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

Hannah Magdalena Baumann hbaumann at uci.edu
Wed Jun 12 20:42:09 CEST 2019


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,

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