jade-hpc-gpu / jade-hpc-gpu.github.io

Joint Academic Data Science Endeavour (JADE) is the largest GPU facility in the UK supporting world-leading research in machine learning (and this is the repo that powers its website)

http://www.jade.ac.uk/

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I am trying to run an MD simulation using AMBER. #137

Open magbada88 opened 4 years ago

magbada88 commented 4 years ago

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magbada88 commented 4 years ago

The job is failing with the following error message: Error: an illegal memory access was encountered launching kernel kNLSkinTest

Here an example of my slurm job file:

!/bin/bash

SBATCH --nodes=1

SBATCH --gres=gpu:1

SBATCH --time=24:00:00

SBATCH -J job1

SBATCH -p small

module load amber/18

pmemd.cuda -O -i step4.1_equilibration.mdin -p helicase_rna_atp_wat.top -c helicase_rna_atp_wat.crd -o step4.1_equilibration.mdout -r step4.1_equilibration.rst7 -inf step4.1_equilibration.mdinfo -ref helicase_rna_atp_wat.crd -x step4.1_equilibration.nc

Thanks

jimboid commented 4 years ago

Hi, Before I start debugging this issue. I had to recompile AMBER 18 yesterday evening due to unexpected removal of Cuda 9.0. I finished compilation and made the module available at about 17:45 yesterday evening. Has this error happened since this time?

Thanks

James