Hi Sasha,
Can you try with cut=8.0. I assume that should work fine. Also send me the
files and I'll see if the problem is still there in the development version.
All the best
Ross
> -----Original Message-----
> From: Sasha Buzko [mailto:obuzko.ucla.edu]
> Sent: Friday, April 15, 2011 1:52 PM
> To: AMBER Mailing List
> Subject: [AMBER] pmemd.cuda: max pairlist problem with a large system
>
> Ross, Scott,
> I guess it's mostly question for you.
>
> I'm simulating a large protein in a mixture of solvents
> (water-isopropanol). Minimization and hearing are going well, but at
> the
> stage of density equilibration I end up with two different errors,
> depending on whether it's run as the serial or the parallel version.
> When pmemd.cuda is used, I get "maximum pairlist cutoff must be less
> than unit cell max sphere radius".
> With pmemd.cuda.MPI on 4 cores the process fails with "unspecified
> launch failure launching kernel kClearNBForces".
>
> The system is a bit over 230k atoms and the simulation is run on Tesla
> 2050. Below is the output file for the serial version. I can email you
> the prmtop and inpcrd files offlist, if you'd like to reproduce the
> issue.
>
> Thanks for any suggestions.
>
> Sasha
>
>
>
>
> -------------------------------------------------------
> Amber 11 SANDER 2010
> -------------------------------------------------------
>
> | PMEMD implementation of SANDER, Release 11
>
> | Run on 04/15/2011 at 12:00:27
>
> [-O]verwriting output
>
> File Assignments:
> | MDIN:
> wat_density.in
> | MDOUT:
> ad5_ipr_1pct_density.out
> | INPCRD:
> ad5_ipr_1pct_heat.rst
> | PARM:
> ad5_ipr_1pct.prmtop
> | RESTRT:
> ad5_ipr_1pct_density.rst
> | REFC:
> ad5_ipr_1pct_heat.rst
> | MDVEL:
> mdvel
> | MDEN:
> mden
> | MDCRD:
> ad5_ipr_1pct_density.mdcrd
> | MDINFO:
> mdinfo
>
>
> Here is the input file:
>
> protein:
> density
> &cntrl
>
> imin =
> 0,
> irest =
> 1,
> ntx =
> 5,
> ntb =
> 2,
> cut =
> 12,
> ntr =
> 1,
> ntp =
> 1,
> ntc =
> 2,
> ntf =
> 2,
> temp0 =
> 300.0,
> ntt =
> 3,
> gamma_ln =
> 2.0,
> nstlim = 50000, dt =
> 0.001,
> ntpr = 500, ntwx = 500, ntwr =
> 10000
> /
>
> Keep protein fixed with weak
> restraints
> 10.0
>
> RES 1
> 2480
> END
>
> END
>
>
>
>
> |--------------------- INFORMATION ----------------------
> | GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
> | Version 2.1
> |
> | 12/20/2010
> |
> |
> | Implementation by:
> | Ross C. Walker (SDSC)
> | Scott Le Grand (nVIDIA)
> | Duncan Poole (nVIDIA)
> |
> | CAUTION: The CUDA code is currently experimental.
> | You use it at your own risk. Be sure to
> | check ALL results carefully.
> |
> | Precision model in use:
> | [SPDP] - Hybrid Single/Double Precision (Default).
> |
> |--------------------------------------------------------
>
> |------------------- GPU DEVICE INFO --------------------
> |
> | CUDA Capable Devices Detected: 8
> | CUDA Device ID in use: 7
> | CUDA Device Name: Tesla C2050
> | CUDA Device Global Mem Size: 2687 MB
> | CUDA Device Num Multiprocessors: 14
> | CUDA Device Core Freq: 1.15 GHz
> |
> |--------------------------------------------------------
>
>
> | Conditional Compilation Defines Used:
> | DIRFRC_COMTRANS
> | DIRFRC_EFS
> | DIRFRC_NOVEC
> | PUBFFT
> | FFTLOADBAL_2PROC
> | MKL
> | CUDA
>
> | Largest sphere to fit in unit cell has radius = 61.768
>
> | New format PARM file being parsed.
> | Version = 1.000 Date = 04/14/11 Time = 11:46:45
>
> | Note: 1-4 EEL scale factors were NOT found in the topology file.
> | Using default value of 1.2.
>
> | Note: 1-4 VDW scale factors were NOT found in the topology file.
> | Using default value of 2.0.
> | Duplicated 0 dihedrals
>
> | Duplicated 0 dihedrals
>
> -----------------------------------------------------------------------
> ---------
> 1. RESOURCE USE:
> -----------------------------------------------------------------------
> ---------
>
> getting new box info from bottom of inpcrd
>
> NATOM = 231564 NTYPES = 17 NBONH = 214278 MBONA = 17008
> NTHETH = 42292 MTHETA = 22432 NPHIH = 80922 MPHIA = 50896
> NHPARM = 0 NPARM = 0 NNB = 452360 NRES = 67504
> NBONA = 17008 NTHETA = 22432 NPHIA = 50896 NUMBND = 48
> NUMANG = 96 NPTRA = 42 NATYP = 36 NPHB = 1
> IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0
> NCOPY = 0
>
> | Coordinate Index Table dimensions: 19 19 23
> | Direct force subcell size = 6.6072 6.5019 6.7625
>
> BOX TYPE: RECTILINEAR
>
> -----------------------------------------------------------------------
> ---------
> 2. CONTROL DATA FOR THE RUN
> -----------------------------------------------------------------------
> ---------
>
>
>
>
> General flags:
> imin = 0, nmropt = 0
>
> Nature and format of input:
> ntx = 5, irest = 1, ntrx = 1
>
> Nature and format of output:
> ntxo = 1, ntpr = 500, ntrx = 1, ntwr
> = 10000
> iwrap = 0, ntwx = 500, ntwv = 0, ntwe
> = 0
> ioutfm = 0, ntwprt = 0, idecomp = 0,
> rbornstat= 0
>
> Potential function:
> ntf = 2, ntb = 2, igb = 0, nsnb
> = 25
> ipol = 0, gbsa = 0, iesp = 0
> dielc = 1.00000, cut = 12.00000, intdiel = 1.00000
>
> Frozen or restrained atoms:
> ibelly = 0, ntr = 1
>
> Molecular dynamics:
> nstlim = 50000, nscm = 0, nrespa = 1
> t = 0.00000, dt = 0.00100, vlimit = -1.00000
>
> Langevin dynamics temperature regulation:
> ig = 71277
> temp0 = 300.00000, tempi = 0.00000, gamma_ln= 2.00000
>
> Pressure regulation:
> ntp = 1
> pres0 = 1.00000, comp = 44.60000, taup = 1.00000
>
> SHAKE:
> ntc = 2, jfastw = 0
> tol = 0.00001
>
> | Intermolecular bonds treatment:
> | no_intermolecular_bonds = 1
>
> | Energy averages sample interval:
> | ene_avg_sampling = 500
>
> Ewald parameters:
> verbose = 0, ew_type = 0, nbflag = 1, use_pme
> = 1
> vdwmeth = 1, eedmeth = 1, netfrc = 1
> Box X = 125.537 Box Y = 123.537 Box Z = 155.537
> Alpha = 90.000 Beta = 90.000 Gamma = 90.000
> NFFT1 = 128 NFFT2 = 128 NFFT3 = 160
> Cutoff= 12.000 Tol =0.100E-04
> Ewald Coefficient = 0.22664
> Interpolation order = 4
>
> LOADING THE CONSTRAINED ATOMS AS GROUPS
>
>
> 5. REFERENCE ATOM COORDINATES
>
>
>
> ----- READING GROUP 1; TITLE:
> Keep protein fixed with weak
> restraints
>
> GROUP 1 HAS HARMONIC CONSTRAINTS 10.00000
> GRP 1 RES 1 TO 2480
> Number of atoms in this group = 36276
> ----- END OF GROUP READ -----
>
> -----------------------------------------------------------------------
> ---------
> 3. ATOMIC COORDINATES AND VELOCITIES
> -----------------------------------------------------------------------
> ---------
>
>
>
> begin time read from input coords = 50.000 ps
>
>
> Number of triangulated 3-point waters found: 65000
>
> Sum of charges from parm topology file = 0.00000064
> Forcing neutrality...
>
> | Dynamic Memory, Types Used:
> | Reals 7862102
> | Integers 8626215
>
> | Nonbonded Pairs Initial Allocation: 115162566
>
> | GPU memory information:
> | KB of GPU memory in use: 2011231
> | KB of CPU memory in use: 219916
>
> -----------------------------------------------------------------------
> ---------
> 4. RESULTS
> -----------------------------------------------------------------------
> ---------
>
> ---------------------------------------------------
> APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
> using 5000.0 points per unit in tabled values
> TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
> | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
> | CHECK d/dx switch(x): max rel err = 0.7967E-11 at 2.716640
> ---------------------------------------------------
> |---------------------------------------------------
> | APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
> | with 50.0 points per unit in tabled values
> | Relative Error Limit not exceeded for r .gt. 2.27
> | APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
> | with 50.0 points per unit in tabled values
> | Relative Error Limit not exceeded for r .gt. 2.78
> |---------------------------------------------------
> | ERROR: max pairlist cutoff must be less than unit cell max sphere
> radius!
>
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Received on Fri Apr 15 2011 - 14:30:03 PDT
