Hi Ross,
still fails with the reduced cutoff. I'm sending you the input files off
the list.
Thanks
Sasha
Ross Walker wrote:
> 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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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Fri Apr 15 2011 - 15:00:03 PDT
