Extend CPU limit for c3g_gmx project

IFB Core Cluster Gestion de comptes et de projets
1

Hello ,

While running a quite simple R code in the project c3g_gmx, I got the message error "reached CPU time limit"

Could I t be possible to extend?

Thank you +++

MSM

2

Hello,

There is no limit on CPU time.

However, a default account called "demo" is usable with limited CPU time.
You have to switch your default account to use a created one (c3g_gmx)

More information and procedure: https://ifb-elixirfr.gitlab.io/cluster/doc/troubleshooting/#explanation-1

3

Thank you for your answer.

If I undersand well, I am supposed to run this command
"# Remove (rm) or move (mv) RStudio files

mv ~/.rstudio ~/.rstudio.backup-2022-27-02

rm -rf ~/.rstudio
rm -rf ~/.local/share/rstudio
rm .RData"

but it gives me error in the syntax
"> # Remove (rm) or move (mv) RStudio files

mv ~/.rstudio ~/.rstudio.backup-2022-27-02

rm -rf ~/.rstudio
Error: unexpected '/' in "rm -rf ~/"
rm -rf ~/.local/share/rstudio
Error: unexpected '/' in "rm -rf ~/"
rm .RData
Error: unexpected symbol in "rm .RData""

Thank you for your help

MSM

4

Nope. You are supposed to run this command:

sacctmgr update user $USER set defaultaccount=c3g_gmx

Sorry if it wasn't clear

5

Thank you for your answer :slight_smile:

I got an error while running this commande (in R studio)

"> sacctmgr update user $USER set defaultaccount=c3g_gmx
Error: unexpected symbol in "sacctmgr update" "

6

You have to do this in a terminal (bash)

7

OK thank you :slight_smile:
And stupid question, how do I access to the terminal...?
Sorry and thank you for your help :slight_smile:

8
9

Thank you very much.
Using the Terminal in R I still have an error message =

"[mmeuleman@rstudio ~]$ sacctmgr update user $USER set defaultaccount=c3g_gmx
bash: sacctmgr: command not found"

thank ou for your help,

MSM

10

Please try with another terminal (SSH, with Jupyter...).

11

Hi,
I managed to change default account to the project c3g_gmx and still have the same error message
"Error in match.fun(FUN) : reached CPU time limit"

Could you help?

Thank you

12

Hi,

From my point of view, it's ok.
Could you relaunch your session or try with JupyterHUB (RStudio inside JupyterHUB) ?

13

Thank you for your answer.

I relaunch my session : It does not change anything.

I have never use JupyterHUB

I read here R / RStudio - IFB Core Cluster Documentation

That CPU is limited to 56, is it right?

Maybe that Is why I get this error message? (reminder : "reached CPU time limit")

So I tried to follow the advices on this page, and run my script for my terminal , with the following commands :

module load r/4.1.1

sbatch -A c3g_gmx --mem=200G --partition=fast --wrap "/shared/ifbstor1/projects/c3g_gmx/mmeuleman/C3G-GeoMx-MSM20231211/Script-20231212_MSM.R"

But I did not worked and got an error message, in R studio, saying "permission non accordée"

Could you help ?

Thank you a lot +++

Marie-Sophie