Denied permission when running my srun command

HPC Support HPC issues
1

Hello all,

I am writing because I cannot run my script on the baobab2 cluster.

I tried with an old script that was working back then and I always have the same message:

srun: job 5815111 queued and waiting for resources

srun: job 5815111 has been allocated resources

srun: error: cpu001: task 0: Exited with exit code 13

slurmstepd: error: execve(): test.sh: Permission denied

Here is the .sh file I try to run :

#!/bin/sh

#SBATCH --partition=public-cpu
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=6000
#SBATCH --time=10:00:00


module load GCC/10.3.0  OpenMPI/4.1.1  R/4.1.0 nodejs

srun R CMD BATCH test_smartvote_GE_candidates.R

Am I doing something wrong here? Anyone else had this issue? Any idea how I could solve this?

Thanks a lot for all the help you can provide!!

2

Hi @Maxime.Walder

For the next time please create your post in category “HPC support > HPC Issue”.

Do you have a file name test.sh (maybe your sbatch file) ?

Could you give the output of :

ls -ls test.sh

It seems you have a permission issue on this file

3

Hi @Adrien,

Thanks a lot for your reply, and sorry for the misclassification, I’ll be more careful next time!

So the command you indicated gived the following:

1 -rw-r–r-- 1 walderm hpc_users 224 May 22 11:16 test.sh

What I don’t get is that it was working before, I just tried this because I was trying to run another code and it was not working, so I ran something that was working before and it gives the message indicatd above!

Many thanks!

4

Are you running your jobs like that ? :

srun test.sh

Using a sbatch file, you should use sbatch test.sh

Let me know if it’s working fine ?

5

Hi Adrien,

Thank you so much for helping me fixe! I had not used this for a while and confused the two commands. Using the sbatch command fixed it thank you!

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