Dear Filip,
thank you very much for your valuable contribution to this story !
For those who interested below is the relevant OUT part from this
Filip.s verification run.
We have the identical OS and similar HW.
#####We have differences in gcc versions:
My: gcc version 4.5.0 20100604 [gcc-4_5-branch revision 160292] (SUSE
Linux)
Filip.s: gcc (SUSE Linux) 4.3.4 [gcc-4_3-branch revision 152973]
#####and in CUDA SW.
My:
CUDA spec:
devdriver_3.2_linux_64_260.24.run
cudatoolkit_3.2.16_linux_64_suse11.2.run
gpucomputingsdk_3.2.16_linux.run
Filip.s
NVIDIA 260.19.36
Cuda 3.1,
Based on these new information it seems that the source of the problem is
the gcc compiler (some
problem with random generator ?) or eventually version of Cuda SW or the
combination.
So let say the first thing which came on my mind is recompilation of our
Amber11 using older gcc version,
that which Filip used for example and let us see ...
I have one question here for Filip:
Did you ever obtained any error on your system (some of that described in
this thread sooner or some else) ?
Thanks again !
Best wishes,
Marek
******** Relevant part of the Filip.s verification test**********
******** Relevant part of the Filip.s verification test**********
******** Relevant part of the Filip.s verification test**********
-------------------------------------------------------
Amber 11 SANDER 2010
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 11
| Run on 01/27/2011 at 16:25:27
[-O]verwriting output
File Assignments:
| MDIN: 1.in
| MDOUT: 1.out
| INPCRD: 1.rst
| PARM: 1.prmtop
| RESTRT: 1out.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: 1out.mdcrd
| MDINFO: mdinfo
Here is the input file:
heat ras-raf
&cntrl
imin=0,irest=1,ntx=5,
nstlim=50000,dt=0.002,
ntc=2,ntf=2,
cut=10.0, ntb=2, ntp=1, taup=1.0,
ntpr=5000, ntwx=5000,
ntt=3, gamma_ln=2.0, ig=676075,
temp0=298,
/
|--------------------- 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: 1
| CUDA Device ID in use: 0
| CUDA Device Name: GeForce GTX 470
| CUDA Device Global Mem Size: 1279 MB
| CUDA Device Num Multiprocessors: 14
| CUDA Device Core Freq: 1.22 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 = 43.365
| New format PARM file being parsed.
| Version = 1.000 Date = 01/21/11 Time = 18:45:59
| 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 = 92246 NTYPES = 16 NBONH = 89280 MBONA = 2945
NTHETH = 6302 MTHETA = 4240 NPHIH = 11120 MPHIA = 8029
NHPARM = 0 NPARM = 0 NNB = 147846 NRES = 29261
NBONA = 2945 NTHETA = 4240 NPHIA = 8029 NUMBND = 33
NUMANG = 67 NPTRA = 38 NATYP = 25 NPHB = 1
IFBOX = 2 NMXRS = 77 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Coordinate Index Table dimensions: 17 17 17
| Direct force subcell size = 6.2484 6.2484 6.2484
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
= 500
iwrap = 0, 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 = 10.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 50000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = -1.00000
Langevin dynamics temperature regulation:
ig = 676075
temp0 = 298.00000, 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 = 106.223 Box Y = 106.223 Box Z = 106.223
Alpha = 109.471 Beta = 109.471 Gamma = 109.471
NFFT1 = 108 NFFT2 = 108 NFFT3 = 108
Cutoff= 10.000 Tol =0.100E-04
Ewald Coefficient = 0.27511
Interpolation order = 4
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 3700.000 ps
Number of triangulated 3-point waters found: 28820
Sum of charges from parm topology file = -0.00266701
Forcing neutrality...
| Dynamic Memory, Types Used:
| Reals 2846082
| Integers 2613755
| Nonbonded Pairs Initial Allocation: 27902108
| GPU memory information:
| KB of GPU memory in use: 876823
| KB of CPU memory in use: 77099
--------------------------------------------------------------------------------
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 = 0.8314E-11 at 2.736960
---------------------------------------------------
|---------------------------------------------------
| APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.33
| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
| with 50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt. 2.80
|---------------------------------------------------
NSTEP = 5000 TIME(PS) = 3710.000 TEMP(K) = 297.79 PRESS =
60.2
Etot = -207528.7559 EKtot = 55465.7266 EPtot =
-262994.4824
BOND = 12722.7807 ANGLE = 5383.2634 DIHED =
1782.5626
1-4 NB = 1253.2627 1-4 EEL = 32582.7471 VDWAALS =
45110.7010
EELEC = -361829.7998 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 25878.0000 VIRIAL = 24678.2848 VOLUME =
923047.1445
Density =
1.0163
------------------------------------------------------------------------------
NSTEP = 10000 TIME(PS) = 3720.000 TEMP(K) = 296.80 PRESS =
-12.9
Etot = -208476.2108 EKtot = 55281.8750 EPtot =
-263758.0858
BOND = 12894.4298 ANGLE = 5343.3677 DIHED =
1798.8020
1-4 NB = 1205.0200 1-4 EEL = 32543.9225 VDWAALS =
45182.6696
EELEC = -362726.2974 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 25760.0657 VIRIAL = 26016.4707 VOLUME =
921773.9291
Density =
1.0177
------------------------------------------------------------------------------
NSTEP = 15000 TIME(PS) = 3730.000 TEMP(K) = 296.47 PRESS
= 2.1
Etot = -207826.4718 EKtot = 55219.9375 EPtot =
-263046.4093
BOND = 12817.7798 ANGLE = 5348.0198 DIHED =
1769.2348
1-4 NB = 1228.9614 1-4 EEL = 32562.1284 VDWAALS =
44912.9028
EELEC = -361685.4363 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 25785.1440 VIRIAL = 25743.7122 VOLUME =
922364.9202
Density =
1.0170
------------------------------------------------------------------------------
NSTEP = 20000 TIME(PS) = 3740.000 TEMP(K) = 297.74 PRESS =
-1.0
Etot = -207983.5671 EKtot = 55455.3867 EPtot =
-263438.9538
BOND = 12911.8300 ANGLE = 5304.5698 DIHED =
1780.6825
1-4 NB = 1219.8619 1-4 EEL = 32660.1010 VDWAALS =
44948.5692
EELEC = -362264.5682 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 25935.6954 VIRIAL = 25956.3596 VOLUME =
921616.9026
Density =
1.0178
------------------------------------------------------------------------------
NSTEP = 25000 TIME(PS) = 3750.000 TEMP(K) = 297.48 PRESS =
-143.3
Etot = -207726.0675 EKtot = 55408.5313 EPtot =
-263134.5987
BOND = 13021.7387 ANGLE = 5253.2554 DIHED =
1795.5507
1-4 NB = 1246.4234 1-4 EEL = 32614.4983 VDWAALS =
44693.4432
EELEC = -361759.5086 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 25633.4157 VIRIAL = 28488.1980 VOLUME =
922455.8130
Density =
1.0169
------------------------------------------------------------------------------
NSTEP = 30000 TIME(PS) = 3760.000 TEMP(K) = 297.22 PRESS =
33.3
Etot = -208300.4298 EKtot = 55359.6914 EPtot =
-263660.1212
BOND = 12859.0691 ANGLE = 5368.4443 DIHED =
1799.1768
1-4 NB = 1214.7949 1-4 EEL = 32473.7844 VDWAALS =
45181.8227
EELEC = -362557.2134 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 25940.3133 VIRIAL = 25277.2747 VOLUME =
922317.7516
Density =
1.0171
------------------------------------------------------------------------------
> Hi Marek,
> I performed 50 000 steps. You can find the outputs as an attache file.
> Update: Because the output files are about 2.7mb and attachment needs to
> be approved by moderator I am sending you the results privately too
> (just in case).
>
> My system:
> --------------------------------------
> Linux 2.6.34-12-desktop x86_64
> openSUSE 11.3 (x86_64)
> GeForce GTX 470
> NVIDIA 260.19.36
> AMD Phenom(tm) II X6 1090T Processor
> RAM: 7.8 GiB
> --------------------------------------
> Cuda 3.1, everything compiled by gcc (SUSE Linux) 4.3.4 [gcc-4_3-branch
> revision 152973] due to described issues with CUDA and newer versions.
>
> Regards,
> Filip
>
>
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> __________ Informace od ESET NOD32 Antivirus, verze databaze 5824
> (20110127) __________
>
> Tuto zpravu proveril ESET NOD32 Antivirus.
>
> http://www.eset.cz
>
>
>
--
Tato zpráva byla vytvořena převratným poštovním klientem Opery:
http://www.opera.com/mail/
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Received on Thu Jan 27 2011 - 08:30:09 PST
