Antw: [gmx-users] NaN error using mdrun-gpu
Szilárd Páll
szilard.pall at cbr.su.se
Wed Dec 15 15:49:13 CET 2010
Hi,
Tesla C1060 and S1070 should is definitely supported so it's strange
that you get that warning. The only thing I can think of is that for
some reason the CUDA runtime reports the name of the GPUS other than
C1060/S1070. Could you please run the deviceQuery from the SDK and
provide the output here?
However, that should not be causing the NaN issue. Does the same
simulation run on the CPU?
Cheers,
--
Szilárd
2010/12/15 Bongkeun Kim <bkim at chem.ucsb.edu>:
> 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 <Emanuel.Peter at chemie.uni-regensburg.de>:
>
>> 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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>>
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>>
>>
>>
>
>
>
>
> --
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