Hi, 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 particles.
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! Mark On Wed., 12 Jun. 2019, 20:42 Hannah Magdalena Baumann, <hbaum...@uci.edu> wrote: > 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 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
