[gmx-users] error: 1 particles communicated to PME node 3 (...)

[Berk Hess]

Hi,

This sounds like the bug in domdec.c that I fixed a month ago:
revision 1.146
date: 2008/07/11 12:09:43;  author: hess;  state: Exp;  lines: +307 -193
fixed incorrect computation of the PME coordinate communication range with dlb and change some formatting

Is your version from before that date?

Berk.


From: regafan at hotmail.com
To: gmx-users at gromacs.org
Date: Tue, 12 Aug 2008 17:15:59 +0000
Subject: [gmx-users] error: 1 particles communicated to PME node 3 (...)








Hello,

I am trying to equilibrate a protein+membrane system in Gromacs 4. The minimization went OK, but in the equilibration at constant pressure I got this error:

 

 

Fatal error:
1 particles communicated to PME node 3 are more than a cell length out of the domain decomposition cell of their charge group
-------------------------------------------------------

"O My God, They Killed Kenny !" (South Park)

Error on node 15, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 15 out of 32

gcq#254: "O My God, They Killed Kenny !" (South Park)

[15] MPI Abort by user Aborting program !
mx_finalize() called while some endpoints are still open.
MX:s23c2b13:mx_finalize:error 20(errno=2):Busy
srun: error: s23c2b13: task15: Exited with exit code 1
MX:s23c2b06:Remote endpoint is closed, peer=00:60:dd:48:46:62 (s23c2b13:0)
srun: error: s23c2b06: task11: Exited with exit code 1
srun: error: s23c2b13: task[12-14]: Killed
srun: Job Failed

 

The calculations stops after 2000 steps:

 

           Step           Time         Lambda
           2000        4.00000        0.00000

   Energies (kJ/mol)
          Angle Ryckaert-Bell.          LJ-14     Coulomb-14        LJ (SR)
    6.17238e+05    4.06472e+05    1.89810e+05    5.82538e+05    3.71263e+06
        LJ (LR)   Coulomb (SR)   Coul. recip. Position Rest.      Potential
   -5.12910e+04   -9.09326e+06   -1.97121e+06    1.69698e+06   -3.91010e+06
    Kinetic En.   Total Energy    Temperature Pressure (bar)  Cons. rmsd ()
    2.12885e+06   -1.78125e+06    3.56627e+02   -2.35301e+04    2.99204e-05

 

As input I use:

 

title           = EQUILIBRADO
cpp             = /usr/bin/cpp
include         = -I../top
define          = -DPOSRES_D -DPOSRES_P
constraints     = all-bonds
integrator      = md
dt              = 0.002
nsteps          = 10000
nstxout         = 1000
nstvout         = 1000
nstlog          = 1000
nstenergy       = 1000
nstxtcout       = 1000
nstlist         = 10
ns_type         = grid
rlist           = 1.0
coulombtype     = PME
rcoulomb        = 1.0
vdwtype         = cut-off
rvdw            = 1.4
pme_order       = 4
ewald_rtol      = 1e-5
optimize_fft    = yes
;Berendsen temperature coupling is on
Tcoupl          = berendsen
tau_t           = 0.1     0.1    0.1
tc-grps         = Protein dop SOL_Na_Cl
ref_t           = 310     310    310
; Pressure coupling
Pcoupl                   = Parrinello-Rahman
Pcoupltype               = Semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p                    = 1.0 1.0
compressibility          = 4.6E-5 4.6E-5
ref-p                    = 1.0 1.0
;Generate velocities is on at 310 K
gen_vel         = yes
gen_temp        = 310
gen_seed        = 173529


Does anybody which could be the problem?

 

Thank you very much for your help.

 

Best wishes,

 

Rebeca Garcia Fandiño

Parc Cientific de Barcelona



 

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