Antw: Re: Antw: [gmx-users] NaN error using mdrun-gpu
Emanuel Peter
Emanuel.Peter at chemie.uni-regensburg.de
Wed Dec 15 14:04:00 CET 2010
Hello
Did you use constraints = none instead of LINCS.
It could work better
bests,
Emanuel
>>> Bongkeun Kim 15.12.10 9.42 Uhr >>>
Hello,
I tried using 1fs timestep and it did not work.
I'm using nvidia T10 gpus(c1060 or s1070) and mdrun-gpu said it's not
supported gpu and I had to use "force-device=y". Do you think this is
the reason of the error?
Thanks.
Bongkeun Kim
Quoting Emanuel Peter :
> 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
>
>
>
>
>
> --
>
> gmx-users mailing list gmx-users at gromacs.org
>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
>
> Please search the archive at
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>
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