[gmx-users] mpispawn.c:303 Unexpected exit status

[Justin A. Lemkul]

shivkumar bale wrote:
> Hi Gromacs Users,
> 
> when I am trying to run the simulation I am getting the following error:
> 
> mpispawn.c:303 Unexpected exit status
> 
> Child exited abnormally!
> Killing remote processes...DONE
> 
> I read about this online and it says that simulation is running out of 
> memory and it depends upon the grid spacing. It also talks about PP/PME 
> ratio. But I am not able to figure how to make that changes in the mdp file?
> 

Can you provide a link to the information you found?

PP/PME ratio is either guessed, or explicitly set using mdrun -npme.  Assuming 
the "grid spacing" you refer to is the PME grid spacing, then the fourierspacing 
parameter is what you need to set.  Usually a default of 0.12 is reasonable; 
yours is set at 0.10.

Also, you shouldn't be using -DFLEXIBLE with the md integrator, see here:

http://lists.gromacs.org/pipermail/gmx-users/2008-October/037571.html

-Justin

> title                    = bilayer
> cpp                      = /lib/cpp
> include                  =
> define                   = -DFLEXIBLE
> integrator               = md
> emstep             = 0.1
> emtol             = 10.0
> nstcgsteep         = 10
> dt                       = 0.001
> nsteps                   = 2000000
> nstxout                  = 10000
> nstvout                  = 10000
> nstlog                   = 10000
> nstenergy                = 10000
> nstxtcout                = 10000
> xtc_grps                 =
> energygrps               =
> nstlist                  = 10
> ns_type                  = grid
> pbc                      = xyz
> rlist                    = 1.0
> vdw-type                 = Cut-off
> rvdw                     = 1.0
> coulombtype              = PME
> rcoulomb                 = 1.0
> DispCorr                 = EnerPres
> fourierspacing           = 0.1
> pme_order                = 6
> ewald_rtol               = 1e-05
> ewald_geometry           = 3d
> epsilon_surface          = 0
> optimize_fft             = yes
> tcoupl                   = Berendsen
> tc_grps                  = system
> tau_t                    = 1.0 
> ref_t                    = 300
> Pcoupl                   = Berendsen
> Pcoupltype               = isotropic
> tau_p                    = 4.0
> compressibility          = 4.5e-5
> ref_p                    = 1.0
> gen_vel                  = yes
> gen_temp                 = 300
> gen_seed                 = 173529
> constraints              = none
> constraint_algorithm     = lincs
> lincs_order              = 8
> lincs_iter               = 2
> 
> 
> Regards,
> 
> Shivkumar Bale
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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