Dear List,
I installed AMBER16 recently and compiled the cuda version both parallel
and serial.
The .out log files look complete but it seems the .rst file has issues
(AMBER16). I think it is in binary format ..there are no coordinates
written to it but the size of the file seems correct. I tried compiling
twice and it didn't give any errors.
Upon running the same with AMBER14, it outputs coordinates in the right
format in the .rst file.
Here is the output file with AMBER16
| PMEMD implementation of SANDER, Release 16
| Run on 06/15/2016 at 07:07:25
| Executable path: /home/gandhin/amber16/bin/pmemd.cuda.MPI
| Working directory: /home/gandhin/caroline/pep4
| Hostname: cl2n002
[-O]verwriting output
File Assignments:
| MDIN: heat.in
| MDOUT:
heat.out
| INPCRD:
sys_min.rst
| PARM:
solvated.prmtop
| RESTRT:
heat.rst
| REFC:
sys_min.rst
| MDVEL:
mdvel
| MDEN:
mden
| MDCRD:
mdcrd
| MDINFO:
mdinfo
|LOGFILE:
logfile
| MDFRC:
mdfrc
Here is the input file:
Heating
System
&cntrl
imin=0,
nmropt=1,
ntx=1,
irest=0,
ntpr=500, ntwr=500, ntwx=500,
iwrap=1,
ntf=2, ntb=1, cut=12.0,
nsnb=20,
igb=0,
ibelly=0,
ntr=1,
nstlim=250000, nscm=500,
dt=0.002,
ntt=1, temp0=0.0, tempi=0.0,
tautp=0.5
ntc=2,restraintmask=':1-20',
restraint_wt=10.0,
&end
&wt type='REST', istep1=0, istep2=0, value1=1.0, value2=1.0,
&end
&wt type='TEMP0', istep1=0, istep2=250000, value1=0.0, value2=293,
&end
&wt type='END'
&end
Note: ig = -1. Setting random seed to 545793 based on wallclock time in
microseconds and disabling the synchronization of random numbers
between tasks to improve performance.
| INFO: The nsnb ctrl option does not affect nonbonded list update
frequency.
| It does affect steepest descent minimization freq if ntmin == 0
|--------------------- INFORMATION ----------------------
| GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
| Version 16.0.0
|
| 02/25/2016
|
| Implementation by:
| Ross C. Walker (SDSC)
| Scott Le Grand (nVIDIA)
|
| Precision model in use:
| [SPFP] - Single Precision Forces, 64-bit Fixed Point
| Accumulation. (Default)
|
|--------------------------------------------------------
|----------------- CITATION INFORMATION -----------------
|
| When publishing work that utilized the CUDA version
| of AMBER, please cite the following in addition to
| the regular AMBER citations:
|
| - Romelia Salomon-Ferrer; Andreas W. Goetz; Duncan
| Poole; Scott Le Grand; Ross C. Walker "Routine
| microsecond molecular dynamics simulations with
| AMBER - Part II: Particle Mesh Ewald", J. Chem.
| Theory Comput., 2013, 9 (9), pp3878-3888,
| DOI: 10.1021/ct400314y.
|
| - Andreas W. Goetz; Mark J. Williamson; Dong Xu;
| Duncan Poole; Scott Le Grand; Ross C. Walker
| "Routine microsecond molecular dynamics simulations
| with AMBER - Part I: Generalized Born", J. Chem.
| Theory Comput., 2012, 8 (5), pp1542-1555.
|
| - Scott Le Grand; Andreas W. Goetz; Ross C. Walker
| "SPFP: Speed without compromise - a mixed precision
| model for GPU accelerated molecular dynamics
| simulations.", Comp. Phys. Comm., 2013, 184
| pp374-380, DOI: 10.1016/j.cpc.2012.09.022
|
|--------------------------------------------------------
|------------------- GPU DEVICE INFO --------------------
|
| Task ID: 0
| CUDA_VISIBLE_DEVICES: 0,1
| CUDA Capable Devices Detected: 2
| 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_VISIBLE_DEVICES: 0,1
| CUDA Capable Devices Detected: 2
| CUDA Device ID in use: 1
| CUDA Device Name: Tesla M2090
| CUDA Device Global Mem Size: 5375 MB
| CUDA Device Num Multiprocessors: 16
| CUDA Device Core Freq: 1.30 GHz
|
|--------------------------------------------------------
|---------------- GPU PEER TO PEER INFO -----------------
|
| Peer to Peer support: DISABLED
|
| (Selected GPUs cannot communicate over P2P)
|
|--------------------------------------------------------
| Conditional Compilation Defines Used:
| MPI
| PUBFFT
| BINTRAJ
| CUDA
| EMIL
| Largest sphere to fit in unit cell has radius = 36.851
| New format PARM file being parsed.
| Version = 1.000 Date = 04/29/16 Time = 14:56:38
| 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 = 39632 NTYPES = 20 NBONH = 39470 MBONA = 152
NTHETH = 330 MTHETA = 209 NPHIH = 671 MPHIA = 637
NHPARM = 0 NPARM = 0 NNB = 54069 NRES = 13141
NBONA = 152 NTHETA = 209 NPHIA = 637 NUMBND = 56
NUMANG = 122 NPTRA = 125 NATYP = 34 NPHB = 1
IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Coordinate Index Table dimensions: 10 10 10
| Direct force subcell size = 7.3739 7.3897 7.3701
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
default_name
General flags:
imin = 0, nmropt = 1
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 2, ntpr = 500, ntrx = 1, ntwr =
500
iwrap = 1, ntwx = 500, ntwv = 0, ntwe
= 0
ioutfm = 1, ntwprt = 0, idecomp = 0,
rbornstat= 0
Potential function:
ntf = 2, ntb = 1, igb = 0, nsnb
= 20
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 12.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 1
restraint_wt = 10.00000
Molecular dynamics:
nstlim = 250000, nscm = 0, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = -1.00000
Berendsen (weak-coupling) temperature regulation:
temp0 = 0.00000, tempi = 0.00000, tautp = 0.50000
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
NMR refinement options:
iscale = 0, noeskp = 1, ipnlty = 1, mxsub
= 1
scalm = 100.00000, pencut = 0.10000, tausw = 0.10000
| 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 = 73.739 Box Y = 73.897 Box Z = 73.701
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 80 NFFT2 = 80 NFFT3 = 80
Cutoff= 12.000 Tol =0.100E-04
Ewald Coefficient = 0.22664
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
LOADING THE CONSTRAINED ATOMS AS GROUPS
5. REFERENCE ATOM COORDINATES
default_name
Mask :1-20; matches 295 atoms
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
default_name
begin time read from input coords = 0.000 ps
Begin reading energy term weight changes/NMR restraints
WEIGHT CHANGES:
REST 0 0 1.000000 1.000000 0 0
TEMP0 0 250000 0.000000 293.000000 0 0
RESTRAINTS:
** No restraint defined **
Done reading weight changes/NMR restraints
Number of triangulated 3-point waters found: 13108
Sum of charges from parm topology file = -0.00000002
Forcing neutrality...
| Dynamic Memory, Types Used:
| Reals 1820586
| Integers 1441862
| Nonbonded Pairs Initial Allocation: 12293846
| GPU memory information (estimate):
| KB of GPU memory in use: 85032
| KB of CPU memory in use: 56682
| Running AMBER/MPI version on 2 nodes
--
Regards,
Dr. Neha S. Gandhi,
Vice Chancellor's Research Fellow,
Queensland University of Technology,
2 George Street, Brisbane, QLD 4000
Australia
LinkedIn
Research Gate
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Received on Tue Jun 14 2016 - 14:30:02 PDT
