Problem launching Python job on Baobab

HPC Support HPC issues
1

Primary informations

Username: avilamar
Cluster: Baobab

Description

I want to submit a Python job on Baobab using a batch file and the command sbatch, but I get the following error:

Running main.py on cpu001.baobab
slurmstepd: error: execve(): Python: No such file or directory
srun: error: cpu001: task 0: Exited with exit code 2

Steps to Reproduce

My batch file is called main.sh and contains:

#!/bin/bash

#SBATCH --mem=3G
#SBATCH --cpus-per-task=1
#SBATCH --ntasks=1
#SBATCH --licenses=matlab@matlablm.unige.ch
#SBATCH --time=00:15:00
#SBATCH --mail-user=monika.avila@unige.ch
#SBATCH --partition=debug-cpu

module load GCCcore/8.3.0
module load Python

BASE_MFILE_NAME=main

unset DISPLAY

echo “Running ${BASE_MFILE_NAME}.py on $(hostname)”

srun Python ${BASE_MFILE_NAME}.py

Expected Result

I expect to obtain a job that is running

Actual Result

I get an error

Running main.py on cpu001.baobab
slurmstepd: error: execve(): Python: No such file or directory
srun: error: cpu001: task 0: Exited with exit code 2

I also replaced the las line of my batch file by

srun ${BASE_MFILE_NAME}.py

And in that case I get the mistake

Running main.py on cpu001.baobab
slurmstepd: error: execve(): main.py: Permission denied
srun: error: cpu001: task 0: Exited with exit code 13

2

Dear Monika,

It seems you just have a typo in your sbatch scripts. You call “Python” but the software name is “python” lowercase.

Best regards,

3

Thanks, Gael! You are very kind for taking the time to answer my post. However, it was not the upper or lower case that made a difference in my case. Actually, I solved the issue with the following line:

module load GCC/8.2.0-2.31.1 OpenMPI/3.1.3 Python/3.7.2 SciPy-bundle/2019.03

4

Hi Monika,
the module command lets you manage the software versions you want to use. In your case, you’re only loading a different version of python installed by default on the server.
According to the following tests, it’s python in lower case that works (regardless of the version used)

## check command
(baobab)-[alberta@login2 ~]$ Python --version
-bash: Python: command not found
(baobab)-[alberta@login2 ~]$ python --version
Python 3.6.8
(baobab)-[alberta@login2 ~]$ module load GCC/8.2.0-2.31.1 OpenMPI/3.1.3 Python/3.7.2 SciPy-bundle/2019.03
(baobab)-[alberta@login2 ~]$ Python --version
-bash: Python: command not found
(baobab)-[alberta@login2 ~]$ python --version
Python 3.7.2

## Launching job on debug-cpu
(baobab)-[alberta@login2 ~]$ srun Python --version
srun: job 9927929 queued and waiting for resources
srun: job 9927929 has been allocated resources
slurmstepd: error: execve(): Python: No such file or directory
srun: error: cpu001: task 0: Exited with exit code 2
(baobab)-[alberta@login2 ~]$ srun python --version
srun: job 9927931 queued and waiting for resources
srun: job 9927931 has been allocated resources
Python 3.7.2

Best Regards