[gmx-users] Query regarding Domain decomposition
suhani nagpal
suhani.nagpal at gmail.com
Wed Jun 25 08:14:51 CEST 2014
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.
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)
Note: file tpx version 73, software tpx version 83
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.
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