HPC for training (INFO)

Fir Janick

• open ssh key format for the variant analysis training (conversion)
  https://man.openbsd.org/ssh-keygen

keygen by default creats a open ssh key type.

needed for some tools!

now we are using rsa keys

Accounts for the VSC

• Those with academic accounts (KULeuven, Ugent, UHasselt, Uantwerp)
  • Can request an VCS account, and this can be used in any of the HPCs (KUleuven, Ugent, VIB)
  • KULeuven HPC can create accounts for
    • KULeuven
    • UHasselt
    • Exeternal
  • Ugent HPC can create acconts for
    • UGhent
    • External

KULeuven Training services

Students have for training

• $SCRATCH :
  • for intermediate files, unused files are kept for 30 days
  • Keeps existing after training (space:?)
• $STAGING :
  • less space (space:500GB)
  • make sure students delete data afterwards

Reserve nodes for training

• Sending the specifics in advance
• Send list of participants in advance (priorities and data access if needed)

Training dataset

• Download estimated time: 1TB/hour
• If saved in Tier1 can be downloaded either in KULeuven or UGent
  • Long term storage
  • Easy sharing among diff. services
• If in KULeuven server
  • Can be open and shared with all
  • Can be restrict
  • Some internal data is only available for KULeuven students

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Training storage ≠ Group storage

For further analysis of own data, that might need large storage sutdents need to turn to Group storage offers intestad of the trainign setup ($$$)

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Ugent Training service

Issues and Solutions Ugent server

1. (issue september 2023) Participant has an account but its changing intitutions (from UGent to VIB) contract.

• can he still use the account during the training since is withing 1-2 weeks of the change
• can he already resquest another account?
• can we ask for his account to be kept funcitonal during the training?

Solution
a. Ask the HPC number so the procedure can be clarified with the HPC help desk, taking in account already the personal account in case is possible to keep account during training time.

b. HPC answered the account was already expired, so participant should ask a new VSC-id using the new institution e-mail (it took about 3 working days to answer and the student has 1 week time to activiate his account). If it is not the case of having already a new e-mail, the same solution for industry participants apply (see bellow).

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2. (issue september 2023)Participant joing from industry, cannot have an account request on regular request as in the website.

Solution
a. We request an account for them and the HPC will get in touch with them. PArticipant to be informed by e-mail. This observation should be sent in the 1st informative e-mail.

b. HPC answered they will create a mini Ugent account for the participant. For that they contacted the participant by e-mial and have kindly inlcuded Alex and me (Bruna) in CC.

Summary of the e-mail

Dear researcher,

Within the context of a workshop at VIB, we will give you access to the Tier2 HPC infrastructure of >Ghent University.

For this purpose, we have created a central UGent ‘welkom' account for you. >You should just now have received a ‘welkom’ invite mail from UGent.

By following the link in the mail, you should be able to choose a password for your username >'[e-mail]'.

(We advise to copy-paste the link in a New Private Browsing window.)

This username and password can then be used to log in on the VSC accountpage >https://account.vscentrum.be.

Don't forget to select ‘UGent’ as home institution.
Select a Research Field from the pull-down menu, and then you can choose to upload a public ssh key now >(upload one) or do it later (Submit without key).

3. (issue september 2023) Participant has created a SSH key but can't connect with VSCode

Participant msg:
I am facing some problems connecting to my VSC-HPC account.
So far I have created the public-private key pair as described here: https://www.ugent.be/hpc/en/access/faq/access#Howtocreateapublic/privatesshkeypair [ugent.be]?
and uploaded my public key on the VSC portal. I then tried to access my account through terminal, though I got this error:

ERROR MSG
PS C:\Users|____> ssh [e-mail]
[e-mail]: Permission denied (publickey,gssapi-keyex,gssapi-with-mic)

Solution
In this case, what is been observed is that students that create their SSH Key using Putty can not acces it from the command line, they can only access via the Putty interface or tool linked to it. To use it from VSCode command line they need to generate their key using the Linux/MAC instruction session from the instructions page. To do so they can use VSCode with WSL or GitBash.