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crest-lab / crest

CREST - A program for the automated exploration of low-energy molecular chemical space.
https://crest-lab.github.io/crest-docs/
GNU Lesser General Public License v3.0
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Segmentation Fault from Linux #170

Closed rtm82 closed 1 year ago

rtm82 commented 1 year ago

Hi, I'm using the precompiled linux binaries for CREST 2.2.0 and xtb 6.6.0 and 6.4.0, but after trying to run it with my submission script sub.sh:

`#!/bin/bash

SBATCH -p vega

SBATCH --job-name=sub_pw

SBATCH --ntasks=8

SBATCH --cpus-per-task=2

SBATCH --nodes=2

SBATCH --mem-per-cpu=4GB

OUTFILE="confGen.out"

echo "starting at date on hostname"

export OMP_NUM_THREADS=2 export OMP_STACKSIZE=4G

crest struc.xyz --cinp .xcontrol_sample --subrmsd

echo "ended at date on hostname" exit 0`

I get the following error for both xtb versions:

`

xTB Geometry Optimization

sh: line 1: 55662 Segmentation fault xtb tmpcoord --gfn2 --opt > xtb.out 2> /dev/null

Initial geometry optimization failed! Please check your input. ended at Fri Feb 10 14:17:29 EST 2023 on c0101 `

Any idea what might be happening? Let me know if you need any more info.

Thanks,

Rob

rtm82 commented 1 year ago

Very sorry about this, solved. Issue was that there was not enough memory allocated to xtb for my relatively large system (as per https://xtb-docs.readthedocs.io/en/latest/setup.html). Making their suggested tweaks to my submission script solved everything.