AutodE only runs as an interactive job

[ATsybizova]

Dear AutodE community,
I have been testing AutodE on our university cluster for quite a bit, and I have only managed to run it as an interactive job. My understanding that this should not be the case, however whenever I am submitting it as a batch job, I get the following error:

qt.qpa.xcb: could not connect to display localhost:16.0
qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.
This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.

Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, webgl, xcb.

/var/spool/slurm/slurmd/state/job60065625/slurm_script: line 15: 86830 Aborted                 python input.py

It seems as if autodE tries to open a graphical window and fails when the job is submitted to the queue. Do you have any idea where the Qt dependency comes from? I could not find any mentioning of qt in the autodE documentation.

To Reproduce
I am using a simple Diels-Alder reaction as a test, and here are my input file and submission script:

import autode as ade

ade.Config.hcode = 'orca'
ade.Config.n_cores = 8
ade.Config.max_core = 500

rxn = ade.Reaction("C=CC=C.C=C>>C1=CCCCC1", name="DA")
rxn.calculate_reaction_profile()

Submission script:

#!/bin/bash

#SBATCH -n 8
#SBATCH --time=30:00
#SBATCH --mem-per-cpu=200
#SBATCH --tmp=4000                        # per node!!
#SBATCH --job-name=analysis1
#SBATCH --output=analysis1.out
#SBATCH --error=analysis1.err

module load  gcc/8.2.0 python/3.9.9
module load libxkbcommon/0.8.0 xcb-util-wm/0.4.1 xcb-util-image/0.4.0 xcb-util-keysyms/0.4.0 xcb-util-renderutil/0.3.9
source $HOME/autode_env/bin/activate
module load orca/5.0.3
python input.py

Expected behavior
Calculated reaction profile

Environment
Operating System: Linux CentOS 7
Python version: 3.9
autodE version: 1.3.5

[t-young31]

autodE uses matplotlib to render pdf profiles, which needs a backend. if there isn't one I think you should just be able to do

conda install -c conda-forge matplotlib

[ATsybizova]

Unfortunately, I cannot use conda on our cluster.
I loaded tk/8.6.10 separately, however, the calculation resulted in the same error message.

[t-young31]

annoying!

what's this line for? can it be removed?

module load libxkbcommon/0.8.0 xcb-util-wm/0.4.1 xcb-util-image/0.4.0 xcb-util-keysyms/0.4.0 xcb-util-renderutil/0.3.9

looking at the error (qt.qpa.xcb: could not connect to display localhost:16.0) it seems like it's complaining about xcb?

[ATsybizova]

Huh, it seems that line does not affect anything. I removed it and got the same error. Originally I thought I need to load these additional modules exactly because autodE complained about xcb

[t-young31]

I've got no experience with installing autodE without using conda for the dependencies so I'm not sure what to suggest. maybe pip install matplotlib will bring in qt?

[kjelljorner]

I'm fairly sure that you can change the backend using the environment variable: https://matplotlib.org/stable/install/environment_variables_faq.html#envvar-MPLBACKEND