Dear Gromacs users, I am performing simulations on a server which contains two 20 core CPUs, and 4 GTX1080 GPUs using gromacs version 5.1.4. However my simulations are being stopped during production run in the middle. I have not seen any problems up to equilibriation (NVT and NPT). When i use only 2 GPUs the simulation was successful, however with 4 GPUs it is being *reported a fatal error like below. *Any suggestions please....
Program gmx mdrun, VERSION 5.1.4 Source code file: /home/gosu/gromacs-5.1.4/src/gromacs/domdec/domdec.cpp, line: 2848 Fatal error: Step 18622600: The domain decomposition grid has shifted too much in the Y-direction around cell 0 1 0. This should not have happened. Running with fewer ranks might avoid this issue. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Program gmx mdrun, VERSION 5.1.4 Source code file: /home/gosu/gromacs-5.1.4/src/gromacs/domdec/domdec.cpp, line: 2848 Fatal error: Step 18622600: The domain decomposition grid has shifted too much in the Y-direction around cell 1 1 0. This should not have happened. Running with fewer ranks might avoid this issue. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- : Unknown error 255 *I have used the below commands* gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr gmx mdrun -deffnm md_0_1 -v *MDP file parameter are given below (**amber99sb-ildn.ff**)* ; Run parameters integrator = md ; leap-frog integrator nsteps = 100000000 dt = 0.002 ; 2 fs ; Output control nstxout = 0 nstvout = 0 nstenergy = 1000 nstlog = 1000 nstxout-compressed = 1000 compressed-x-grps = System ; Bond parameters continuation = yes constraint_algorithm = lincs constraints = all-bonds lincs_iter = 1 lincs_order = 4 ; Neighborsearching cutoff-scheme = Verlet ns_type = grid nstlist = 20 rcoulomb = 1.0 rvdw = 1.0 ; Electrostatics coulombtype = PME pme_order = 4 fourierspacing = 0.16 ; Temperature coupling is on tcoupl = V-rescale tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 310 310 ; Pressure coupling is on pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 2.0 ref_p = 1.0 compressibility = 4.5e-5 ; Periodic boundary conditions pbc = xyz ; Dispersion correction DispCorr = EnerPres ; Velocity generation gen_vel = no *Thanks * *Vijayakumar gosu.* -- 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 [email protected].
