Hi Ross,
I compiled the new code and performed many tests and the results are really impressive! I will post later.
However, I am in a big trouble with my systems (116K atoms) and hope that you will be able to help me.
The problem is that with the new code I am not able to simulate these proteins (116K) with GTX590 (1.5GB per core), because of some memory issue/bug:
cudaMalloc GpuBuffer::Allocate failed out of memory
With the older code I had no any problems with same input files and configuration. I tried both NPT and NVT but the same problem...
Then I use GTX580 3GB and it works fine. From output you can see that the requested memory is just 882MB:
For NPT:
| GPU memory information:
| KB of GPU memory in use: 882413
| KB of CPU memory in use: 104090
and for restrained NVT:
| GPU memory information:
| KB of GPU memory in use: 1006146
| KB of CPU memory in use: 99724
Thus I shouldn’t have any problem.
What could be the issue and how I can solve it?
Regards,
Filip
Below is the output file (my NPT density.out) and heat.in:
-------------------------------------------------------
Amber 11 SANDER 2010
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 11
| Run on 08/20/2011 at 01:42:20
[-O]verwriting output
File Assignments:
| MDIN: densityF.in
| MDOUT: 0densitytest580Karti.out
| INPCRD: heattest.rst
| PARM: MyosinWT.prmtop
| RESTRT: density1test.rst
| REFC: heattest.rst
| MDVEL: mdvel
| MDEN: mden
| MDCRD: density1test.mdcrd
| MDINFO: mdinfo
Here is the input file:
Ligand9 density
&cntrl
imin=0,irest=1, ntx=5,
nstlim=5000,dt=0.002,
ntc=2,ntf=2, ig=-1, iwrap=1,
cut=8.0, ntb=2, ntp=1, taup=1.0,
ntpr=5000, ntwx=5000, ntwr=10000,
ntt=3, gamma_ln=2.0,
temp0=300.0,
/
Note: ig = -1. Setting random seed based on wallclock time in microseconds.
|--------------------- INFORMATION ----------------------
| GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
| Version 2.2
|
| 08/16/2011
|
|
| 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: 1
| CUDA Device ID in use: 0
| CUDA Device Name: GeForce GTX 580
| CUDA Device Global Mem Size: 3071 MB
| CUDA Device Num Multiprocessors: 16
| CUDA Device Core Freq: 1.57 GHz
|
|--------------------------------------------------------
| Conditional Compilation Defines Used:
| DIRFRC_COMTRANS
| DIRFRC_EFS
| DIRFRC_NOVEC
| PUBFFT
| FFTLOADBAL_2PROC
| BINTRAJ
| CUDA
| Largest sphere to fit in unit cell has radius = 48.492
| New format PARM file being parsed.
| Version = 1.000 Date = 05/27/11 Time = 11:50:53
| 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 = 116271 NTYPES = 21 NBONH = 109977 MBONA = 6423
NTHETH = 14190 MTHETA = 8659 NPHIH = 27033 MPHIA = 21543
NHPARM = 0 NPARM = 0 NNB = 207403 NRES = 35368
NBONA = 6423 NTHETA = 8659 NPHIA = 21543 NUMBND = 59
NUMANG = 124 NPTRA = 64 NATYP = 40 NPHB = 1
IFBOX = 2 NMXRS = 43 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Coordinate Index Table dimensions: 23 23 23
| Direct force subcell size = 5.1644 5.1644 5.1644
BOX TYPE: TRUNCATED OCTAHEDRON
--------------------------------------------------------------------------------
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 = 5000, ntrx = 1, ntwr = 10000
iwrap = 1, ntwx = 5000, 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 = 8.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 5000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = -1.00000
Langevin dynamics temperature regulation:
ig = 974683
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 = 5000
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
vdwmeth = 1, eedmeth = 1, netfrc = 1
Box X = 118.781 Box Y = 118.781 Box Z = 118.781
Alpha = 109.471 Beta = 109.471 Gamma = 109.471
NFFT1 = 128 NFFT2 = 128 NFFT3 = 128
Cutoff= 8.000 Tol =0.100E-04
Ewald Coefficient = 0.34864
Interpolation order = 4
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 10.000 ps
Number of triangulated 3-point waters found: 34583
Sum of charges from parm topology file = -0.00000040
Forcing neutrality...
| Dynamic Memory, Types Used:
| Reals 3524690
| Integers 3800219
| Nonbonded Pairs Initial Allocation: 19420163
| GPU memory information:
| KB of GPU memory in use: 882413
| KB of CPU memory in use: 104090
--------------------------------------------------------------------------------
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 = 0.8332E-11 at 2.782960
---------------------------------------------------
|---------------------------------------------------
| APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.47
| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.89
|---------------------------------------------------
wrapping first mol.: 38.333512154956900 54.211771142609109 93.897534410964738
wrapping first mol.: 38.333512154956900 54.211771142609109 93.897534410964738
NSTEP = 5000 TIME(PS) = 20.000 TEMP(K) = 300.01 PRESS = -23.7
Etot = -281399.8069 EKtot = 71193.9609 EPtot = -352593.7679
BOND = 2490.5718 ANGLE = 6429.0655 DIHED = 8582.5720
1-4 NB = 2942.3115 1-4 EEL = 32655.1879 VDWAALS = 42104.9713
EELEC = -447798.4479 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 30939.5460 VIRIAL = 31538.3575 VOLUME = 1170788.5879
Density = 1.0106
------------------------------------------------------------------------------
A V E R A G E S O V E R 1 S T E P S
NSTEP = 5000 TIME(PS) = 20.000 TEMP(K) = 300.01 PRESS = -23.7
Etot = -281399.8069 EKtot = 71193.9609 EPtot = -352593.7679
BOND = 2490.5718 ANGLE = 6429.0655 DIHED = 8582.5720
1-4 NB = 2942.3115 1-4 EEL = 32655.1879 VDWAALS = 42104.9713
EELEC = -447798.4479 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 30939.5460 VIRIAL = 31538.3575 VOLUME = 1170788.5879
Density = 1.0106
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 5000 TIME(PS) = 20.000 TEMP(K) = 0.00 PRESS = 0.0
Etot = 0.0000 EKtot = 0.0000 EPtot = 0.0000
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 0.0000
EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT = 0.0000
------------------------------------------------------------------------------
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| NonSetup CPU Time in Major Routines:
|
| Routine Sec %
| ------------------------------
| Nonbond 97.05 92.22
| Bond 0.00 0.00
| Angle 0.00 0.00
| Dihedral 0.00 0.00
| Shake 2.47 2.34
| RunMD 5.71 5.43
| Other 0.00 0.00
| ------------------------------
| Total 105.24
| PME Nonbond Pairlist CPU Time:
|
| Routine Sec %
| ---------------------------------
| Set Up Cit 0.00 0.00
| Build List 0.00 0.00
| ---------------------------------
| Total 0.00 0.00
| PME Direct Force CPU Time:
|
| Routine Sec %
| ---------------------------------
| NonBonded Calc 0.00 0.00
| Exclude Masked 0.00 0.00
| Other 0.00 0.00
| ---------------------------------
| Total 0.00 0.00
| PME Reciprocal Force CPU Time:
|
| Routine Sec %
| ---------------------------------
| 1D bspline 0.00 0.00
| Grid Charges 0.00 0.00
| Scalar Sum 0.00 0.00
| Gradient Sum 0.00 0.00
| FFT 0.00 0.00
| ---------------------------------
| Total 0.00 0.00
| Final Performance Info:
| -----------------------------------------------------
| Average timings for last 0 steps:
| Elapsed(s) = 0.00 Per Step(ms) = +Infinity
| ns/day = 0.00 seconds/ns = +Infinity
|
| Average timings for all steps:
| Elapsed(s) = 105.26 Per Step(ms) = 21.05
| ns/day = 8.21 seconds/ns = 10525.53
| -----------------------------------------------------
| Setup CPU time: 0.90 seconds
| NonSetup CPU time: 105.24 seconds
| Total CPU time: 106.13 seconds 0.03 hours
| Setup wall time: 1 seconds
| NonSetup wall time: 105 seconds
| Total wall time: 106 seconds 0.03 hours
heat Ligand9
&cntrl
irest=0, ntx=1,
nstlim=5000, dt=0.002,
ntc=2,ntf=2, iwrap=1,
cut=8.0, ntb=1, ig=-1,
ntpr=1000, ntwx=1000, ntwr=10000,
ntt=3, gamma_ln=2.0,
tempi=0.0, temp0=300.0,
ioutfm=1, ntr=1,
ntr=1,
/
Group input for restrained atoms
2.0
RES 1 790
END
END
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Aug 19 2011 - 16:30:03 PDT
