[gmx-users] parallel calculation problem in implicit solvent modeling

[Ming Tang]

Dear all,

I had a problems with parallel calculation of a implicit solvent problem. My gromacs is compiled with mpi, so technically, I run mdrun_mpi for my simulation. I am calling 12 cpus for my simulation and started 12 treads.

When I put a limited rlist in the simulation, say rlist=4, 12 cpus calculation runs good. However, when I put an infinite one, which is rlist=rvdw=rcoulmb=rgbradii=0, the parallel calculation doesn't move anymore, and doesn't give me error msg, either. The output window is freezed, showing a note:


Non-default thread affinity set probably by the OpenMP library,
disabling internal thread affinity

If I change it to one CPU calculation, the simulation will still run, with rlist=0.

I also tried 'simple' method for ns algorithm, but the mpi compiles parallel calculation does not allow to use it due to the default 'Domain decomposition' algrithm.

Can any mate give me some hints? Thanks in advance.

Cheers
Tony

My running command is:

export OMP_NUM_THREADS=1
mdrun_mpi -v -ntomp 1 -cpi -cpo -c nvt.pdb

My mdp file is:

define                   = -DPOSRES
; RUN CONTROL PARAMETERS
integrator               = steep
; Start time and timestep in ps
tinit                    = 0
dt                       = 0.001
nsteps                   = 50000
; For exact run continuation or redoing part of a run
simulation_part          = 1
init_step                = 0
; mode for center of mass motion removal
comm-mode                = Linear
; number of steps for center of mass motion removal
nstcomm                  = 1
; group(s) for center of mass motion removal
comm-grps                =

; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd-fric                  = 0
ld-seed                  = 1993

; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol                    = 5
emstep                   = 0.1
; Max number of iterations in relax_shells
niter                    = 20
; Step size (ps^2) for minimization of flexible constraints
fcstep                   = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep               = 1000
nbfgscorr                = 10

; TEST PARTICLE INSERTION OPTIONS
rtpi                     = 0.05

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout                  = 100
nstvout                  = 100
nstfout                  = 100
; Output frequency for energies to log file and energy file
nstlog                   = 100
nstenergy                = 100
; Output frequency and precision for xtc file
nstxtcout                = 100
xtc-precision            = 100

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist                  = 40
; ns algorithm (simple or grid)
ns_type                  = grid
; Periodic boundary conditions: xyz, no, xy
pbc                      = no
; nblist cut-off
cutoff-scheme         = group
rlist                    = 0

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype              = cut-off
rcoulomb-switch          = 1
rcoulomb                 = 0

; Method for doing Van der Waals
vdw-type                 = cut-off
; cut-off lengths
rvdw-switch              = 1
rvdw                     = 0

; IMPLICIT SOLVENT ALGORITHM
implicit-solvent         = GBSA
gb-algorithm             = still
rgbradii                 = 0
sa_surface_tension     = 2.05016