[gmx-users] Query regarding Domain decomposition

[suhani nagpal]

Thanks for the insights.

So, now using the .tpr file generated with grompp whose version matches the
mdrun.

files are generated again but after time step 0 and time 0 nothing gets
written and the jobs reaches an error state and stops.

in the error file,

mpirun noticed that process rank 41 with PID 35866 on node cn0286. exited
on signal 11 (Segmentation fault).


I'm not able to scale over 160 processors. I have 32600 atoms in the
system.

Kindly assist

thanks


Suhani






On Wed, Jun 25, 2014 at 5:53 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> On Jun 25, 2014 8:15 AM, "suhani nagpal" <suhani.nagpal at gmail.com> wrote:
> >
> > Greetings
> >
> > I have been trying to run a few set of simulations using high number of
> > processors.
> >
> > Using the tutorial -
> >
>
> http://compchemmpi.wikispaces.com/file/view/Domaindecomposition_KKirchner_27Apr2012.pdf
> >
> > I have done calculations to evaluate the set of nodes which would be
> > optimal for the protein.
> >
> >
> > So the all the files are generated, but error occurs and the trajectory
> > files remain empty with no error mentioned in the log file.
>
> Hard to say. The problem could be anywhere, since we don't yet know when
> mdrun does work...
>
> > Number of nodes to be used in multiple of 16
> >
> > box in x and y dimension 8 nm
> >
> >
> >
> > In the error file,
> >
> >
> > Reading file 400K_SIM2.tpr, VERSION 4.5.5 (single precision)
>
> Why use a slow, old version if you want parallel performance?
>
> > Note: file tpx version 73, software tpx version 83
>
> You should prefer to use grompp whose version matches mdrun.
>
> > The number of OpenMP threads was set by environment variable
> > OMP_NUM_THREADS to 1
> > Using 320 MPI processes
> >
> > NOTE: The load imbalance in PME FFT and solve is 116%.
> >       For optimal PME load balancing
> >       PME grid_x (54) and grid_y (54) should be divisible by #PME_nodes_x
> > (140)
> >       and PME grid_y (54) and grid_z (54) should be divisible by
> > #PME_nodes_y (1)
> >
> >
> >
> > mdp file for reference
> >
> > ; Bond parameters
> > continuation    = yes           ; Restarting after NPT
> > constraint_algorithm = lincs    ; holonomic constraints
> > constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
> > constrained
> > lincs_iter      = 1             ; accuracy of LINCS
> > lincs_order     = 4             ; also related to accuracy
> > ; Neighborsearching
> > ns_type         = grid          ; search neighboring grid cells
> > nstlist         = 5             ; 10 fs
> > rlist           = 1.0           ; short-range neighborlist cutoff (in nm)
> > rcoulomb        = 1.0           ; short-range electrostatic cutoff (in
> nm)
> > rvdw            = 1.0           ; short-range van der Waals cutoff (in
> nm)
> > ; Electrostatics
> > coulombtype     = PME           ; Particle Mesh Ewald for long-range
> > electrostatics
> > pme_order       = 4             ; cubic interpolation
> > fourierspacing  = 0.16          ; grid spacing for FFT
> > ; Temperature coupling is on
> > tcoupl          = nose-hoover   ; nose-hoover coupling
> > tc-grps         = Protein Non-Protein   ; two coupling groups - more
> > accurate
> > tau_t           = 0.2   0.2     ; time constant, in ps
> > ref_t           = 400   400     ; reference temperature, one for each
> > group, in K
> > ; Pressure coupling is off
> > pcoupl          = no            ;
> > ; Periodic boundary conditions
> > pbc             = xyz           ; 3-D PBC
> > ; Dispersion correction
> > DispCorr        = EnerPres      ; account for cut-off vdW scheme
> > ; Velocity generation
> > gen_vel         = yes           ; assign velocities from Maxwell
> > distribution
> > gen_temp        = 400           ; temperature for Maxwell distribution
> > gen_seed        = -1            ; generate a random seed
> >
> >
> > Kindly help.
> >
> > I have to run simulations at 250 to 300 processors.
>
> Maybe. You can't efficiently parallelize an algorithm over arbitrary
> amounts of hardware. You need 100-1000 atoms per core, depending on
> hardware, simulation settings and GROMACS version.
>
> Mark
>
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