[gmx-users] simulations being stopped during production run

[vijayakumar gosu]

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.*