---
tags: user support coffee break
---

# Weekly CSC coffee break

:::danger
**Link to this HedgeDoc:** https://siili.rahtiapp.fi/weekly-user-zoom
**Link to this page:** https://hackmd.io/@CSC-research-support/support-session
Introduction slides: https://a3s.fi/usersupportsession/First%20meeting%20info.pdf
Link to feedback: https://link.webropolsurveys.com/S/94AB9F77D8EFF054
**Link to archive:**
https://hackmd.io/@CSC-research-support/weekly_session_archive
:::

**Contents of this documents and quicklinks**
[TOC]

:::success
This is the Q&A info page for the CSC's open support session organised every **Wednesday at 14:00** in Zoom (see link at: https://ssl.eventilla.com/usersupportcoffee) to discuss current issues in CSC services and to provide direct support for our users. You can submit your questions beforehand or during the session, or check what others have asked!
You can ask both in English and Finnish - or any other language our specialists speak :)
Note that if you are typing a question in here, we expect you to join the Zoom session :) Otherwise, probably best to send a support request to [e-mail] !
:::

You can think of these sessions as walking into our office to ask for help. If you are not sure whether we can help you, come and chat with us anyway and we can figure out a solution together!

Join the coffee session, if you want to:
* Get started with CSC services
* Solve problems
* Discuss and figure out what your problem really is
* Brainstorm the best uses of our services in your work
* Work with someone on your issues in real time
* Network with others who are doing similar work and learn something new

:::info
:bulb: **Hint:** HackMD is great for sharing information! To edit, switch to Edit mode (the pencil) or Both mode (the two boxes) on the top left corner. **It's like a Google doc**: it allows simultaneous editing, but code formatting is made nice & easy with MarkDown: just add 3 ticks (``` ` ```) for the``` code blocks ```. Might look scary, but this is very easy to use! Scroll to the bottom of the page for a "testing area"
:::

:::success
:bulb: **Tip:** Did you know that we have self-learning courses on several topics?
* [Getting started with CSC computing services](https://e-learn.csc.fi/course/view.php?id=75)
* [CSC Computing Services](https://e-learn.csc.fi/course/view.php?id=76)
* [Research Data Management](https://e-learn.csc.fi/course/view.php?id=63)
:::

[ToC]

## Code of conduct

We strive to follow the [Code of Conduct developed by The Carpentries organisation](https://docs.carpentries.org/topic_folders/policies/code-of-conduct.html) to foster a welcoming environment for everyone. In short:
- Use welcoming and inclusive language
- Be respectful of different viewpoints and experiences
- Gracefully accept constructive criticism
- Focus on what is best for the community
- Show courtesy and respect towards other community members

---
## Recordings, slides etc material from short talks

7.9. Puhti web interface ([recording](https://video.csc.fi/media/t/0_j18nkvvh))
14.9. LUMI ([slides](https://a3s.fi/mlehtiva-2004306-pub/LUST_CSC_coffee_break_20220914.pdf), [recording](https://video.csc.fi/media/t/0_bz8m2kbn))
21.9. CSC Notebooks ([slides](https://a3s.fi/mlehtiva-2001659-pub/CSC_Notebooks_Sept2022.pdf), [recording](https://video.csc.fi/media/t/0_uhgggpml))
28.9. Puhti OS update ([slides](https://a3s.fi/swift/v1/AUTH_53f5b0ae8e724b439a4cd16d1237015f/mlehtiva-2001659-pub/RHEL8-flash.pdf))
5.10. Tykky ([slides](https://a3s.fi/swift/v1/AUTH_53f5b0ae8e724b439a4cd16d1237015f/mlehtiva-2001659-pub/tykky.pdf), [recording](https://video.csc.fi/media/t/0_3qy1o8uv))
12.10. SD services (slides, [recording](https://video.csc.fi/media/t/0_yde0f1iq) )
19.10. No short talk (autumn holidays)
26.10. Machine Learning guide (no slides, all information in [docs](https://docs.csc.fi/support/tutorials/ml-guide/), [recording](https://video.csc.fi/media/t/0_na3upt7e))
2.11. CSC cloud services Pouta and Rahti ([slides](https://cloud-solutions.a3s.fi/researchsupportweeklyzooms/index.html), [recording](https://video.csc.fi/media/t/0_auvrto32))
9.11. Workflows and Hyperqueue ([recording](https://video.csc.fi/media/t/0_1u744x4n))
16.11. CSC training materials

### General and practical matters

- [x] **Q1: I have difficulty pasting my questions into HackMD (here). Do you have some instructions on how to write here?**

- A: Can you see these three icons on top left corner, next to HackMD text? There’s pencil, this side-by-side symbol, and an eye. In eye view, you can’t edit, you are just viewing. The other two reveal the markdown (MD) version of the page, which you can edit. I find it easiest to edit with the side-by-side view.
:::info
:bulb: **Hint:** You can also apply styling from the toolbar at the top :arrow_upper_left: of the editing area.
:::

- [x] **Q2: What is the correct reference form for acknowledge CSC in a scientific publication?**
- A: See here how to cite CSC in a paper: https://docs.csc.fi/support/faq/how-to-cite-csc/

:::warning
**You can find all previous questions and answers here:**
https://hackmd.io/@CSC-research-support/weekly_session_archive
:::

## 2022-11-09 session

Short talk: Workflows and hyperqueue

### CSC Specialists available

Maria Lehtivaara - Host, Bio stuff :)
Maria Dimitrova - Co-host
Rasmus Kronberg - Short talk about workflows & hyperqueue
Mats Sjöberg - Machine learning
Anni Järvenpää - Language bank

### Room and topic

Room 1 - Tykky & LUMI, Rasmus
Room 2 - VSCode & ssh connection to Puhti, AnniJ, MariaD, Laxman & Mats
Room 3 -

### Questions:

**Q38:** Where are we to find the other questions (<Q38)? Thanks!
A: In the archive! Link is in the box at the top of this document, and here: https://hackmd.io/@CSC-research-support/weekly_session_archive

**Q39:** How can I download NDVI data from NASA MODIS database? https://lpdaac.usgs.gov/products/mod13q1v006/ I have gps coordinates of my study sites and need to extract NDVI values from a given time period for these for further analyses. I have trouble getting the data downloaded in raster format that I could use. Or perhaps there is some R code ready that can be used for this, as I will be continuing analyses in R (package LEA)?
**A:** There seems to be some instructions for R here: https://rspatial.org/terra/modis/2-download.html and here: https://flograttarola.com/post/modis-downloads/ (no experience with them though). In the latter there is some possibility to define the output format which might help?

**Q40:** Do you have container wrapper tykky on Lumi? & which workflow tools do you have here?
A: Yes, https://docs.lumi-supercomputer.eu/software/installing/container-wrapper/. Although it is not named Tykky, it is basically the same tool. Regarding workflow tools, HyperQueue is projected to be on LUMI at some point. Latest versions of the program also support dependencies, although only through the Python API.

**Q41:** I used Visual Studio Code to connect to puhti.csc.fi but since last week I am not able to connect anymore. I haven't been able to solve the solution myself. (x2)
A: After the RHEL8 operating system update, the public key of the server has changed, making the ssh client suspect that you are not connecting to the intended machine but to a possibly malicious agent instead. To remove the outdated key from your computer, remove "puhti.csc.fi" lines from `.ssh/known_hosts` file. On unix machines the `.ssh` directory is usually found in your home directory, on Windows machines it typically is in `C:\Users\<username>\.ssh` unless a program has saved it to a specific location.

**Q42:** One RT ticket discussed in main room :) Hyperqueue might be the solution there.

Q43: It would be helpful for the newbies like me if there was an example of how to write a batch job to execute a Jupyter notebook (using Tensorflow for high intensive deep learning). Thanks in advance!
A: Good idea! Unfortunately I cannot join the call today, but you could take a look at the papermill tool. I can try to create some examples on how to use it on Puhti when I have some more free time. If you send a request to [e-mail] I can reply to you directly there once I have some examples ready.

**NOTE: 16.11. notes in [HedgeDoc](https://siili.rahtiapp.fi/s/weekly-user-zoom)!!!**

## Test area for HackMD first timers

Just type here :)
pllaaplaa **plaa** *plaplaa* `pllaplaa`

**Please add an "o" if you found this place and can edit the document**
I can edit here: oooo oo

Testings testings

Test area ending here :)

---

:::danger
**Please give us feedback:** https://link.webropolsurveys.com/S/94AB9F77D8EFF054
:::