Hi Marek,
Just to let you know, i started your run couple minutes ago. I will
keep you informed.
best
peker
2011/1/26 Marek Maly <marek.maly.ujep.cz>:
> Hi Ross and All,
>
> here are some system specifications. Moreover I already confirmed
> reproducibility of the given NaN error on another PC equipped with
> GTX 470 GPU (with identical architecture as the first PC where I originally
> discovered the error). On the other hand the error was NOT
> reproduced on our Tesla C2050 ! - see below.
>
> I am really curious if you or anyone else will be able to reproduce NaN
> error on GTX 470 GPU system,
> using my previously posted input files.
>
>
> Best wishes,
>
> Marek
>
>
>
>
> ****************GTX 470 MACHINES*****************
>
> SW:
>
> OS spec:
>
> Linux 2.6.34-12-desktop (OpenSuSE)
>
> GNU Amber11 compilation with bugfixes applied up to bugfix 12.
>
> gcc version 4.5.0 20100604 [gcc-4_5-branch revision 160292] (SUSE Linux)
>
> (obtained with command gcc -v or gfortran -v)
>
> 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
>
> Regarding to HW, I know for this moment that PCs are equipped with
> six-core AMD CPUs and GTX 470 GPUs,
> I will learn the details from the responsible guy and will send during
> tomorrow.
>
> ****************TESLA MACHINE*****************
>
> SW:
>
> OS spec:
>
> Ubuntu 10.04.1 LTS (Ubuntu server)
>
>
> GNU Amber11 compilation with bugfixes applied up to bugfix 11 (for the
> moment).
>
> gcc version 4.4.3 (Ubuntu 4.4.3-4ubuntu5)
>
> CUDA spec:
>
> devdriver_3.2_linux_64_260.19.26.run
> cudatoolkit_3.2.16_linux_64_ubuntu10.04.run
>
> HW:
>
> CASE: COOLERMASTER DOMINATOR /Xcalade
> CPU: AMD Phenom II X4 955 Black Edition (3,2GHz, s. AM3, 125W, C3) BOX
> HDD: Seagate Barracuda 7200.12, 3,5" SATA II, 32MB - 1TB
> MB: Asus M4N98TD EVO - nForce 980a, DDR3, s. AM3, ATX
> RAM: Corsair 4x2GB DDR3 1600MHz CL8 (CMP4GX3M2A1600C8)
> POWER: CoolerMaster Silent Pro Gold Active - 700W
> 2 x TESLA C2050
>
> ############ GXT 470 OUTPUT #################
> ############ GXT 470 OUTPUT #################
> ############ GXT 470 OUTPUT #################
> ############ GXT 470 OUTPUT #################
> ############ GXT 470 OUTPUT #################
>
> -------------------------------------------------------
> Amber 11 SANDER 2010
> -------------------------------------------------------
>
> | PMEMD implementation of SANDER, Release 11
>
> | Run on 01/26/2011 at 17:52:17
>
> [-O]verwriting output
>
> File Assignments:
> | MDIN: equil_G4malTRI_10BIL.in
> | MDOUT: equil8_G4malTRI_10BIL.out
> | INPCRD: equil7_G4malTRI_10BIL.rst
> | PARM: G4malTRI_10BIL.prmtop
> | RESTRT: equil8_G4malTRI_10BIL.rst
> | REFC: refc
> | MDVEL: mdvel
> | MDEN: mden
> | MDCRD: equil8_G4malTRI_10BIL.mdcrd
> | MDINFO: mdinfo
>
>
> Here is the input file:
>
> heat ras-raf
> &cntrl
> imin=0,irest=1,ntx=5,
> nstlim=250000,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 = 250000, 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) = 298.54 PRESS =
> 19.7
> Etot = -208138.5945 EKtot = 55606.0703 EPtot =
> -263744.6648
> BOND = 12770.3337 ANGLE = 5327.0090 DIHED =
> 1796.1712
> 1-4 NB = 1220.6297 1-4 EEL = 32614.9838 VDWAALS =
> 44968.0029
> EELEC = -362441.7951 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 25890.2734 VIRIAL = 25498.7611 VOLUME =
> 920970.7237
> Density =
> 1.0185
> ------------------------------------------------------------------------------
>
>
> NSTEP = 10000 TIME(PS) = 3720.000 TEMP(K) = 296.22 PRESS =
> 73.8
> Etot = -208072.6867 EKtot = 55172.7422 EPtot =
> -263245.4289
> BOND = 12797.2804 ANGLE = 5280.3633 DIHED =
> 1793.7009
> 1-4 NB = 1236.9252 1-4 EEL = 32530.0890 VDWAALS =
> 45147.6190
> EELEC = -362031.4066 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 25827.2976 VIRIAL = 24357.5606 VOLUME =
> 921836.9062
> Density =
> 1.0176
> ------------------------------------------------------------------------------
>
>
> NSTEP = 15000 TIME(PS) = 3730.000 TEMP(K) = 299.32 PRESS =
> 133.8
> Etot = -207140.0864 EKtot = 55750.0508 EPtot =
> -262890.1372
> BOND = 12813.3463 ANGLE = 5316.1231 DIHED =
> 1777.2270
> 1-4 NB = 1214.8564 1-4 EEL = 32504.7227 VDWAALS =
> 45134.9078
> EELEC = -361651.3206 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 26061.3868 VIRIAL = 23397.2429 VOLUME =
> 922304.1794
> Density =
> 1.0171
> ------------------------------------------------------------------------------
>
>
> NSTEP = 20000 TIME(PS) = 3740.000 TEMP(K) = NaN PRESS
> = NaN
> Etot = NaN EKtot = NaN EPtot
> = NaN
> BOND = 0.0000 ANGLE = 795708.3759 DIHED =
> 0.0000
> 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
> -1408.8764
> EELEC = NaN EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 0.0000 VIRIAL = NaN VOLUME
> = NaN
> Density
> = NaN
> ------------------------------------------------------------------------------
>
>
> NSTEP = 25000 TIME(PS) = 3750.000 TEMP(K) = NaN PRESS
> = NaN
> Etot = NaN EKtot = NaN EPtot
> = NaN
> BOND = 0.0000 ANGLE = 795708.3759 DIHED =
> 0.0000
> 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
> -1408.8764
> EELEC = NaN EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 0.0000 VIRIAL = NaN VOLUME
> = NaN
> Density
> = NaN
> ------------------------------------------------------------------------------
>
>
> NSTEP = 30000 TIME(PS) = 3760.000 TEMP(K) = NaN PRESS
> = NaN
> Etot = NaN EKtot = NaN EPtot
> = NaN
> BOND = 0.0000 ANGLE = 795708.3759 DIHED =
> 0.0000
> 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
> -1408.8764
> EELEC = NaN EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 0.0000 VIRIAL = NaN VOLUME
> = NaN
> Density
> = NaN
> ------------------------------------------------------------------------------
>
> ############ TESLA OUTPUT #################
> ############ TESLA OUTPUT #################
> ############ TESLA OUTPUT #################
> ############ TESLA OUTPUT #################
> ############ TESLA OUTPUT #################
>
>
> -------------------------------------------------------
> Amber 11 SANDER 2010
> -------------------------------------------------------
>
> | PMEMD implementation of SANDER, Release 11
>
> | Run on 01/26/2011 at 21:54:14
>
> [-O]verwriting output
>
> File Assignments:
> | MDIN: equil_G4malTRI_10BIL.in
> | MDOUT: equil8_G4malTRI_10BIL.out
> | INPCRD: equil7_G4malTRI_10BIL.rst
> | PARM: G4malTRI_10BIL.prmtop
> | RESTRT: equil8_G4malTRI_10BIL.rst
> | REFC: refc
> | MDVEL: mdvel
> | MDEN: mden
> | MDCRD: equil8_G4malTRI_10BIL.mdcrd
> | MDINFO: mdinfo
>
>
> Here is the input file:
>
> heat ras-raf
> &cntrl
> imin=0,irest=1,ntx=5,
> nstlim=250000,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.
> |
> | 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: 2
> | CUDA Device ID in use: 1
> | CUDA Device Name: Tesla C2050
> | CUDA Device Global Mem Size: 3071 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
> | 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 = 250000, 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
>
> --------------------------------------------------------------------------------
> 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) = 298.17 PRESS =
> -65.0
> Etot = -208105.5602 EKtot = 55536.2500 EPtot =
> -263641.8102
> BOND = 12866.3112 ANGLE = 5342.0912 DIHED =
> 1767.6154
> 1-4 NB = 1260.5860 1-4 EEL = 32577.8341 VDWAALS =
> 45096.1019
> EELEC = -362552.3502 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 25784.6613 VIRIAL = 27079.4346 VOLUME =
> 922977.4720
> Density =
> 1.0163
> ------------------------------------------------------------------------------
>
>
> NSTEP = 10000 TIME(PS) = 3720.000 TEMP(K) = 298.45 PRESS =
> -21.0
> Etot = -207729.1303 EKtot = 55589.4570 EPtot =
> -263318.5874
> BOND = 12890.8807 ANGLE = 5253.2612 DIHED =
> 1777.9787
> 1-4 NB = 1222.3407 1-4 EEL = 32539.5469 VDWAALS =
> 45053.4545
> EELEC = -362056.0500 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 25763.3611 VIRIAL = 26182.4102 VOLUME =
> 922146.5473
> Density =
> 1.0172
> ------------------------------------------------------------------------------
>
>
> NSTEP = 15000 TIME(PS) = 3730.000 TEMP(K) = 298.37 PRESS =
> 98.2
> Etot = -207996.7778 EKtot = 55573.0195 EPtot =
> -263569.7973
> BOND = 12785.0173 ANGLE = 5270.3883 DIHED =
> 1784.1405
> 1-4 NB = 1220.4520 1-4 EEL = 32552.7635 VDWAALS =
> 45295.2640
> EELEC = -362477.8230 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 25963.8604 VIRIAL = 24009.0863 VOLUME =
> 922094.0380
> Density =
> 1.0173
> ------------------------------------------------------------------------------
>
>
> NSTEP = 20000 TIME(PS) = 3740.000 TEMP(K) = 298.20 PRESS =
> 67.7
> Etot = -208293.8436 EKtot = 55542.7656 EPtot =
> -263836.6093
> BOND = 12872.9016 ANGLE = 5363.9036 DIHED =
> 1795.2137
> 1-4 NB = 1213.2018 1-4 EEL = 32466.5915 VDWAALS =
> 45424.6127
> EELEC = -362973.0342 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 25522.4362 VIRIAL = 24176.4890 VOLUME =
> 921096.1611
> Density =
> 1.0184
> ------------------------------------------------------------------------------
>
>
> NSTEP = 25000 TIME(PS) = 3750.000 TEMP(K) = 299.33 PRESS =
> -129.9
> Etot = -207342.5575 EKtot = 55752.0117 EPtot =
> -263094.5692
> BOND = 12831.1293 ANGLE = 5359.5763 DIHED =
> 1781.3044
> 1-4 NB = 1241.1887 1-4 EEL = 32550.6750 VDWAALS =
> 44670.0979
> EELEC = -361528.5407 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 25933.6779 VIRIAL = 28525.6386 VOLUME =
> 923959.6257
> Density =
> 1.0153
> ------------------------------------------------------------------------------
>
>
> NSTEP = 30000 TIME(PS) = 3760.000 TEMP(K) = 299.23 PRESS =
> -48.6
> Etot = -207514.9903 EKtot = 55734.1758 EPtot =
> -263249.1661
> BOND = 12685.1313 ANGLE = 5395.4329 DIHED =
> 1767.0411
> 1-4 NB = 1226.7051 1-4 EEL = 32517.0993 VDWAALS =
> 45071.9541
> EELEC = -361912.5299 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 26018.3035 VIRIAL = 26987.2669 VOLUME =
> 922634.0169
> Density =
> 1.0167
> ------------------------------------------------------------------------------
>
>
>
>
>
>
>
>
> Dne Wed, 26 Jan 2011 17:45:07 +0100 Ross Walker <ross.rosswalker.co.uk>
> napsal/-a:
>
>> Hi Marek,
>>
>> Can you please send me the exact input files for the run that reproduces
>> the
>> error you see. Specifically the one that sets the ig value to the setting
>> that causes the issue. My suspicion is, given this is reproducible, that
>> something is going crazy in the random number generator. I assume these
>> are
>> all ntt=3 runs.
>>
>> Can you also include the exact nvcc compiler version, driver version,
>> card
>> specs (deviceQuery will give this, since I need bios revision etc) as
>> well
>> as the exact compiler and version you used to build pmemd.cuda, for
>> example
>> the gcc / gfortran version numbers.
>>
>> The interesting thing will be if this problem is reproducible on an
>> identical system to the one you see it on. I.e. the exact same model
>> card,
>> driver, compiler versions etc. If it is then we can make progress pretty
>> quickly to fix it. If it isn't then well errrr.... ugh...
>>
>> All the best
>> Ross
>>
>>> -----Original Message-----
>>> From: Marek Maly [mailto:marek.maly.ujep.cz]
>>> Sent: Wednesday, January 26, 2011 8:23 AM
>>> To: AMBER Mailing List
>>> Subject: Re: [AMBER] NaN error in .rst files
>>>
>>> Hello All,
>>>
>>> it seems that the error is reproducible as indicated
>>> Peker sooner - see data below (the verification test was done on the
>>> same
>>> machine as the original one, with the same random seed) (although that
>>> restarted simulation with ig=-1
>>> helped here to continue simulation from the critical point, but of
>>> course,
>>> this is not the systematic solution and the given error might occure
>>> also
>>> in
>>> future of this run ...).
>>>
>>> So now I will try to verify this error
>>>
>>> #1 - on another machine (again with GTX 470)
>>>
>>> #2 - on TESLA C2050, unfortunately here I have no bugfix 12 applied, but
>>> box is not small ( 106.2227312 106.2227312 106.2227312 109.4712190
>>> 109.4712190 109.4712190 ) so
>>> there shouldn.t be problems with 10 A cutoff or am I wrong ?. Anyway I
>>> can
>>> later recompile with the
>>> bugfix 12 as well.
>>>
>>> #3
>>> on CPUs which can also help to find out the source of the error.
>>>
>>> When I have some results I will post them here.
>>>
>>> Best wishes,
>>>
>>> Marek
>>>
>>>
>>>
>>> ############### ORIGINAL RUN ##########################
>>> ############### ORIGINAL RUN ##########################
>>> ############### ORIGINAL RUN ##########################
>>> ############### ORIGINAL RUN ##########################
>>> ############### ORIGINAL RUN ##########################
>>>
>>>
>>>
>>> -------------------------------------------------------
>>> Amber 11 SANDER 2010
>>> -------------------------------------------------------
>>>
>>> | PMEMD implementation of SANDER, Release 11
>>>
>>> | Run on 01/24/2011 at 00:12:00
>>>
>>> [-O]verwriting output
>>>
>>> File Assignments:
>>> | MDIN: equil_G4malTRI_10BIL.in
>>> | MDOUT: equil8_G4malTRI_10BIL.out
>>> | INPCRD: equil7_G4malTRI_10BIL.rst
>>> | PARM: G4malTRI_10BIL.prmtop
>>> | RESTRT: equil8_G4malTRI_10BIL.rst
>>> | REFC: refc
>>> | MDVEL: mdvel
>>> | MDEN: mden
>>> | MDCRD: equil8_G4malTRI_10BIL.mdcrd
>>> | MDINFO: mdinfo
>>>
>>>
>>> Here is the input file:
>>>
>>> heat ras-raf
>>> &cntrl
>>> imin=0,irest=1,ntx=5,
>>> nstlim=250000,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=-1,
>>> 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 = 250000, 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) = 298.54 PRESS =
>>> 19.7
>>> Etot = -208138.5945 EKtot = 55606.0703 EPtot =
>>> -263744.6648
>>> BOND = 12770.3337 ANGLE = 5327.0090 DIHED =
>>> 1796.1712
>>> 1-4 NB = 1220.6297 1-4 EEL = 32614.9838 VDWAALS =
>>> 44968.0029
>>> EELEC = -362441.7951 EHBOND = 0.0000 RESTRAINT =
>>> 0.0000
>>> EKCMT = 25890.2734 VIRIAL = 25498.7611 VOLUME =
>>> 920970.7237
>>> Density =
>>> 1.0185
>>>
>> ----------------------------------------------------------------------------
>> --
>>>
>>>
>>> NSTEP = 10000 TIME(PS) = 3720.000 TEMP(K) = 296.22 PRESS =
>>> 73.8
>>> Etot = -208072.6867 EKtot = 55172.7422 EPtot =
>>> -263245.4289
>>> BOND = 12797.2804 ANGLE = 5280.3633 DIHED =
>>> 1793.7009
>>> 1-4 NB = 1236.9252 1-4 EEL = 32530.0890 VDWAALS =
>>> 45147.6190
>>> EELEC = -362031.4066 EHBOND = 0.0000 RESTRAINT =
>>> 0.0000
>>> EKCMT = 25827.2976 VIRIAL = 24357.5606 VOLUME =
>>> 921836.9062
>>> Density =
>>> 1.0176
>>>
>> ----------------------------------------------------------------------------
>> --
>>>
>>>
>>> NSTEP = 15000 TIME(PS) = 3730.000 TEMP(K) = 299.32 PRESS =
>>> 133.8
>>> Etot = -207140.0864 EKtot = 55750.0508 EPtot =
>>> -262890.1372
>>> BOND = 12813.3463 ANGLE = 5316.1231 DIHED =
>>> 1777.2270
>>> 1-4 NB = 1214.8564 1-4 EEL = 32504.7227 VDWAALS =
>>> 45134.9078
>>> EELEC = -361651.3206 EHBOND = 0.0000 RESTRAINT =
>>> 0.0000
>>> EKCMT = 26061.3868 VIRIAL = 23397.2429 VOLUME =
>>> 922304.1794
>>> Density =
>>> 1.0171
>>>
>> ----------------------------------------------------------------------------
>> --
>>>
>>>
>>> NSTEP = 20000 TIME(PS) = 3740.000 TEMP(K) = NaN PRESS
>>> = NaN
>>> Etot = NaN EKtot = NaN EPtot
>>> = NaN
>>> BOND = 0.0000 ANGLE = 795708.3759 DIHED =
>>> 0.0000
>>> 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
>>> -1408.8764
>>> EELEC = NaN EHBOND = 0.0000 RESTRAINT =
>>> 0.0000
>>> EKCMT = 0.0000 VIRIAL = NaN VOLUME
>>> = NaN
>>> Density
>>> = NaN
>>>
>> ----------------------------------------------------------------------------
>> --
>>>
>>>
>>> NSTEP = 25000 TIME(PS) = 3750.000 TEMP(K) = NaN PRESS
>>> = NaN
>>> Etot = NaN EKtot = NaN EPtot
>>> = NaN
>>> BOND = 0.0000 ANGLE = 795708.3759 DIHED =
>>> 0.0000
>>> 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
>>> -1408.8764
>>> EELEC = NaN EHBOND = 0.0000 RESTRAINT =
>>> 0.0000
>>> EKCMT = 0.0000 VIRIAL = NaN VOLUME
>>> = NaN
>>> Density
>>> = NaN
>>>
>> ----------------------------------------------------------------------------
>> --
>>>
>>>
>>>
>>>
>>> ############### VERIFICATION RUN ######################
>>> ############### VERIFICATION RUN ######################
>>> ############### VERIFICATION RUN ######################
>>> ############### VERIFICATION RUN ######################
>>> ############### VERIFICATION RUN ######################
>>>
>>>
>>>
>>> -------------------------------------------------------
>>> Amber 11 SANDER 2010
>>> -------------------------------------------------------
>>>
>>> | PMEMD implementation of SANDER, Release 11
>>>
>>> | Run on 01/26/2011 at 15:38:33
>>>
>>> [-O]verwriting output
>>>
>>> File Assignments:
>>> | MDIN: equil_G4malTRI_10BIL.in
>>> | MDOUT: equil8_G4malTRI_10BIL.out
>>> | INPCRD: equil7_G4malTRI_10BIL.rst
>>> | PARM: G4malTRI_10BIL.prmtop
>>> | RESTRT: equil8_G4malTRI_10BIL.rst
>>> | REFC: refc
>>> | MDVEL: mdvel
>>> | MDEN: mden
>>> | MDCRD: equil8_G4malTRI_10BIL.mdcrd
>>> | MDINFO: mdinfo
>>>
>>>
>>> Here is the input file:
>>>
>>> heat ras-raf
>>> &cntrl
>>> imin=0,irest=1,ntx=5,
>>> nstlim=250000,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 = 250000, 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) = 298.54 PRESS =
>>> 19.7
>>> Etot = -208138.5945 EKtot = 55606.0703 EPtot =
>>> -263744.6648
>>> BOND = 12770.3337 ANGLE = 5327.0090 DIHED =
>>> 1796.1712
>>> 1-4 NB = 1220.6297 1-4 EEL = 32614.9838 VDWAALS =
>>> 44968.0029
>>> EELEC = -362441.7951 EHBOND = 0.0000 RESTRAINT =
>>> 0.0000
>>> EKCMT = 25890.2734 VIRIAL = 25498.7611 VOLUME =
>>> 920970.7237
>>> Density =
>>> 1.0185
>>>
>> ----------------------------------------------------------------------------
>> --
>>>
>>>
>>> NSTEP = 10000 TIME(PS) = 3720.000 TEMP(K) = 296.22 PRESS =
>>> 73.8
>>> Etot = -208072.6867 EKtot = 55172.7422 EPtot =
>>> -263245.4289
>>> BOND = 12797.2804 ANGLE = 5280.3633 DIHED =
>>> 1793.7009
>>> 1-4 NB = 1236.9252 1-4 EEL = 32530.0890 VDWAALS =
>>> 45147.6190
>>> EELEC = -362031.4066 EHBOND = 0.0000 RESTRAINT =
>>> 0.0000
>>> EKCMT = 25827.2976 VIRIAL = 24357.5606 VOLUME =
>>> 921836.9062
>>> Density =
>>> 1.0176
>>>
>> ----------------------------------------------------------------------------
>> --
>>>
>>>
>>> NSTEP = 15000 TIME(PS) = 3730.000 TEMP(K) = 299.32 PRESS =
>>> 133.8
>>> Etot = -207140.0864 EKtot = 55750.0508 EPtot =
>>> -262890.1372
>>> BOND = 12813.3463 ANGLE = 5316.1231 DIHED =
>>> 1777.2270
>>> 1-4 NB = 1214.8564 1-4 EEL = 32504.7227 VDWAALS =
>>> 45134.9078
>>> EELEC = -361651.3206 EHBOND = 0.0000 RESTRAINT =
>>> 0.0000
>>> EKCMT = 26061.3868 VIRIAL = 23397.2429 VOLUME =
>>> 922304.1794
>>> Density =
>>> 1.0171
>>>
>> ----------------------------------------------------------------------------
>> --
>>>
>>>
>>> NSTEP = 20000 TIME(PS) = 3740.000 TEMP(K) = NaN PRESS
>>> = NaN
>>> Etot = NaN EKtot = NaN EPtot
>>> = NaN
>>> BOND = 0.0000 ANGLE = 795708.3759 DIHED =
>>> 0.0000
>>> 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
>>> -1408.8764
>>> EELEC = NaN EHBOND = 0.0000 RESTRAINT =
>>> 0.0000
>>> EKCMT = 0.0000 VIRIAL = NaN VOLUME
>>> = NaN
>>> Density
>>> = NaN
>>>
>> ----------------------------------------------------------------------------
>> --
>>>
>>>
>>> NSTEP = 25000 TIME(PS) = 3750.000 TEMP(K) = NaN PRESS
>>> = NaN
>>> Etot = NaN EKtot = NaN EPtot
>>> = NaN
>>> BOND = 0.0000 ANGLE = 795708.3759 DIHED =
>>> 0.0000
>>> 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
>>> -1408.8764
>>> EELEC = NaN EHBOND = 0.0000 RESTRAINT =
>>> 0.0000
>>> EKCMT = 0.0000 VIRIAL = NaN VOLUME
>>> = NaN
>>> Density
>>> = NaN
>>>
>> ----------------------------------------------------------------------------
>> --
>>>
>>>
>>>
>>>
>>>
>>>
>>> Dne Wed, 26 Jan 2011 15:04:16 +0100 case <case.biomaps.rutgers.edu>
>>> napsal/-a:
>>>
>>> > On Wed, Jan 26, 2011, Marek Maly wrote:
>>> >>
>>> >> I recently also obtained NaN problem in one of my simulation using
>>> >> pmemd.cuda on GTX 470:
>>> >> see - relevant data below. Unfortunately it is unreproducable as I am
>>> >> using ig=-1.
>>> >
>>> > You *can* re-run things in this circumstance: pmemd will print out the
>>> > value
>>> > of the random seed that was actually used, and you can put that back
>> into
>>> > your input file. This can be helpful to see if the problem is the
>>> same
>>> > every
>>> > time.
>>> >
>>> > ....dac
>>> >
>>> > _______________________________________________
>>> > AMBER mailing list
>>> > AMBER.ambermd.org
>>> > http://lists.ambermd.org/mailman/listinfo/amber
>>> >
>>> > __________ Informace od ESET NOD32 Antivirus, verze databaze 5820
>>> > (20110126) __________
>>> >
>>> > Tuto zpravu proveril ESET NOD32 Antivirus.
>>> >
>>> > http://www.eset.cz
>>> >
>>> >
>>> >
>>>
>>>
>>> --
>>> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
>>> http://www.opera.com/mail/
>>>
>>> _______________________________________________
>>> 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
>>
>> __________ Informace od ESET NOD32 Antivirus, verze databaze 5821
>> (20110126) __________
>>
>> Tuto zpravu proveril ESET NOD32 Antivirus.
>>
>> http://www.eset.cz
>>
>>
>>
>
>
> --
> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
> http://www.opera.com/mail/
>
> _______________________________________________
> 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 Thu Jan 27 2011 - 07:30:03 PST
