Antw: [gmx-users] NaN error using mdrun-gpu
Justin A. Lemkul
jalemkul at vt.edu
Wed Dec 15 14:13:00 CET 2010
Bongkeun Kim wrote:
> 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?
Probably. Please note the documentation and the specific warning about this option:
http://www.gromacs.org/Downloads/Installation_Instructions/Gromacs_on_GPUs?highlight=gromacs+on+gpu#Gromacs-GPU_specific_mdrun_features
Also, when using PME, I don't think there's any real benefit to using the GPU
version of mdrun. I seem to recall posts that doing so actually results in
poorer performance than the standard CPU binary. GPU is particularly beneficial
for implicit solvent simulations.
-Justin
> 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
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>
>> Please don't post (un)subscribe requests to the list. Use the
>>
>> www interface or send it to gmx-users-request at gromacs.org.
>>
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>
>
>
>
--
========================================
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
========================================
More information about the gromacs.org_gmx-users
mailing list