Hello all,
Although I couldn't join this email traffic fast enough, i need to let
you know about my case. But this time i will be more specific (i
hope). I applied all patches in bugfixes and i actually made a clean
(from scratch) installation. My system is Ubuntu 10.04 with kernel
version 2.6.37-9. My gcc version is 4.4.3. Below is my nvcc --version
output
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2010 NVIDIA Corporation
Built on Wed_Nov__3_16:16:57_PDT_2010
Cuda compilation tools, release 3.2, V0.2.1221
Machine has two intel nehalem cpu packs on it. It has 8 physical 16
logical cores. Our graphics card is GTX 480. Its idle state
temperature is 47 C. When it runs it can reach 90 C quickly (less than
a minute). Then it stabilizes itself at this temperature. The actual
simulation consists of many 500 pico second runs. I decided to use
this time scale right after i had this NaN errors in the first time.
My reasoning based on the observation of first set of NaN s in a
longer run. Back in that time fine part of the .rst file was close to
800 pico seconds. Then this leads me to divide it into 500 pico second
steps. Again for those runs, i am using a cutoff distance 10 A.
iwrap=1 flag/options is included. But, I am not utilizing ig=-1
flag/option. Basically my input file is exactly same with the input
file
in advanced web tutorial for explicit solvent case except this iwrap option.
In my case, i can run pmemd.MPI without seen any errors similar to
this NaN issue. I tested it recently, and a sort of long time ago (say
1-2 mounts). As Marek said ,unfortunately this error comes from
nowhere and at least for me it is not reproducable.
Meanwhile, what bothering me is not facing with this problem. It is
rather not to be able to see any kind of warnings or a sign of it. In
other words i don't know how to debug it or observing it among system
messages. For example, again in Marek's email he was
showing a notice like below
-----------------------------------
Error: unspecified launch failure launching kernel kClearForces
cudaFree GpuBuffer::Deallocate failed unspecified launch failure
STOP PMEMD Terminated Abnormally!
-----------------------------------
I didn't get this error even in .out file. I have no idea how i should
understand this. If anybody wants to take a look at the any of the
resultant files i can gladly send you a link or attach to my email.
Also, if anybody can tell me in which file or among which messages i
should see a notice/warning/error related with this behavior i will be
so happy. Otherwise this problem will stay as a mistery for me, and
this is highly sad.
thank you million times
all the best
peker
2011/1/26 Jason Swails <jason.swails.gmail.com>:
> Ah, so you did. You clearly wrote CPUs, but I was seeing GPUs.
>
> 2011/1/26 Marek Maly <marek.maly.ujep.cz>
>
>> No, as I wrote in my last response I am going to do this test right now.
>>
>> Best,
>>
>> Marek
>>
>> Dne Wed, 26 Jan 2011 17:37:49 +0100 Jason Swails <jason.swails.gmail.com>
>> napsal/-a:
>>
>> > One other comment -- to make sure that this is specific GPU issues, have
>> > you
>> > tried running the same restart simulation using just pmemd (with no GPU)
>> > and
>> > show that it is in fact a GPU issue?
>> >
>> > 2011/1/26 Jason Swails <jason.swails.gmail.com>
>> >
>> >> Hello,
>> >>
>> >> You really should apply bugfix.12 to compare apples to apples. Another
>> >> comment -- the default cut value is 8, not 10, and without bugfix.12 it
>> >> was
>> >> cut != 8 that caused problems.
>> >>
>> >> However, bugfix.12 fixed more issues than just cut != 8 (it also fixed
>> >> issues with GTX 4xx/5xx.
>> >>
>> >> Hope this helps,
>> >> Jason
>> >>
>> >> 2011/1/26 Marek Maly <marek.maly.ujep.cz>
>> >>
>> >> 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
>> >>>
>> >>
>> >>
>> >>
>> >> --
>> >> Jason M. Swails
>> >> Quantum Theory Project,
>> >> University of Florida
>> >> Ph.D. Graduate Student
>> >> 352-392-4032
>> >>
>> >
>> >
>> >
>>
>>
>> --
>> 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
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jan 26 2011 - 16:00:02 PST
