Weekly CSC coffee break

Contents of this documents and quicklinks

• Weekly CSC coffee break
  • Code of conduct
  • Recordings, slides etc material from short talks
    • General and practical matters
  • 2022-11-09 session
    • CSC Specialists available
    • Room and topic
    • Questions:
  • Test area for HackMD first timers

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

• Weekly CSC coffee break
  • Code of conduct
  • Recordings, slides etc material from short talks
    • General and practical matters
  • 2022-11-09 session
    • CSC Specialists available
    • Room and topic
    • Questions:
  • Test area for HackMD first timers

Code of conduct

We strive to follow the Code of Conduct developed by The Carpentries organisation 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)
14.9. LUMI (slides, recording)
21.9. CSC Notebooks (slides, recording)
28.9. Puhti OS update (slides)
5.10. Tykky (slides, recording)
12.10. SD services (slides, recording )
19.10. No short talk (autumn holidays)
26.10. Machine Learning guide (no slides, all information in docs, recording)
2.11. CSC cloud services Pouta and Rahti (slides, recording)
9.11. Workflows and Hyperqueue (recording)
16.11. CSC training materials

General and practical matters

• 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.

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Hint: You can also apply styling from the toolbar at the top

Image Not Showing Possible Reasons

• The image file may be corrupted
• The server hosting the image is unavailable
• The image path is incorrect
• The image format is not supported

Learn More →

of the editing area.

• 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/

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 servicedesk@csc.fi I can reply to you directly there once I have some examples ready.

NOTE: 16.11. notes in HedgeDoc!!!

Test area for HackMD first timers

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Testings testings

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