Hi,
Did you apply all the bug fixes because when i see you information headers i noticed that your AMBER version is not up-to-date.
Stephane
________________________________________
De : Mary Varughese [maryvj1985.gmail.com]
Date d'envoi : jeudi 14 mars 2013 16:04
À : AMBER Mailing List
Objet : [AMBER] PMEMD in amber12
Sir,
We have installed amber12 in a GPU server. Test run fine.
On trying pmemd.cuda.MPI on a protein-ligand system. Its hanging on the
last line of the .out file i attached together. After half an hour (but
without showing any error) i terminated the run. the same with a dna-
ligand system. Please have a look at the .out file which includes all the
inputs given. And i am trying pmemd for the first time. Please give some
suggestions too.
"
The same .out file is given below:
-------------------------------------------------------
Amber 11 SANDER 2010
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 11
| Run on 03/14/2013 at 19:54:49
[-O]verwriting output
File Assignments:
| MDIN: TbNrb_md9.in
| MDOUT: TbNrb_md9.out
| INPCRD: TbNrb_md8.rst
| PARM: TbNrb.prmtop
| RESTRT: TbNrb_md9.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: TbNrb_md9.mdcrd
| MDINFO: mdinfo
|LOGFILE: logfile
Here is the input file:
Tb-Ntr complex : 200ps MD (production run in NPT)
&cntrl
imin = 0,
irest = 1,
ntx = 5,
ntb = 2, ntp = 1, pres0 = 1.0,
cut = 10,
ntr = 0,
ntc = 2,
ntf = 2,
tempi = 300.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1,
nstlim = 1000, dt = 0.002,
ntpr = 500, ntwx = 500, ntwr = 1000,
/
|--------------------- INFORMATION ----------------------
| GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
| Version 12.0
|
| 03/19/2012
|
| 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 --------------------
|
| Task ID: 0
| CUDA Capable Devices Detected: 1
| CUDA Device ID in use: 0
| CUDA Device Name: Tesla M2090
| CUDA Device Global Mem Size: 5375 MB
| CUDA Device Num Multiprocessors: 16
| CUDA Device Core Freq: 1.30 GHz
|
|
| Task ID: 1
| CUDA Capable Devices Detected: 1
| CUDA Device ID in use: 0
| CUDA Device Name: Tesla M2090
| CUDA Device Global Mem Size: 5375 MB
| CUDA Device Num Multiprocessors: 16
| CUDA Device Core Freq: 1.30 GHz
|
|
| Task ID: 2
| CUDA Capable Devices Detected: 1
| CUDA Device ID in use: 0
| CUDA Device Name: Tesla M2090
| CUDA Device Global Mem Size: 5375 MB
| CUDA Device Num Multiprocessors: 16
| CUDA Device Core Freq: 1.30 GHz
|
|
| Task ID: 3
| CUDA Capable Devices Detected: 1
| CUDA Device ID in use: 0
| CUDA Device Name: Tesla M2090
| CUDA Device Global Mem Size: 5375 MB
| CUDA Device Num Multiprocessors: 16
| CUDA Device Core Freq: 1.30 GHz
|
|
| Task ID: 4
| CUDA Capable Devices Detected: 1
| CUDA Device ID in use: 0
| CUDA Device Name: Tesla M2090
| CUDA Device Global Mem Size: 5375 MB
| CUDA Device Num Multiprocessors: 16
| CUDA Device Core Freq: 1.30 GHz
|
|
| Task ID: 5
| CUDA Capable Devices Detected: 1
| CUDA Device ID in use: 0
| CUDA Device Name: Tesla M2090
| CUDA Device Global Mem Size: 5375 MB
| CUDA Device Num Multiprocessors: 16
| CUDA Device Core Freq: 1.30 GHz
|
|
| Task ID: 6
| CUDA Capable Devices Detected: 1
| CUDA Device ID in use: 0
| CUDA Device Name: Tesla M2090
| CUDA Device Global Mem Size: 5375 MB
| CUDA Device Num Multiprocessors: 16
| CUDA Device Core Freq: 1.30 GHz
|
|
| Task ID: 7
| CUDA Capable Devices Detected: 1
| CUDA Device ID in use: 0
| CUDA Device Name: Tesla M2090
| CUDA Device Global Mem Size: 5375 MB
| CUDA Device Num Multiprocessors: 16
| CUDA Device Core Freq: 1.30 GHz
|
|--------------------------------------------------------
| Conditional Compilation Defines Used:
| DIRFRC_COMTRANS
| DIRFRC_EFS
| DIRFRC_NOVEC
| MPI
| PUBFFT
| FFTLOADBAL_2PROC
| BINTRAJ
| CUDA
| Largest sphere to fit in unit cell has radius = 47.238
| New format PARM file being parsed.
| Version = 1.000 Date = 10/04/12 Time = 11:18:48
| Note: 1-4 EEL scale factors are being read from the topology file.
| Note: 1-4 VDW scale factors are being read from the topology file.
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
getting new box info from bottom of inpcrd
NATOM = 119092 NTYPES = 20 NBONH = 112233 MBONA = 6978
NTHETH = 14955 MTHETA = 9471 NPHIH = 29675 MPHIA = 23498
NHPARM = 0 NPARM = 0 NNB = 214731 NRES = 36118
NBONA = 6978 NTHETA = 9471 NPHIA = 23498 NUMBND = 78
NUMANG = 158 NPTRA = 71 NATYP = 52 NPHB = 1
IFBOX = 2 NMXRS = 44 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Coordinate Index Table dimensions: 17 17 17
| Direct force subcell size = 6.8064 6.8064 6.8064
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 = 500, ntrx = 1, ntwr = 1000
iwrap = 0, ntwx = 500, 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 = 1000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = -1.00000
Langevin dynamics temperature regulation:
ig = 71277
temp0 = 300.00000, tempi = 300.00000, gamma_ln= 1.00000
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 = 500
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
vdwmeth = 1, eedmeth = 1, netfrc = 1
Box X = 115.709 Box Y = 115.709 Box Z = 115.709
Alpha = 109.471 Beta = 109.471 Gamma = 109.471
NFFT1 = 120 NFFT2 = 120 NFFT3 = 120
Cutoff= 10.000 Tol =0.100E-04
Ewald Coefficient = 0.27511
Interpolation order = 4
| PMEMD ewald parallel performance parameters:
| block_fft = 0
| fft_blk_y_divisor = 2
| excl_recip = 0
| excl_master = 0
| atm_redist_freq = 320
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 400.000 ps
Number of triangulated 3-point waters found: 35215
Sum of charges from parm topology file = -0.00000042
Forcing neutrality...
"its hanging at this line"
Thanking you
--
Mary Varughese
Research Scholar
School of Pure and Applied Physics
Mahatma Gandhi University
India
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Received on Thu Mar 14 2013 - 09:00:03 PDT
