OK, perfect !
You should arrive at critical step 20 000 in few minutes I guess ...
Best,
Marek
Dne Thu, 27 Jan 2011 16:07:31 +0100 peker milas <pekermilas.gmail.com>
napsal/-a:
> 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
--
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
Received on Thu Jan 27 2011 - 07:30:03 PST
