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

Berk Hess gmx3 at hotmail.com
Wed Aug 13 15:18:27 CEST 2008


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?


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 (...)


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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