[gmx-users] Simulation terminated after 260 ns of simulation

[Szilárd Páll]

There is a small chance that your crashes are caused by a rare bug that
could affect runs where the GPU is shared by multiple ranks. This was fixed
in 5.0.6, I suggest updating your installation.

For more details see the release notes:
http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_5.0.x

Cheers,

--
Szilárd

On Tue, Jan 19, 2016 at 12:53 PM, anu chandra <anu80125 at gmail.com> wrote:

> Dear Gromcas users,
>
> I have been carrying out a simulation of protein in POPC membrane.  After
> the successful completion of about 260 ns, simulation terminated with the
> following error.
>
> ***************************************************************
> Reading checkpoint file 16md.cpt generated: Sun Jan 17 06:38:52 2016
>
>
> Using 4 MPI processes
> Using 6 OpenMP threads per MPI process
>
> 2 GPUs detected on host tesla68:
>   #0: NVIDIA Tesla K20c, compute cap.: 3.5, ECC: yes, stat: compatible
>   #1: NVIDIA Tesla K20c, compute cap.: 3.5, ECC: yes, stat: compatible
>
> 2 GPUs auto-selected for this run.
> Mapping of GPUs to the 2 PP ranks in this node: #0, #1
>
> Non-default thread affinity set probably by the OpenMP library,
> disabling internal thread affinity
>
> WARNING: This run will generate roughly 5432 Mb of data
> starting mdrun 'Title'
> 133000000 steps, 266000.0 ps (continuing from step 120500000, 241000.0 ps).
>
> NOTE: Turning on dynamic load balancing
>
>
> -------------------------------------------------------
> Program gmx_mpi, VERSION 5.0.5
> Source code file: /tmp/gromacs-5.0.5/src/gromacs/mdlib/pme.c, line: 754
>
> Fatal error:
> 35983 particles communicated to PME rank 2 are more than 2/3 times the
> cut-off out of the domain decomposition cell of their charge group in
> dimension x.
> This usually means that your system is not well equilibrated.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> ********************************************************************
>
>
> I am using the following input parameters for simulation. I also used
> flat-bottom position restrain  during simulation.
>
> ******************************************************************
> define                  = -DPOSRES -DMD -DPOSRES_POT
> ;
> integrator              = md
> dt                      = 0.002
> nsteps                  = 500000
> tinit                   = 0
> init-step               = 0
> ;
> nstlog                  = 1000
> nstxout                 = 20000
> nstvout                 = 20000
> nstfout                 = 20000
> nstcalcenergy           = 100
> nstenergy               = 1000
> nstxout-compressed      = 4000
> compressed-x-grps       = System
> ;
> cutoff-scheme           = Verlet
> nstlist                 = 20
> rlist                   = 1.2
> coulombtype             = pme
> rcoulomb                = 1.2
> vdwtype                 = Cut-off
> vdw-modifier            = Force-switch
> rvdw_switch             = 1.0
> rvdw                    = 1.2
> ;
> pbc                     = xyz
> ;
> tcoupl                  = Nose-Hoover
> tc_grps                 = Protein POPC K_CL_SOL
> tau_t                   = 1.0    1.0     1.0
> ref_t                   = 305.0    305.0    305.0
> ;
> pcoupl                  = Parrinello-Rahman
> pcoupltype              = semiisotropic
> tau_p                   = 5.0     5.0
> compressibility         = 4.5e-5  4.5e-5
> ref_p                   = 1.0     1.0
> ;
> constraints             = h-bonds
> constraint_algorithm    = LINCS
> continuation            = yes
> ;
> nstcomm                 = 100
> comm_mode               = linear
> comm_grps               = Protein_POPC K_CL_SOL
> ;
> refcoord_scaling        = com
>
>
> **********************************************************************************
>
> I just wonder why Gromcas detected an improper system equilibration after
> 250 ns of simulation, though the system looks fine. Can anybody help me to
> get rid off the error here.
>
>
> Many thanks in advance
>
> Anu
> --
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