[gmx-users] segfault(11) -- simulation blows up on first step
Itamar Kass
itamar.kass at gmail.com
Tue Jun 2 13:19:56 CEST 2009
Hi,
I don't see any immediate problem in your file, except the fact that you
have to couple all molecule to a heat bath. Second, has much as I know, you
can't reach 0K, so what the meaning?
Best,
Itamar
On Tue, Jun 2, 2009 at 9:11 PM, Inon Sharony <InonShar at tau.ac.il> wrote:
> Hi everyone!
>
> I'm trying to run a simulation of a single diatomic Sulfur molecule. When I
> run an equilibration scheme (generating velocities from a 300K
> Maxwell-Boltzmann distribution) it runs fine, but when I take the
> equilibrated molecule and couple one atom to a 0K heat bath (using
> Stochastic Dynamics) the simulation segfaults at the first step.
>
> I've enclosed as much information as I could. Notice (at the very bottom)
> that the md.log file shows an initial temperature of 17884.7K, but already
> in the report for step 0 the temperature, as well as many other
> thermodynamic quantities, are NaN.
>
> I've encountered one reference to the same error I'm getting, but itjust
> said that there was some problem with the input files, but didn'tsay what
> was the problem...
>
> I hope you will find some stupid mistake in the *.mdp file, or something
> easily remedied...
>
> P.S.
>
> I know GROMACS is not optimized for simulating tiny molecules, but I don't
> see why it should be such a critical problem...
>
>
> A wholotta supplemental data:
>
>
> MDRUN_MPI STD-I/O:
> ==================
>
> step 0
> [hydrogen:15285] *** Process received signal ***
> [hydrogen:15285] Signal: Segmentation fault (11)
> [hydrogen:15285] Signal code: Address not mapped (1)
> [hydrogen:15285] Failing at address: 0xfffffffe16c50a90
> [hydrogen:15285] [ 0] /lib64/libpthread.so.0 [0x355c00de80]
> [hydrogen:15285] [ 1] mdrun_mpi(gmx_pme_do+0x28b2) [0x4b56f2]
> [hydrogen:15285] [ 2] mdrun_mpi(do_force_lowlevel+0x1023) [0x47f6f3]
> [hydrogen:15285] [ 3] mdrun_mpi(do_force+0xe6e) [0x4c99ce]
> [hydrogen:15285] [ 4] mdrun_mpi(do_md+0x48f0) [0x42c4a0]
> [hydrogen:15285] [ 5] mdrun_mpi(mdrunner+0x831) [0x42d771]
> [hydrogen:15285] [ 6] mdrun_mpi(main+0x3c0) [0x42e6a0]
> [hydrogen:15285] [ 7] /lib64/libc.so.6(__libc_start_main+0xf4)
> [0x355b41d8b4]
> [hydrogen:15285] [ 8] mdrun_mpi [0x4131a9]
> [hydrogen:15285] *** End of error message ***
> ./test-2-6-09.sh: line 16: 15285 Segmentation fault mdrun_mpi -c md -v
>
>
>
> ----------------------------------------------------------------------------------------------------------------
>
> MD.MDP
> ======
>
> integrator = sd ;stochastic dynamics (velocity Langevin) using a
> leap-frog algorithm
> dt = 0.0001
> nsteps = 10000 ; [steps] ==> total
> (nsteps*dt) ps.
> nstxout = 1
> nstvout = 1
> nstfout = 1
> ; nstxtcout = 1
> nstenergy = 1 ; write energies to energy file every 1000 steps
> (default 100)
> nstlog = 1
> energygrps = SL SR
> ns_type = simple
> periodic_molecules = no
> coulombtype = PME
> tc-grps = SL SR
> tau_t = 0 1 ; mass/gamma
> ref_t = 0 0 ; refference (bath) temperature
> Pcoupl = no
> gen_vel = no
> gen_seed = -1 ; random seed based on computer clock
> constraints = none
>
>
> --------------------------------------------------------------------------------------------
>
> 1S2.itp
> =======
>
> [ atomtypes ]
> ;atomtype m (u) q (e) part.type V(cr) W(cr)
> SX 32.0600 0.000 A 1E-03 1E-05
>
> [ moleculetype ]
> ; Name nrexcl
> 1S2 2
>
> [ atoms ]
> ; nr type resnr resid atom cgnr charge mass
> 1 SX 1 1S2 SL 1 0.000 32.0600
> 2 SX 1 1S2 SR 2 0.000 32.0600
>
> [ bonds ]
> ; ai aj fu c0, c1, ...
> 1 2 2 0.2040 5.3E+6 0.2040 5.3E+6 ; SL SR
>
>
> --------------------------------------------------------------------------------------------
>
> TRAJ.TRR
> ========
>
> traj.trr frame 0:
> natoms= 2 step= 0 time=0.0000000e+00 lambda=
> 0
> box (3x3):
> box[ 0]={ 6.37511e+00, 0.00000e+00, 0.00000e+00}
> box[ 1]={ 0.00000e+00, 6.37511e+00, 0.00000e+00}
> box[ 2]={ 0.00000e+00, 0.00000e+00, 6.37511e+00}
> x (2x3):
> x[ 0]={ 3.19756e+00, 3.20532e+00, 3.18725e+00}
> x[ 1]={ 3.03044e+00, 3.21568e+00, 3.08875e+00}
> v (2x3):
> v[ 0]={ 2.22763e+00, -2.56083e-01, 1.38905e+00}
> v[ 1]={-2.22763e+00, 2.56083e-01, -1.38905e+00}
> f (2x3):
> f[ 0]={ 3.43615e+03, -2.13216e+02, 2.02509e+03}
> f[ 1]={-3.43615e+03, 2.13216e+02, -2.02509e+03}
>
>
>
> --------------------------------------------------------------------------------------------
>
> MD.LOG
> ======
>
>
>
> Input Parameters:
> integrator = sd
> nsteps = 10000
> init_step = 0
> ns_type = Simple
> nstlist = 10
> ndelta = 2
> nstcomm = 1
> comm_mode = Linear
> nstlog = 1
> nstxout = 1
> nstvout = 1
> nstfout = 1
> nstenergy = 1
> nstxtcout = 0
> init_t = 0
> delta_t = 0.0001
> xtcprec = 1000
> nkx = 54
> nky = 54
> nkz = 54
> pme_order = 4
> ewald_rtol = 1e-05
> ewald_geometry = 0
> epsilon_surface = 0
> optimize_fft = FALSE
> ePBC = xyz
> bPeriodicMols = FALSE
> bContinuation = FALSE
> bShakeSOR = FALSE
> etc = No
> epc = No
> epctype = Isotropic
> tau_p = 1
> ref_p (3x3):
> ref_p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> ref_p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> compress (3x3):
> compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> refcoord_scaling = No
> posres_com (3):
> posres_com[0]= 0.00000e+00
> posres_com[1]= 0.00000e+00
> posres_com[2]= 0.00000e+00
> posres_comB (3):
> posres_comB[0]= 0.00000e+00
> posres_comB[1]= 0.00000e+00
> posres_comB[2]= 0.00000e+00
> andersen_seed = 815131
> rlist = 1
> rtpi = 0.05
> coulombtype = PME
> rcoulomb_switch = 0
> rcoulomb = 1
> vdwtype = Cut-off
> rvdw_switch = 0
> rvdw = 1
> epsilon_r = 1
> epsilon_rf = 1
> tabext = 1
> implicit_solvent = No
> gb_algorithm = Still
> gb_epsilon_solvent = 80
> nstgbradii = 1
> rgbradii = 2
> gb_saltconc = 0
> gb_obc_alpha = 1
> gb_obc_beta = 0.8
> gb_obc_gamma = 4.85
> sa_surface_tension = 2.092
> DispCorr = No
> free_energy = no
> init_lambda = 0
> sc_alpha = 0
> sc_power = 0
> sc_sigma = 0.3
> delta_lambda = 0
> nwall = 0
> wall_type = 9-3
> wall_atomtype[0] = -1
> wall_atomtype[1] = -1
> wall_density[0] = 0
> wall_density[1] = 0
> wall_ewald_zfac = 3
> pull = no
> disre = No
> disre_weighting = Conservative
> disre_mixed = FALSE
> dr_fc = 1000
> dr_tau = 0
> nstdisreout = 100
> orires_fc = 0
> orires_tau = 0
> nstorireout = 100
> dihre-fc = 1000
> em_stepsize = 0.01
> em_tol = 10
> niter = 20
> fc_stepsize = 0
> nstcgsteep = 1000
> nbfgscorr = 10
> ConstAlg = Lincs
> shake_tol = 0.0001
> lincs_order = 4
> lincs_warnangle = 30
> lincs_iter = 1
> bd_fric = 0
> ld_seed = 1993
> cos_accel = 0
> deform (3x3):
> deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> userint1 = 0
> userint2 = 0
> userint3 = 0
> userint4 = 0
> userreal1 = 0
> userreal2 = 0
> userreal3 = 0
> userreal4 = 0
> grpopts:
> nrdf: 1.5 1.5
> ref_t: 0 0
> tau_t: 0 1
> anneal: No No
> ann_npoints: 0 0
> acc: 0 0 0
> nfreeze: N N N
> energygrp_flags[ 0]: 0 0
> energygrp_flags[ 1]: 0 0
> efield-x:
> n = 0
> efield-xt:
> n = 0
> efield-y:
> n = 0
> efield-yt:
> n = 0
> efield-z:
> n = 0
> efield-zt:
> n = 0
> bQMMM = FALSE
> QMconstraints = 0
> QMMMscheme = 0
> scalefactor = 1
> qm_opts:
> ngQM = 0
> Table routines are used for coulomb: TRUE
> Table routines are used for vdw: FALSE
> Will do PME sum in reciprocal space.
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen
> A smooth particle mesh Ewald method
> J. Chem. Phys. 103 (1995) pp. 8577-8592
> -------- -------- --- Thank You --- -------- --------
>
> Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
> Cut-off's: NS: 1 Coulomb: 1 LJ: 1
> System total charge: 0.000
> Generated table with 4000 data points for Ewald.
> Tabscale = 2000 points/nm
> Generated table with 4000 data points for LJ6.
> Tabscale = 2000 points/nm
> Generated table with 4000 data points for LJ12.
> Tabscale = 2000 points/nm
> Configuring nonbonded kernels...
> Testing x86_64 SSE2 support... present.
>
>
> Removing pbc first time
> Center of mass motion removal mode is Linear
> We have the following groups for center of mass motion removal:
> 0: rest
> There are: 2 Atoms
> Max number of connections per atom is 1
> Total number of connections is 2
> Max number of graph edges per atom is 1
> Total number of graph edges is 2
> Initial temperature: 17884.7 K
>
> Started mdrun on node 0 Tue Jun 2 13:38:03 2009
>
> Step Time Lambda
> 0 0.00000 0.00000
>
> Energies (kJ/mol)
> G96Bond LJ (SR) Coulomb (SR) Coul. recip. Potential
> 1.99416e+01 0.00000e+00 0.00000e+00 0.00000e+00 1.99416e+01
> Kinetic En. Total Energy Temperature Pressure (bar)
> nan nan nan nan
>
> Step Time Lambda
> 1 0.00010 0.00000
>
>
> --
> Inon Sharony
> ינון שרוני
> +972(3)6407634
> atto.TAU.ac.IL/~inonshar
> Please consider your environmental responsibility before printing this
> e-mail.
>
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