I had one problem with R stuido in the server i.e, I am trying to run the genomic prediction of my work in the R stuido server but, serval times I had a problem related to "CPU" and the error message is below. Would you please help me How I will solve this problem?
Thanks.
Error in makeRestartList(...) : reached CPU time limit
En complément, le problème se pose en utilisant la fonction BGLR du package R du même nom. Elle est censée faire une analyse bayésienne sur un jeu de données un peu important (quelques dizaines de milliers d'individus phénotypés, avec un modèle linéaire mixte comprenant une demi douzaine d'effets fixes ou aléatoires).
L'analyse tourne correctement quelques minutes avant de donner le message d'erreur indiqué.
On a essayé setTimeLimit(cpu = Inf) mais ça n'a rien changé.
Merci !
Hello,
We set limit-cpu-time-minutes=60 to prevent long compute on this server more dedicated to interactive work.
I don't know precisely why it failed after some minutes..
Could you try to launch your job/script on the cluster with Slurm ?
Moreover, you will benefit of the computing power of the cluster without time limit (at least much higher).
Hi
I had the same error message on the RStudio server after ~2 minutes computing, but I am using R packages doParallel and foreach, which 25 CPUs. I guess the CPU time limit takes into account the product of the number of CPUs and the actual time.
@dbenaben , is this the case ?
Thanks
Jacques
Hello @jvanhelden ,
I must admit that I don't know where this error comes from, and if limit-cpu-time-minutes is really effective... 
I didn't find anything relevant in the logs or in the documentation.
Your jobs seems to run, so...
Actually I am running the jobs on the command line (Rscript), so I guess I escaped the limit-cpu-time-minutes setting, which affects the RStudio environment.
If that can help, here a little tutorial to migration from RStudio to Rscript:
https://ifb-elixirfr.gitlab.io/cluster/doc/r/