[gmx-users] mdrun segmentation fault
Sikandar Mashayak
symashayak at gmail.com
Thu May 20 23:37:39 CEST 2010
It happens immediately at step 0., and the log file looks like :
Input Parameters:
integrator = md
nsteps = 20000
init_step = 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 0
comm_mode = Linear
nstlog = 1000
nstxout = 600
nstvout = 600
nstfout = 600
nstenergy = 1000
nstxtcout = 1000
init_t = 0
delta_t = 0.001
xtcprec = 10000
nkx = 44
nky = 42
nkz = 120
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 1
epsilon_surface = -1
optimize_fft = FALSE
ePBC = xyz
bPeriodicMols = FALSE
bContinuation = FALSE
bShakeSOR = FALSE
etc = Nose-Hoover
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 = 1.1
rtpi = 0.05
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1.1
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1.1
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 = EnerPres
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 = 100
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: 0 12822
ref_t: 0 300
tau_t: 0 0.2
anneal: No No
ann_npoints: 0 0
acc: 0 0 0
nfreeze: Y Y Y N
N N
energygrp_flags[ 0]: 1 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 the Ewald3DC correction for systems with a slab geometry.
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
Y. In-Chul and M. L. Berkowitz
Ewald summation for systems with slab geometry
J. Chem. Phys. 111 (1999) pp. 3155-3162
-------- -------- --- Thank You --- -------- --------
Using a Gaussian width (1/beta) of 0.352179 nm for Ewald
Cut-off's: NS: 1.1 Coulomb: 1.1 LJ: 1.1
System total charge: 0.000
Generated table with 4200 data points for Ewald.
Tabscale = 2000 points/nm
Generated table with 4200 data points for LJ6.
Tabscale = 2000 points/nm
Generated table with 4200 data points for LJ12.
Tabscale = 2000 points/nm
Enabling SPC water optimization for 2137 molecules.
Configuring nonbonded kernels...
Testing ia32 SSE2 support... present.
Removing pbc first time
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- --- Thank You --- -------- --------
There are: 7699 Atoms
Max number of connections per atom is 2
Total number of connections is 8548
Max number of graph edges per atom is 2
Total number of graph edges is 8548
Constraining the starting coordinates (step 0)
Constraining the coordinates at t0-dt (step 0)
RMS relative constraint deviation after constraining: 0.00e+00
Initial temperature: 304.27 K
Started mdrun on node 0 Thu May 20 16:33:38 2010
Step Time Lambda
0 0.00000 0.00000
Grid: 5 x 5 x 14 cells
Long Range LJ corr.: <C6> 1.1930e-03
Long Range LJ corr.: Epot -415.301, Pres: -51.4754, Vir: 415.301
Energies (kJ/mol)
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
6.44979e+04 -4.15301e+02 -1.00185e+05 -4.94669e+03 -4.10490e+04
Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
1.72141e+04 -2.38349e+04 -2.38347e+04 3.22940e+02 1.36187e+04
On Thu, May 20, 2010 at 4:30 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Sikandar Mashayak wrote:
>
>> Hi
>>
>> I have gromacs input files for md simulation, with these set up files
>> (*.mdp,*.top,*.itp *.gro), I can successfully run grompp and mdrun on one
>> machine, but when I move it to other machine, I get segmentation fault when
>> I do mdrun. Both the machines have exactly same types of installation of
>> gromacs 4.0.7 . Also, I can run water tutorials successfully on both the
>> machines.
>>
>> So what could be the source of segmentation fault?
>>
>>
> MD is chaotic, so you may not get the same result every time you run a
> simulation. Since you've not said how quickly the seg fault occurs it is
> exceptionally hard to diagnose. Generally, seg faults with mdrun occur
> because the system crashes from an instability. Without substantially more
> information (system contents, .mdp settings, relevant log file output, etc)
> there is not much more to suggest.
>
> -Justin
>
> thanks
>> sikandar
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
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