[gmx-users] Is it possible to run implicit solvent simulations in parallel?
Ozlem Ulucan
ulucan.oz at googlemail.com
Wed May 4 16:05:06 CEST 2011
Dear Justin, this was only a test run and I ran the simulations on my
multi-core workstations (4 cores actually). MPI is no longer required for
such a situation. Since I did not set -nt option to 1, this can be accepted
as a parallel run. So the command I sent in my previous e-mail was for the
parallel run and for serial run I set -nt to 1.
Dear Justin, as I said I am using a workstation of 4 processors. I have
approximately 2200 atoms in my system. That means for one processor I have
slightly more than 550 atoms. I set all the cut-offs to 0. I really need to
run this system in parallel. Any suggestions to make it work out?
Here is my run input file :
;
; File 'mdout.mdp' was generated
; By user: onbekend (0)
; On host: onbekend
; At date: Sun May 1 16:19:29 2011
;
; VARIOUS PREPROCESSING OPTIONS
; Preprocessor information: use cpp syntax.
; e.g.: -I/home/joe/doe -I/home/mary/roe
include =
; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)
define =
; RUN CONTROL PARAMETERS
integrator = SD
; Start time and timestep in ps
tinit = 0
dt = 0.002
nsteps = 500000
; For exact run continuation or redoing part of a run
init_step = 0
; Part index is updated automatically on checkpointing (keeps files
separate)
simulation_part = 1
; mode for center of mass motion removal
comm-mode = Angular
; number of steps for center of mass motion removal
nstcomm = 10
; group(s) for center of mass motion removal
comm-grps = system
; 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 = 10.0
emstep = 0.01
; 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 = 1000
nstvout = 1000
nstfout = 0
; Output frequency for energies to log file and energy file
nstlog = 1000
nstcalcenergy = -1
nstenergy = 1000
; Output frequency and precision for .xtc file
nstxtcout = 0
xtc-precision = 500
; This selects the subset of atoms for the .xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps = Protein
; Selection of energy groups
energygrps = Protein
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 0
; ns algorithm (simple or grid)
ns_type = simple
; Periodic boundary conditions: xyz, no, xy
pbc = no
periodic_molecules = no
; nblist cut-off
rlist = 0
; long-range cut-off for switched potentials
rlistlong = -1
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = cut-off
rcoulomb-switch = 0
rcoulomb = 0
; Relative dielectric constant for the medium and the reaction field
epsilon_r = 1
epsilon_rf = 1
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths
rvdw-switch = 0
rvdw = 0
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = No
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1
; Seperate tables between energy group pairs
energygrp_table =
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = yes
; IMPLICIT SOLVENT ALGORITHM
implicit_solvent = GBSA
; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm = OBC
; Frequency of calculating the Born radii inside rlist
nstgbradii = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii = 0
; Dielectric coefficient of the implicit solvent
gb_epsilon_solvent = 80
; Salt concentration in M for Generalized Born models
gb_saltconc = 0
; Scaling factors used in the OBC GB model. Default values are OBC(II)
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
gb_dielectric_offset = 0.009
sa_algorithm = Ace-approximation
; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
; The value -1 will set default value for Still/HCT/OBC GB-models.
sa_surface_tension = -1
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl = v-rescale
nsttcouple = -1
nh-chain-length = 10
; Groups to couple separately
tc-grps = Protein
; Time constant (ps) and reference temperature (K)
tau-t = 0.1
ref-t = 300
; Pressure coupling
Pcoupl = Parrinello-Rahman
Pcoupltype = isotropic
nstpcouple = -1
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p = 1
compressibility = 4.5e-5
ref-p = 1.0
; Scaling of reference coordinates, No, All or COM
refcoord_scaling = No
; Random seed for Andersen thermostat
andersen_seed = 815131
; OPTIONS FOR QMMM calculations
QMMM = no
; Groups treated Quantum Mechanically
QMMM-grps =
; QM method
QMmethod =
; QMMM scheme
QMMMscheme = normal
; QM basisset
QMbasis =
; QM charge
QMcharge =
; QM multiplicity
QMmult =
; Surface Hopping
SH =
; CAS space options
CASorbitals =
CASelectrons =
SAon =
SAoff =
SAsteps =
; Scale factor for MM charges
MMChargeScaleFactor = 1
; Optimization of QM subsystem
bOPT =
bTS =
; SIMULATED ANNEALING
; Type of annealing for each temperature group (no/single/periodic)
annealing =
; Number of time points to use for specifying annealing in each group
annealing_npoints =
; List of times at the annealing points for each group
annealing_time =
; Temp. at each annealing point, for each group.
annealing_temp =
; GENERATE VELOCITIES FOR STARTUP RUN
gen-vel = no
gen-temp = 300
gen-seed = 173529
; OPTIONS FOR BONDS
constraints = all-bonds
; Type of constraint algorithm
constraint-algorithm = Lincs
; Do not constrain the start configuration
continuation = no
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR = no
; Relative tolerance of shake
shake-tol = 0.0001
; Highest order in the expansion of the constraint coupling matrix
lincs-order = 4
; Number of iterations in the final step of LINCS. 1 is fine for
; normal simulations, but use 2 to conserve energy in NVE runs.
; For energy minimization with constraints it should be 4 to 8.
lincs-iter = 1
; Lincs will write a warning to the stderr if in one step a bond
; rotates over more degrees than
lincs-warnangle = 30
; Convert harmonic bonds to morse potentials
morse = no
; ENERGY GROUP EXCLUSIONS
; Pairs of energy groups for which all non-bonded interactions are excluded
energygrp_excl =
; WALLS
; Number of walls, type, atom types, densities and box-z scale factor for
Ewald
nwall = 0
wall_type = 9-3
wall_r_linpot = -1
wall_atomtype =
wall_density =
wall_ewald_zfac = 3
; COM PULLING
; Pull type: no, umbrella, constraint or constant_force
pull = no
; NMR refinement stuff
; Distance restraints type: No, Simple or Ensemble
disre = No
; Force weighting of pairs in one distance restraint: Conservative or Equal
disre-weighting = Conservative
; Use sqrt of the time averaged times the instantaneous violation
disre-mixed = no
disre-fc = 1000
disre-tau = 0
; Output frequency for pair distances to energy file
nstdisreout = 100
; Orientation restraints: No or Yes
orire = no
; Orientation restraints force constant and tau for time averaging
orire-fc = 0
orire-tau = 0
orire-fitgrp =
; Output frequency for trace(SD) and S to energy file
nstorireout = 100
; Dihedral angle restraints: No or Yes
dihre = no
dihre-fc = 1000
; Free energy control stuff
free-energy = no
init-lambda = 0
delta-lambda = 0
foreign_lambda =
sc-alpha = 0
sc-power = 0
sc-sigma = 0.3
nstdhdl = 10
separate-dhdl-file = yes
dhdl-derivatives = yes
dh_hist_size = 0
dh_hist_spacing = 0.1
couple-moltype =
couple-lambda0 = vdw-q
couple-lambda1 = vdw-q
couple-intramol = no
; Non-equilibrium MD stuff
acc-grps =
accelerate =
freezegrps =
freezedim =
cos-acceleration = 0
deform =
; Electric fields
; Format is number of terms (int) and for all terms an amplitude (real)
; and a phase angle (real)
E-x =
E-xt =
E-y =
E-yt =
E-z =
E-zt =
; User defined thingies
user1-grps =
user2-grps =
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
Regards,
Ozlem
On Wed, May 4, 2011 at 3:44 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
> On 4/05/2011 11:23 PM, Justin A. Lemkul wrote:
>
>>
>>
>> Ozlem Ulucan wrote:
>>
>>>
>>> Dear Gromacs Users,
>>>
>>> I have been trying to simulate a protein in implicit solvent. When I used
>>> a single processor by setting -nt to 1 , I did not encounter any problem.
>>> But when I tried to run the simulations using more than 1 processor I get
>>> the following error.
>>>
>>> Fatal error:
>>> Constraint dependencies further away than next-neighbor
>>> in particle decomposition. Constraint between atoms 2177--2179 evaluated
>>> on node 3 and 3, but atom 2177 has connections within 4 bonds
>>> (lincs_order)
>>> of node 1, and atom 2179 has connections within 4 bonds of node 3.
>>> Reduce the # nodes, lincs_order, or
>>> try domain decomposition.
>>>
>>> I set the lincs_order parameter in .mdp file to different values. But
>>> it did not help. I have some questions regarding the information above.
>>>
>>
> See comments about lincs_order in 7.3.18. Obviously, only smaller values of
> lincs_order can help (but if this is not obvious, please consider how
> obvious "it did not help" is :-))
>
>
> 1) Is it possible to run implicit solvent simulations in parallel?
>>>
>>>
>> Yes.
>>
>> 2) As far as I know gromacs uses domain decomposition as default. Why
>>> does in my simulations gromacs use the particle decomposition which I do not
>>> ask for.
>>>
>>>
>> Without seeing the exact commands you gave, there is no plausible
>> explanation. DD is used by default.
>>
>
> Not quite true, unfortunately. With the cutoffs set to zero, the use of the
> all-against-all GB loops is triggered, and that silently requires PD. It
> should write something to the log file.
>
>
>
>> -Justin
>>
>> Any suggestions are appreciated very much.
>>> I am ussing gromacs-4.5.4 with charmm force field and the OBC implicit
>>> solvent model. If you need further informations, probably a run input file,
>>> let me know.
>>>
>>
> A run input file would have helped me avoid guessing above about those
> cutoffs :-)
>
> The real issue is that not all systems can be effectively parallelized by a
> given implementation. How many processors and atoms are we talking about? If
> there's not hundreds of atoms per processor, then parallelism is not going
> to be worthwhile.
>
> Mark
>
> --
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