Antw: [gmx-users] NaN error using mdrun-gpu
Emanuel Peter
Emanuel.Peter at chemie.uni-regensburg.de
Wed Dec 15 09:15:39 CET 2010
Hello,
If you use for your timestep 1fs instead of 2fs, it could run better.
Bests,
Emanuel
>>> Bongkeun Kim 15.12.10 8.36 Uhr >>>
Hello,
I got an error log when I used gromacs-gpu on npt simulation.
The error is like:
---------------------------------------------------------------
Input Parameters:
integrator = md
nsteps = 50000000
init_step = 0
ns_type = Grid
nstlist = 5
ndelta = 2
nstcomm = 10
comm_mode = Linear
nstlog = 1000
nstxout = 1000
nstvout = 1000
nstfout = 0
nstcalcenergy = 5
nstenergy = 1000
nstxtcout = 1000
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 32
nky = 32
nkz = 32
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bPeriodicMols = FALSE
bContinuation = TRUE
bShakeSOR = FALSE
etc = V-rescale
nsttcouple = 5
epc = Parrinello-Rahman
epctype = Isotropic
nstpcouple = 5
tau_p = 2
ref_p (3x3):
ref_p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00}
ref_p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00}
ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00}
compress (3x3):
compress[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00}
compress[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00}
compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05}
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
rlistlong = 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 = 1
gb_saltconc = 0
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
gb_dielectric_offset = 0.009
sa_algorithm = Ace-approximation
sa_surface_tension = 2.05016
DispCorr = EnerPres
free_energy = no
init_lambda = 0
delta_lambda = 0
n_foreign_lambda = 0
sc_alpha = 0
sc_power = 0
sc_sigma = 0.3
sc_sigma_min = 0.3
nstdhdl = 10
separate_dhdl_file = yes
dhdl_derivatives = yes
dh_hist_size = 0
dh_hist_spacing = 0.1
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: 24715
ref_t: 325
tau_t: 0.1
anneal: No
ann_npoints: 0
acc: 0 0 0
nfreeze: N N N
energygrp_flags[ 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 --- -------- --------
Will do ordinary reciprocal space Ewald sum.
Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
Cut-off's: NS: 1 Coulomb: 1 LJ: 1
Long Range LJ corr.: 2.9723e-04
System total charge: 0.000
Generated table with 1000 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 1000 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 1000 data points for LJ12.
Tabscale = 500 points/nm
Generated table with 1000 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1000 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1000 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Enabling SPC-like water optimization for 3910 molecules.
Configuring nonbonded kernels...
Configuring standard C nonbonded kernels...
Initializing LINear Constraint Solver
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
LINCS: A Linear Constraint Solver for molecular simulations
J. Comp. Chem. 18 (1997) pp. 1463-1472
-------- -------- --- Thank You --- -------- --------
The number of constraints is 626
++++ 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 --- -------- --------
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
G. Bussi, D. Donadio and M. Parrinello
Canonical sampling through velocity rescaling
J. Chem. Phys. 126 (2007) pp. 014101
-------- -------- --- Thank You --- -------- --------
Max number of connections per atom is 103
Total number of connections is 37894
Max number of graph edges per atom is 4
Total number of graph edges is 16892
OpenMM plugins loaded from directory /home/bkim/packages/openmm/lib/plugins:
libOpenMMCuda.so, libOpenMMOpenCL.so,
The combination rule of the used force field matches the one used by OpenMM.
Gromacs will use the OpenMM platform: Cuda
Non-supported GPU selected (#1, Tesla T10 Processor), forced
continuing.Note, th
at the simulation can be slow or it migth even crash.
Pre-simulation ~15s memtest in progress...
Memory test completed without errors.
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
Entry Friedrichs2009 not found in citation database
-------- -------- --- Thank You --- -------- --------
Initial temperature: 0 K
Started mdrun on node 0 Tue Dec 14 23:10:20 2010
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
Potential Kinetic En. Total Energy Temperature Constr. rmsd
-1.40587e+05 3.36048e+04 -1.06982e+05 3.27065e+02 0.00000e+00
Step Time Lambda
1000 2.00000 0.00000
Energies (kJ/mol)
Potential Kinetic En. Total Energy Temperature Constr. rmsd
nan nan nan nan 0.00000e+00
Received the second INT/TERM signal, stopping at the next step
Step Time Lambda
1927 3.85400 0.00000
Energies (kJ/mol)
Potential Kinetic En. Total Energy Temperature Constr. rmsd
nan nan nan nan 0.00000e+00
Writing checkpoint, step 1927 at Tue Dec 14 23:12:07 2010
<====== ############### ==>
<==== A V E R A G E S ====>
<== ############### ======>
Statistics over 3 steps using 3 frames
Energies (kJ/mol)
Potential Kinetic En. Total Energy Temperature Constr. rmsd
nan nan nan nan 0.00000e+00
Box-X Box-Y Box-Z
3.91363e-24 6.72623e-44 -1.71925e+16
Total Virial (kJ/mol)
0.00000e+00 0.00000e+00 0.00000e+00
0.00000e+00 0.00000e+00 0.00000e+00
0.00000e+00 0.00000e+00 0.00000e+00
Pressure (bar)
0.00000e+00 0.00000e+00 0.00000e+00
0.00000e+00 0.00000e+00 0.00000e+00
0.00000e+00 0.00000e+00 0.00000e+00
Total Dipole (D)
0.00000e+00 0.00000e+00 0.00000e+00
------------------------------------------------------------------------
The input mdp file is given by
========================================================
title = OPLS Lysozyme MD
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 50000000 ;
dt = 0.002 ; 2 fs
; Output control
nstxout = 1000 ; save coordinates every 2 ps
nstvout = 1000 ; save velocities every 2 ps
nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps
nstenergy = 1000 ; save energies every 2 ps
nstlog = 1000 ; update log file every 2 ps
; Bond parameters
continuation = yes ; Restarting after NPT
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constraine
d
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist = 1.0 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range
electrostat
ics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = System ; two coupling groups - more accurate
tau_t = 0.1 ; time constant, in ps
ref_t = 325 ; reference temperature, one for each
group, in
K
; Pressure coupling is on
pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no ; Velocity generation is off
=========================================================================
It worked with generic cpu mdrun but gave this error when mdrun-gpu
was used by
mdrun-gpu -deffnm md_0_2 -device
"OpenMM:platform=Cuda,deviceid=1,force-device=y
es"
If you have any idea how to avoid this problem, I will really appreciate it.
Thank you.
Bongkeun Kim
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