[gmx-users] Tabulated potential segmentation fault
Laura Leay
laura.leay at postgrad.manchester.ac.uk
Mon Apr 16 17:50:51 CEST 2012
On Fri, 2012-04-13 at 11:01 +1000, Mark Abraham wrote:
> On 13/04/2012 2:48 AM, Laura Leay wrote:
> > All,
> >
> > I'm trying to run a tabulated soft core potential with the form V =
> > A + Br^2 + Cr^3 up to about r=0.1 A and the normal LJ 6-12 potential
> > after this.
> >
> > I've chosen the parameters of this equation to be the same for all
> > atoms in my system (a polymer containing carbon, nitrogen and
> > hydrogen). I've not assigned any charges to the system.
> >
> > Running on Gromacs version 4.5.4 single precision on a high
> > perfomance computing cluster the first 50 or so steps run fine,
> > energies seem reasonable but then the simulation crashes with a
> > segmentation fault. I submitted the job using the comand mdrun
> > -table table.xvg -v -nt $NSLOTS -pd
> >
> > The job seems to run ok on my own desktop PC although I've not tried
> > running it for more than a few minutes to check that it would indeed
> > run.
> >
> > If anyone can tell me why this won't run on the computing cluster
> > I'd appreciate it.
> >
> > the first few lines of my table file look like this:
> >
> > 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00
> > 0.0000000E+00 0.1500000E+05 0.0000000E+00
> > 0.2000000E-02 0.0000000E+00 0.0000000E+00 0.3045913E-01
> > -0.4568869E+02 0.1499547E+05 0.4525801E+04
> > 0.4000000E-02 0.0000000E+00 0.0000000E+00 0.2436730E+00
> > -0.1827548E+03 0.1498190E+05 0.9051602E+04
> > 0.6000000E-02 0.0000000E+00 0.0000000E+00 0.8223965E+00
> > -0.4111982E+03 0.1495927E+05 0.1357740E+05
> > 0.8000000E-02 0.0000000E+00 0.0000000E+00 0.1949384E+01
> > -0.7310191E+03 0.1492759E+05 0.1810320E+05
> > 0.1000000E-01 0.0000000E+00 0.0000000E+00 0.3807391E+01
> > -0.1142217E+04 0.1488685E+05 0.2262901E+05
> > 0.1200000E-01 0.0000000E+00 0.0000000E+00 0.6579172E+01
> > -0.1644793E+04 0.1483707E+05 0.2715481E+05
> > 0.1400000E-01 0.0000000E+00 0.0000000E+00 0.1044748E+02
> > -0.2238746E+04 0.1477824E+05 0.3168061E+05
> > 0.1600000E-01 0.0000000E+00 0.0000000E+00 0.1559507E+02
> > -0.2924076E+04 0.1471035E+05 0.3620641E+05
> > 0.1800000E-01 0.0000000E+00 0.0000000E+00 0.2220471E+02
> > -0.3700784E+04 0.1463341E+05 0.4073221E+05
> > 0.2000000E-01 0.0000000E+00 0.0000000E+00 0.3045913E+02
> > -0.4568869E+04 0.1454742E+05 0.4525801E+05
> > 0.2200000E-01 0.0000000E+00 0.0000000E+00 0.4054110E+02
> > -0.5528332E+04 0.1445238E+05 0.4978381E+05
> >
> > This is my mdp file (note that I turned dispersion correction off to
> > see if this was the problem but it would seem that it is not):
> >
> > ; VARIOUS PREPROCESSING OPTIONS
> > title = Yo
> > cpp = /usr/bin/cpp
> > include =
> > define =
> >
> > ; RUN CONTROL PARAMETERS
> > integrator = md ;md for simulation, steep for Emin
> > ; Start time and timestep in ps
> > tinit = 0
> > dt = 0.001
> > nsteps =100000; 1000000 ;for simulation
> > ; For exact run continuation or redoing part of a run
> > 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
> > ; Temperature, friction coefficient (amu/ps) and random seed
> > ;bd-temp = 300
> > bd-fric = 0
> > ld-seed = 1993
> >
> > ; ENERGY MINIMIZATION OPTIONS
> > ; Force tolerance and initial step-size
> > emtol = 100
> > emstep = 0.01
> > ; Max number of iterations in relax_shells
> > niter = 20
> > ; Step size (1/ps^2) for minimization of flexible constraints
> > fcstep = 0
> > ; Frequency of steepest descents steps when doing CG
> > fcstep = 0
> > ; Frequency of steepest descents steps when doing CG
> > nstcgsteep = 1000
> > nbfgscorr = 10
> >
> > ; OUTPUT CONTROL OPTIONS
> > ; Output frequency for coords (x), velocities (v) and forces (f)
> > nstxout = 0
> > nstvout = 0
> > nstfout = 0
> > ; Checkpointing helps you continue after crashes
> > nstcheckpoint = 1000
> > ; Output frequency for energies to log file and energy file
> > nstlog = 50
> > nstenergy = 50
> > ; Output frequency and precision for xtc file
> > nstxtcout = 50
> > xtc-precision = 1000
> > ; This selects the subset of atoms for the xtc file. You can
> > ; select multiple groups. By default all atoms will be written.
> > xtc-grps =
> > ; Selection of energy groups
> > energygrps =
> >
> > ; NEIGHBORSEARCHING PARAMETERS
> > ; nblist update frequency
> > nstlist = 10
> > ; ns algorithm (simple or grid)
> > ns_type = simple
> > ; Periodic boundary conditions: xyz (default), no (vacuum)
> > ; or full (infinite systems only)
> > pbc = xyz
> > ; nblist cut-off
> > rlist = 0.9
> > domain-decomposition = no
> >
> > ; OPTIONS FOR ELECTROSTATICS AND VDW
> > ; Method for doing electrostatics
> > coulombtype = user
> > rcoulomb-switch = 0
> > rcoulomb = 0.9
> > ; Dielectric constant (DC) for cut-off or DC of reaction field
> > epsilon-r = 1
> > ; Method for doing Van der Waals
> > vdw-type = user
> > ; cut-off lengths
> > rvdw-switch = 0
> > rvdw = 0.9
> > ; Apply long range dispersion corrections for Energy and Pressure
> > DispCorr = no ;EnerPres
> > ; Extension of the potential lookup tables beyond the cut-off
> > table-extension = 2.0
> > ; 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 = no
> >
> > ; GENERALIZED BORN ELECTROSTATICS
> > ; Algorithm for calculating Born radii
> > gb_algorithm = Still
> > ; 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 = 2
> > ; Salt concentration in M for Generalized Born models
> > gb_saltconc = 0
> >
> > ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
> > implicit_solvent = No
> >
> > ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> > ; Temperature coupling
> > Tcoupl = berendsen
> > ; Groups to couple separately
> > tc-grps = System
> > ; Time constant (ps) and reference temperature (K)
> > tau_t = 0.1
> > ref_t = 300
> > ; Pressure coupling
> > Pcoupl = no ;berendsen
> > Pcoupltype = isotropic
> > ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> > tau_p = 1.0
> > compressibility = 4.5e-5
> > ref_p = 1.0
> > ; Random seed for Andersen thermostat
> > andersen_seed = 815131
> >
> > ; SIMULATED ANNEALING
> > ; Type of annealing for each temperature group (no/single/periodic)
> > annealing = no
> > ; 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 = yes
> > gen_temp = 300
> > gen_seed = 1993
> >
> > ; OPTIONS FOR BONDS
> > ;constraints = all-bonds
> > ; Type of constraint algorithm
> > constraint-algorithm = Lincs
> > ; Do not constrain the start configuration
> > unconstrained-start = no
> > ; Use successive overrelaxation to reduce the number of shake
> > iterations
> > Shake-SOR = no
> > ; Relative tolerance of shake
> > shake-tol = 1e-04
> > ; 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 =
> >
> >
>
> You're probably just
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up. I suggest
> equilibrating with a normal potential, and then shifting to your
> special regime. Then you can exclude initial conditions as the source
> of the problem, so long as your special regime is not wildly different
> from a normal potential.
>
> Mark
The system was first energy minimised without the tabulated potential.
It seems as if it is not blowing up on my desktop PC. Its currently up
to step 4800 (compared to step 50 running on the cluster) and still
going. I'm going to continue to run the job on my desktop PC to see if
it will complete.
The problem definitely seems to lie with the job running on the
computing cluster but I don't know enough about parallel computing etc
to know what the problem is. Any help would be appreciated,
Laura
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