doyle-lab-ucla / auto-qchem

Auto-QChem is an automated workflow for the generation and storage of DFT calculations for organic molecules.
https://doyle-lab-ucla.github.io/auto-qchem/
GNU General Public License v3.0
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How to compute dft on computing cluster? #3

Closed stephenokj78 closed 2 years ago

stephenokj78 commented 3 years ago

When I run sm.submit_jobs() in Tutorial_creating_descriptor_sets.ipynb file

An error like the message below occurs.

**UnexpectedExit: Encountered a bad command exit code!

Command: 'cd /scratch/a1422a01/gaussian && sbatch /scratch/a1422a01/gaussian/C15H24N4O6S2_e5f2_conf_0.sh'

Exit code: 1

Stdout:

Stderr:

sbatch: error: Batch job submission failed: Unspecified error**

As a result of checking the computing cluster,

Two files were created.

C15H24N4O6S2_e5f2_conf_0.gif C15H24N4O6S2_e5f2_conf_0.sh

As a result of checking the contents of the ‘C15H24N4O6S2_e5f2_conf_0.sh’ file

A file was created with the following contents.

!/bin/bash

SBATCH -N 1

SBATCH --ntasks-per-node=8

SBATCH -t 23:59:00

SBATCH --constraint="skylake"

input=C15H24N4O6S2_e5f2_conf_0

run the code

cd /scratch/a1422a01/gaussian g16 ${input}.gjf

I want the contents of the C15H24N4O6S2_e5f2_conf_0.sh file to be as follows.

!/bin/sh

SBATCH -J test

SBATCH -p ivy_V100_2 # Neurons use tesla_node partition.

SBATCH -N 1

SBATCH -n 20

SBATCH -o gautest.o%j # Define the filename of the standard output

SBATCH -e gautest.e%j # Define filename for standard error

SBATCH -t 12:00:00

SBATCH --gres=gpu:2

SBATCH --comment gaussian

module load gaussian/g16

input=C15H24N4O6S2_e5f2_conf_0

run the code

cd /scratch/a1422a01/gaussian g16 ${input}.gjf

I would like some help on how to modify the code in slurm_manager.py .

I tried modifying the latter part of the slurm_manager.py file, but didn't get any good results.

I need your help.