Questions and answers from HPC on-boarding Apr 2023, Day 0 (Apr 18)

Icebreaker Question 

Have you used HPC before
- Yes - 0000000000
- No - 00000000
Do I need to log in here or do I remain anonymous?

Sessions 

https://documentation.sigma2.no/training/events/2023-04-hpc-on-boarding.html

What are the methods you know for interacting with a computer ?

Talking to it
Using terminal, using mouse and keyboard, GUI programs, USB/CDs/other storage devices
Typing with a keyboard
Using an on-screen keyboard
GUI
Hitting it with a wrench :laughing:
Tactile screens
navigate in 3D space :)
internett or similar protocols, coding, sequential operations via suite

Have you found the terminal 

I have found the terminal: 00000000000000000000o
I have not found the terminal:
I am lost, what you mean by terminal:

Have you found SSH 

Use the interactive document to vote for

I have ssh 000000000000
I do not have ssh 0
- Do you have windows, linux or mac? Windows 11
  - https://learn.microsoft.com/en-us/windows-server/administration/openssh/openssh_install_firstuse?tabs=gui
    - Thanks, I’ll try it in a break, and use git for now
    - By the way, you only ned OpenSSH Client, not server
    - I’ll have to try as an admin later, since the ‘easy way’ of installing isn’t working now. But at least I can access with GitBash, so no real issue for today. Thanks for the help!
I am lost, what you mean by ssh

*Affirmative USER SSH is a protocol for connecting securely to remote resources and the corresponding tools. For unix-type operating systems this protocol is integrated, for Windows it comes as a plugin/add-in. Basically it is a way to log in to a remote resource in a secure way. (coded connection). We typically use it as “log in to a remote machine” type statement.

Have you connected to FRAM?

yes:00000000000000000
no:

Account/username/password problems 

The access to the sigma is being denied for me (my username: ******). I have changed the password, waited for 20 minutes, repeated the login but still the access is denied.
- Ok, you just recently changed it?
- First, I tried to login with the password from yesterday session, the access was denied, then I changed, but still the access was denied. Yesterday everything worked fine.
- Are you 100% sure that you typed the correct password? :) You said you managed to log in yesterday with the default password right?
- I managed to login in yesterday with a changed password, which did not work today morning. Then I do suspect you might have typed the wrong password. Could you check that, and also type in cleartext to see what you are typing - otherwise, maybe try to change the password again
- Ok.
It seems I have a problem with the username and therefore my password does not work. I was told my username is ****** but in the terminal I have to write it as with capital first letter. Then, my password is not recognized, so I couldn’t log in.
- Your username is in small caps. What platform/operating system are you coming from? Windows has this tendency of always putting capital letters on first letter disregarding.

Have you managed to download the demo-moving-around folder:

yes: 00000
no:
- What is the problem with copy and paste?
- You can paste into terminal by right-clicking on the line, no menu will pop-up NOW IT WORKS - good! :)
- Windows key + v will let you select from several of the last things you copied too

Session: Composing commands with pipes 

Have you managed to download the exercise-pipes folder and untar it?
- yes:
- no:

Ask Your Questions 

What is ssh ? 2. The course material explains a bit what ssh is: https://training.pages.sigma2.no/tutorials/unix-for-hpc/episodes/intro.html#what-is-ssh-secure-shell - it is basically a program that allows save connection between computers
Terminal opens as ‘windows powershell’ 3. Did ssh -V work? No, neither in powershell or command prompt (Windows 11). Commands work in Gitbash for proceeding for now. :+1:
What is the difference between command prompt and windows powershell?
- Windows powershell is a command prompt
- Each operating system wil have their own flavor of command prompt/terminal
- On windows, by default, you have both CMD and PowerShell, both will work for this course
Are there any reasons for customizing the prompt? For instance security related?
- Put some color on that prompt, it will likely improve visibility. :) Also, you might be interested in hiding or showing some info depending on what’s important to you.
- Mostly just aesthetical/informational for yourself, and for instance not having a too long prompt if that disturbs you
I do not have password for fram, can I use Fox?
- Yes, you can follow us on Fox
- Got it to work now in Fram too - I am happy :-) :+1:
Install ssh on windows
When we create a sigma2 account is there anything specific we should use as “project”?
- nn9987k
Best way of finding commands: Ask chatGPT :)
- Yes ,that is of course one option nowadays!
what command show invisable files?
- You could check man ls, it is stated there
- ls -a for “all” - shows invisible (dot) files
From where is / how do you use that terminal_hist program?
- That is not a UNIX inbuild command and some thing Sabry made to help show what he typed last. Not well docuemented sorry.
- https://github.com/Sabryr/Terminal_hist
  - Thanks! I’ve starred it ;)
I got stuck after using the less program. Have a lot of lines starting with ~ and last line says (END). How can I get out of this? (GitBash on Win10)
- try pressing the ESC key
- did not help
- sorry: the q key
- Thank you :-)
  - 👍
wget https://gitlab.sigma2.no/training/tutorials/unix-for-hpc/-/raw/master/content/episodes/moving-around/exercise-moving-around.tar.gz is not working on the remote server due to “ERROR: cannot verify gitlab.sigma2.no’s certificate, issued by ‘/C=US/O=Let’s Encrypt/CN=R3’: Issued certificate has expired”. The same command works fine on a local terminal, though. SAME HERE SAME PROBLEM
- The workaround is in the error message itself (use at own risk, I guess): add --no-check-certificate between wget and the URL. Strange that the certificate works for a file but not for the other…
- It is not that it works for some files and not others, but that we have not updated the wget command everywhere in the tutorial with the added --no-certificate-check everywhere. Once the certificate on site is renewed there will be no need for this extra option. Sorry for that!
share screen is disabled in breakout room?
- Allowed for all now :+1:
What happens if we dont have the permission for editing the text file?
- If there is read permission, then you can make a copy somewhere you have permission and then edit
- The person that owns the file needs to give you permission to write to it, or if you are the owner, you need to move it to a place that you have write permissions if you for instance happen to be in a place where you do not have write permission
When I try to use ssh in the windows terminal nothing happens, so I have to use GitBash.
- Does it work with gitbash?
- Yes
- Ok, all good then for you? Which operating system are you on windows 10/11?
- Win 10 with OpenSSH_for_Windows_8.1p1, LibreSSL 3.0.2
- did you restart the terminal after installing ssh?
- ssh was already installed, this is standard UiO desktop PC
- when I do the ssh MY_USER_NAME@saga.sigma2.no (with my user name) just nothing happens
- Is not SAGA down for maintenance now?
- yes. SAGA not available, Please use fram
- From organizer: Workarounds are - using X2Go (see https://documentation.sigma2.no/getting_started/remote-desktop.html?highlight=x2go) or Visual Studio Code (see https://documentation.sigma2.no/code_development/guides/vs_code/connect_to_server.html?highlight=visual%20studio%20code)

Sorry, but fram does not work either from the terminal - but from GitBash
so you are ok with that, gitbash works as expected?
Yes, have been using it for the whole session, but would be nice to be able to use the integrated terminal
understand, then it will be better that we try to find out this with either a zoom session or sending some screenshots to understand what is going on. Which number OS are you on? Windows 10 or 11 ?
Windows 10, I can contact the helpdesk later
Good, do that, good luck.
Are you using a managed machine? (from uit, uio, etc?) I know that at least this is slightly problematic at UiT machines, and an admin need to activate it.
Yes, UiO managed, no fun ;-)
Got this with fram: M:>ssh USER@fram.sigma2.no The authenticity of host ‘fram.sigma2.no (2001:700:4a00:10::2:2)’ can’t be established. ECDSA key fingerprint is SHA256:4z8Jipr50TpYTXH/hpAGZVgMAt0zwT9+hz8L3LLrHF8. Are you sure you want to continue connecting (yes/no/[fingerprint])? Host key verification failed.

When i type tar xzvf finding.tar.gz, I receive the following message tar (child): finding.tar.gz: Cannot open: No such file or directory tar (child): Error is not recoverable: exiting now tar: Child returned status 2 tar: Error is not recoverable: exiting now

you are probably in the wrong folder, do ls to see if the file is there, and pwd to find out where you are
I am in my home directory
where did you wget (download) finding.tar.gz to? If you dont remember you can do cd then find ./ -name finding.tar.gz to find out where it was. If you did not download it, follow the procedure in the tutorial to download with wget and untar it with tar according to the tutorial
Okay, I did the process again and it works now. Thank you :) :+1:

When I try to access the cd exercise-moving-around I get an error that no such file or directory exists. When I type ls I see there is an object called exercise-moving-around.tar.gz in there. When I try to drite cd exercise-moving-around.tar.gz I get an error again saying that it is not a directory
- Can you please use ls and see if the directory is there. And use pwd see where you are
  - pwd command tells me I’m in cluster/home/username
- Did you issue the command tar xvf demo-moving-around.tar.gz ?
  - No. After I did it it worked! Thanks! (didn’t know about the zipping thing)
  - Just follow the tutorial instructions, where the full list of commands (wget and then tar) is shown in the note: https://training.pages.sigma2.no/tutorials/unix-for-hpc/episodes/moving-around.html (and similarly for the other sessions/exercises)
link to exercise?

https://training.pages.sigma2.no/tutorials/unix-for-hpc/episodes/pipes.html#exercise

What does bash mean?
- Bourne again shell
How important is to use #!/bin/bash at the beginning of the file
- It is quite useful if you want to run your file by just typing ./your-file.sh. You can replace it by #!/bin/python for example. The file extension is not really a “thing” in linux, so you can call your bash script “test.py” if you want. or your python script “test.sh”. Running ./my_python_script.py will work if the first line is #!/bin/python, otherwise you will have to run python my_python_script.py
- #!/bin/bash means that bash is the program to run the script if no program is specified
This was really helpful, thanks!

Great support and help accessing FRAM! Great lectures and exercises and help in the breakout rooms! Thank you! It was a great lecture! See you tomorrow :) Having enough people to answer questions in real time Good documentation to support both copying and catching up if someone gets temporarily lost I really like the Hedgedoc format for asking and answering questions, working collaboratively No shame for asking dumb questions Thank you for the course, I am really happy you made a course at this basis level for us who know to little about Unix

what to improve 

Share command line navigation hints at the beginning - ctrl + a to get to the beginning of a line was very helpful Send info about how to test if your login works with the initial email