Use a different gpu foe display I suspect
On Aug 19, 2011 4:09 PM, "filip fratev" <filipfratev.yahoo.com> wrote:
> 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
>
>
>
>
>
>
>
>
>
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Received on Fri Aug 19 2011 - 17:00:03 PDT
