Hi,
I run gmx 2019 using GPU
There are 4 GPUs in my GPU hosts.
I have slurm and configured gres=gpu
1. If I submit a job with --gres=gpu:1 then GPU#0 is identified and used
(-gpu_id $CUDA_VISIBLE_DEVICES).
2. If I submit a second job, it fails: the $CUDA_VISIBLE_DEVICES is 1
and selected, but GPU #0 is identified by gmx as a compatible gpu.
From the output:
gmx mdrun -v -pin on -deffnm equi_nvt -nt 8 -gpu_id 1 -nb gpu -pme gpu
-npme 1 -ntmpi 4
GPU info:
Number of GPUs detected: 1
#0: NVIDIA GeForce GTX 1080 Ti, compute cap.: 6.1, ECC: no, stat:
compatible
Fatal error:
You limited the set of compatible GPUs to a set that included ID #1, but
that
ID is not for a compatible GPU. List only compatible GPUs.
3. If I login to that node and run the mdrun command written into the
output in the previous step then it selects the right gpu and runs as
expected.
$CUDA_DEVICE_ORDER is set to PCI_BUS_ID
I can not decide if this is a slurm config error or something with
gromacs, as $CUDA_VISIBLE_DEVICES is set correctly by slurm and I expect
gromacs to detect all 4GPUs.
Thanks for your help and suggestions,
Tamas
--
Tamas Hegedus, PhD
Senior Research Fellow
Department of Biophysics and Radiation Biology
Semmelweis University | phone: (36) 1-459 1500/60233
Tuzolto utca 37-47 | mailto:ta...@hegelab.org
Budapest, 1094, Hungary | http://www.hegelab.org
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