Antw: [gmx-users] NaN error using mdrun-gpu
Szilárd Páll
szilard.pall at cbr.su.se
Thu Dec 30 16:51:35 CET 2010
Hi,
I've never seen/had my hands on the Tesla T10 so I didn't know that's
the name it reports. I'll fix this for the next release. Rest assured
that on this hardware Gromacs-GPU should run just fine.
On the other hand, your driver version is very strange: CUDA Driver
Version = 4243455, while it should be 3.2. Are you sure your CUDA
setup is not messed up? Do other programs run well?
Cheers,
--
Szilárd
2010/12/15 Bongkeun Kim <bkim at chem.ucsb.edu>:
> Hello,
>
> This is the output from deviceQuery command:
> ./deviceQuery Starting...
>
> CUDA Device Query (Runtime API) version (CUDART static linking)
>
> There are 4 devices supporting CUDA
>
> Device 0: "Tesla T10 Processor"
> CUDA Driver Version: 3.20
> CUDA Runtime Version: 3.20
> CUDA Capability Major revision number: 1
> CUDA Capability Minor revision number: 3
> Total amount of global memory: 4294770688 bytes
> Number of multiprocessors: 30
> Number of cores: 240
> Total amount of constant memory: 65536 bytes
> Total amount of shared memory per block: 16384 bytes
> Total number of registers available per block: 16384
> Warp size: 32
> Maximum number of threads per block: 512
> Maximum sizes of each dimension of a block: 512 x 512 x 64
> Maximum sizes of each dimension of a grid: 65535 x 65535 x 1
> Maximum memory pitch: 2147483647 bytes
> Texture alignment: 256 bytes
> Clock rate: 1.44 GHz
> Concurrent copy and execution: Yes
> Run time limit on kernels: No
> Integrated: No
> Support host page-locked memory mapping: Yes
> Compute mode: Default (multiple host
> threads can use this device simultaneously)
>
> Device 1: "Tesla T10 Processor"
> CUDA Driver Version: 3.20
> CUDA Runtime Version: 3.20
> CUDA Capability Major revision number: 1
> CUDA Capability Minor revision number: 3
> Total amount of global memory: 4294770688 bytes
> Number of multiprocessors: 30
> Number of cores: 240
> Total amount of constant memory: 65536 bytes
> Total amount of shared memory per block: 16384 bytes
> Total number of registers available per block: 16384
> Warp size: 32
> Maximum number of threads per block: 512
> Maximum sizes of each dimension of a block: 512 x 512 x 64
> Maximum sizes of each dimension of a grid: 65535 x 65535 x 1
> Maximum memory pitch: 2147483647 bytes
> Texture alignment: 256 bytes
> Clock rate: 1.44 GHz
> Concurrent copy and execution: Yes
> Run time limit on kernels: No
> Integrated: No
> Support host page-locked memory mapping: Yes
> Compute mode: Default (multiple host
> threads can use this device simultaneously)
>
> Device 2: "Tesla T10 Processor"
> CUDA Driver Version: 3.20
> CUDA Runtime Version: 3.20
> CUDA Capability Major revision number: 1
> CUDA Capability Minor revision number: 3
> Total amount of global memory: 4294770688 bytes
> Number of multiprocessors: 30
> Number of cores: 240
> Total amount of constant memory: 65536 bytes
> Total amount of shared memory per block: 16384 bytes
> Total number of registers available per block: 16384
> Warp size: 32
> Maximum number of threads per block: 512
> Maximum sizes of each dimension of a block: 512 x 512 x 64
> Maximum sizes of each dimension of a grid: 65535 x 65535 x 1
> Maximum memory pitch: 2147483647 bytes
> Texture alignment: 256 bytes
> Clock rate: 1.44 GHz
> Concurrent copy and execution: Yes
> Run time limit on kernels: No
> Integrated: No
> Support host page-locked memory mapping: Yes
> Compute mode: Default (multiple host
> threads can use this device simultaneously)
>
> Device 3: "Tesla T10 Processor"
> CUDA Driver Version: 3.20
> CUDA Runtime Version: 3.20
> CUDA Capability Major revision number: 1
> CUDA Capability Minor revision number: 3
> Total amount of global memory: 4294770688 bytes
> Number of multiprocessors: 30
> Number of cores: 240
> Total amount of constant memory: 65536 bytes
> Total amount of shared memory per block: 16384 bytes
> Total number of registers available per block: 16384
> Warp size: 32
> Maximum number of threads per block: 512
> Maximum sizes of each dimension of a block: 512 x 512 x 64
> Maximum sizes of each dimension of a grid: 65535 x 65535 x 1
> Maximum memory pitch: 2147483647 bytes
> Texture alignment: 256 bytes
> Clock rate: 1.44 GHz
> Concurrent copy and execution: Yes
> Run time limit on kernels: No
> Integrated: No
> Support host page-locked memory mapping: Yes
> Compute mode: Default (multiple host
> threads can use this device simultaneously)
>
> deviceQuery, CUDA Driver = CUDART, CUDA Driver Version = 4243455, CUDA
> Runtime Version = 3.20, NumDevs = 4, Device = Tesla T10 Processor, Device =
> Tesla T10 Processor
>
>
> PASSED
> ----------------------------------------------------------------------------
>
> And this simulation was already done by cpu first and I tried to run the
> second one with gpu.
> Thanks.
> Bongkeun Kim
>
>
> Quoting Szilard Pall <szilard.pall at cbr.su.se>:
>
>> 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,
>> --
>> Szilard
>>
>>
>>
>> 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
>>>> 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
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>>
>>> --
>>> gmx-users mailing list gmx-users at gromacs.org
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>>> Please search the archive at
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>> --
>> 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
>>
>
>
>
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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