[gmx-users] Is it possible to run implicit solvent simulations in parallel?
Ozlem Ulucan
ulucan.oz at googlemail.com
Wed May 4 16:50:54 CEST 2011
Thank you very much for the suggestions, I will try both and compare the
results.
On Wed, May 4, 2011 at 4:13 PM, Per Larsson <per.larsson at sbc.su.se> wrote:
> Hi!
>
> If you are running implicit solvent with no cutoffs, ie using the special
> all-vs-all kernels, then particle decomposition will be used. This exact
> combination (gb, all-vs-all, dd) is quite tricky to implement, and is not
> supported at the moment, IIRC.
> This could be documented better, sorry.
>
> You could try changing constraints from all-bonds to h-bonds, meaning you
> will have only local constraints, which should allow you to run with
> particle decomposition. Or use a cut-off and domain decomposition.
>
> /Per
>
>
>
> 4 maj 2011 kl. 16.05 skrev Ozlem Ulucan:
>
> 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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