue. Can you go to break room to show more details, or send email to support@pdc.kth.se ?
Ok, i will do that. Thank you.
    
    
#### Using python in Dardel
**Post your questions here:**


#### Python and virtual environments
**Post your questions here


#### Singularity
**Post your questions here:**

#### nf-core pipelines
Q: I'm having troubles running nf-core pipelines (https://nf-co.re/pipelines/) on DARDEL. The main problems I see is the versions of java, singularity and nextflow. I've tried following this tutorial: https://nf-co.re/configs/pdc_kth with limited success. For comparison, on UPPMAX loading 2 modules is enough `ml bioinfo-tools nextflow`.

A: It would be good if you send a support ticket with all the details (module list,error messages etc.) so we can take a closer look. 
A: Will do! Cheers