Hi Filip,
My GPU details are:
|------------------- GPU DEVICE INFO --------------------
|
| CUDA Capable Devices Detected: 4
| CUDA Device ID in use: 3
| CUDA Device Name: Tesla S2050
| CUDA Device Global Mem Size: 3071 MB
| CUDA Device Num Multiprocessors: 14
| CUDA Device Core Freq: 1.15 GHz
|
|--------------------------------------------------------
Good day,
Santosh.
On Sat, 20 Aug 2011, filip fratev wrote:
> Hi Santosh,
> What kind of GPU you use?
>
>
> Regards,
> Filip
>
>
>
>
> ________________________________
> From: Santosh Mogurampelly <santosh.physics.iisc.ernet.in>
> To: AMBER Mailing List <amber.ambermd.org>
> Sent: Saturday, August 20, 2011 12:39 PM
> Subject: Re: [AMBER] Major GPU Update Released
>
> For my system of 109K atoms, earlier I get 3.75 ns/day and now with
> new updates I get 6.5 ns/day. Almost double! Great news for us. Thanks a
> lot Prof. Ross and team.
>
> Santosh
>
>
>
> On Sat, 20 Aug 2011, Levi Pierce wrote:
>
>> Had a chance to sit down and test out the new patch. Wow! Very
>> impressive performance boost on a variety of systems I have been running
>> pmemd.cuda on. Great work!
>>
>> On Fri, Aug 19, 2011 at 4:37 PM, Scott Le Grand <varelse2005.gmail.com>wrote:
>>
>>> 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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>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>>
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>>
>>
>>
>>
>
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Received on Sat Aug 20 2011 - 22:30:03 PDT
