[gmx-users] Query regarding Domain decomposition
mark.j.abraham at gmail.com
Wed Jun 25 14:23:45 CEST 2014
On Jun 25, 2014 8:15 AM, "suhani nagpal" <suhani.nagpal at gmail.com> wrote:
> I have been trying to run a few set of simulations using high number of
> Using the tutorial -
> 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
> 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)
> 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
> 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
> 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
> 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.
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