[gmx-users] GPU issue - system that was stable on CPUs crashes

Mark Abraham mark.j.abraham at gmail.com
Wed Jun 12 22:03:47 CEST 2019


The most likely explanation here is that the starting configuration isn't
very happy (box of wrong size? equilibrating with the unsuitable
parrinello-rahman algorithm?). The CPU-only run does a different domain
decomposition than the run with GPUs, leading to a different relaxation
trajectory, which happens to have smaller forces resulting from the unhappy

I suggest you look at the change of volume over the CPU-only NPT run, and
perhaps reconsider the way you did the initial box preparation. Of course,
if problems persist once you're in the production phase, then we should
look deeper into it!


On Wed., 12 Jun. 2019, 20:42 Hannah Magdalena Baumann, <hbaumann at uci.edu>

> Hi,
> I've been running into following issue in my MD simulation:
> While running the simulation on CPUs everything worked fine. But when
> running the simulation with the same input files on GPUs only minimization
> and NVT equilibration run successfully. When starting the NPT equilibration
> the system crashes due to LINCS warnings:
> Step 270, time 0.54 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.000084, max 0.001286 (between atoms 2019 and 2017)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>    1174   1173   34.2    0.1090   0.1090      0.1090
>    1176   1175   34.4    0.1090   0.1090      0.1090
> I ran the simulation both with Gromacs 2018-3 and 2019-beta1 versions,
> both runs crashed because of the same reason.
> This was the command to start the simulation:
> gmx grompp -f $MDP/npt.mdp -c ../NVT/nvt.gro -p $FREE_ENERGY/complex.top
> -t ../NVT/nvt.cpt -o npt.tpr
> gmx mdrun -s npt.tpr -deffnm npt -nt $SLURM_CPUS_PER_TASK -gpu_id
> $CUDA_VISIBLE_DEVICES -nb gpu -pin on
> GPU: NVIDIA GeForce GTX TITAN X, compute cap.: 5.2, ECC:  no, stat:
> compatible
> Can you see any reason why the system crashes on the GPU? Has anyone
> experienced a similar issue?
> Best regards,
> Hannah
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