sbatch FileNotFoundError

[Leimeroth]

While trying to install and setup pyiron on a new machine we got following error when trying to submit a simple Lammps test job:

FileNotFoundError: [Errno 2] No such file or directory: 'sbatch'

When submitting the job directly logged into the cluster using sbatch run_queue.sh it works fine, also when manually starting python and submitting using subprocess.check_output(["sbatch", "run_queue.sh"]) no problems occur. I highly appreciate any ideas what could cause this.

Maybe @jan-janssen has a hint for me?

[jan-janssen]

I presume it is related to the environment. Are you running pyiron from the command line or from a Jupyter notebook? Depending on how the Jupyter installation is configured there might be differences between what you get when you call !env on jupyter vs. env on the command line. In the background pyiron is calling sbatch in a very similar way to what you describe: https://github.com/pyiron/pysqa/blob/main/pysqa/wrapper/slurm.py#L24 we get the sbatch command and then we call it in

pysqa/pysqa/utils/basic.py

Line 412 in 72b8a2a

def _execute_command(

[Leimeroth]

Exporting the path to sbatch in the .bashrc on the cluster fixed it. This was not necessary for any other installation on our system so I am still somewhat confused why the path seems to be messed up in this case.

[jan-janssen]

@Leimeroth I just had a similar issue - Can you check if #201 helps?