SE xtb job with submission to cluster via SGE scheduler

[tanoury1]

Hi, I'm trying to run a SE xtb job using pyGSM. I have used GSM for several years and am switching to pyGSM.
In addition to the SGE stuff required for my submit script, I am using:

gsm -xyzfile reactants.xyz
-isomers isomers.txt
-mode SE_GSM
-package xTB_lot
-ID $SGE_TASK_ID
-coordinate_type DLC > log 2>&1

ID=printf "%0*d\n" 4 ${SGE_TASK_ID}

In my error file, I'm getting
"File "/cluster/home/tanoury/.local/lib/python3.7/site-packages/pyGSM-0.1-py3.7.egg/pygsm/level_of_theories/xtb_lot.py", line 8, in
from xtb.interface import Calculator
ModuleNotFoundError: No module named 'xtb'

When I try to run each line of xtb_lot.py in my conda environment in via command line, I'm getting:
(gsm) [tanoury@tanourylnx:~]$ python
Python 3.9.17 | packaged by conda-forge | (main, Aug 10 2023, 07:02:31)
[GCC 12.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.

import sys
from os import path
import numpy as np
from xtb.interface import Calculator
Traceback (most recent call last):
File "", line 1, in
File "/cluster/home/tanoury/miniconda3/envs/gsm/lib/python3.9/site-packages/xtb/interface.py", line 20, in
from typing_extensions import Literal
ModuleNotFoundError: No module named 'typing_extensions'

Additionally, when running an xtb job, do I need a "-lot_input_file"?

Thank you for your help.
Jerry

[tanoury1]

Hi, this is no longer an issues.

Jerry