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 - 14:00:03 PDT
