Antw: [gmx-users] NaN error using mdrun-gpu

Bongkeun Kim bkim at chem.ucsb.edu
Wed Dec 15 18:37:25 CET 2010


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
>> 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 thewww interface
>> or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
> --
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> 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
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