Can not run short-ranged non bonded interactions on a GPU because there is no GPU?

User discussions
1

Dear Gromacs users,

I used to run gromacs 2022 on the cluster using CPU. For using that I applied theses commands:

source /nfsexports/SOFTWARE/intel/oneapi/compiler/latest/env/vars.sh

source /nfsexports/SOFTWARE/intel/oneapi/mkl/latest/env/vars.sh intel64

srun --propagate=NONE -p parallel -n 2 /nfsexports/SOFTWARE/gromacs-2022/build/bin/gmx_mpi mdrun -deffnm nvt5 &>SC.out &

However, because of the low speed of calculations, I decided to do the simulation on GPU. I ask the administrator to apply GPU. I use this command to run on GPU:
srun --propagate=NONE -p parallel -n 2 /nfsexports/SOFTWARE/gromacs-2022/build/bin/gmx_mpi mdrun -deffnm nvt5 -nb gpu -pme gpu &>SC.out &

But a Fatal Error appeared:
Can not run short-ranged non bonded interactions on a GPU because there is no GPU
I saw similar topics regarding this issue but I could not solve it. Do I have to source something regarding GPU before running command?

Thanks

2

This is probably more related to Slurm than GROMACS. Have you requested any GPUs in your slurm submission, see Slurm Workload Manager - sbatch? Depending on your Slurm environment setup, GPU nodes might also be in a separate partition, Slurm Workload Manager - sbatch. Hopefully, there is documentation available for your cluster.

3

Dear MagnusL,

Thanks for your help.