Hello Debarati,
I have seen errors like this when, for example, there was a mistake in the input files being provided to pmemd.cuda. I advise you to attempt running the same simulation with pmemd (CPU only) and check if everything is fine.
I hope this helps,
Best,
Vinícius Wilian D. Cruzeiro
PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States
Voice: +1(352)846-1633
________________________________
From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Sent: Monday, December 16, 2019 1:43 PM
To: amber.ambermd.org <amber.ambermd.org>
Subject: [AMBER] Any idea on this error and how to troubleshoot
[External Email]
cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered
My output file looks like this:-
-------------------------------------------------------
Amber 18 PMEMD 2018
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 18
| Run on 12/16/2019 at 12:30:15
| Executable path: /usr/local/amber18/bin/pmemd.cuda
| Working directory: /users/debarati/TI_ABL_Kinase/C3N/C3N_in_protein/TI_setup/complex/EQUIL/0.00
| Hostname: grape5
[-O]verwriting output
File Assignments:
| MDIN: equil1B.in
| MDOUT: complex_equil1B.out
| INPCRD: complex_equil1A.rst
| PARM: complex_WAT.prmtop
| RESTRT: complex_equil1B.rst
| REFC: complex_WAT.inpcrd
| MDVEL: mdvel
| MDEN: mden
| MDCRD: complex_equil1B.mdcrd
| MDINFO: mdinfo
| MDFRC: mdfrc
Here is the input file:
&cntrl
imin = 0, nstlim = 5000000, dt = 0.001,
irest = 1, ntx = 5, ig = -1,
tempi = 300.0, temp0 = 300.0,
ntc = 2, ntf = 1, tol = 0.00001,
taup = 2,
ntwx = 1000, ntwe = 0, ntwr = 1000, ntpr = 1000,
cut = 10.0, iwrap = 1,
ntt =3, ntb = 2, ntp = 1, gamma_ln=5.0,
nscm = 0,
ntr=1, restraintmask=':287', restraint_wt=100,
icfe = 1, clambda = 0.00, ifsc=1,
timask1=':C3N',timask2='',
scmask1=':C3N', scmask2=''
/
Note: ig = -1. Setting random seed to 507792 based on wallclock time in
microseconds.
| irandom = 1, using AMBER's internal random number generator (default).
|--------------------- INFORMATION ----------------------
| GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
| Version 18.0.0
|
| 03/25/2018
|
| Implementation by:
| Ross C. Walker (SDSC)
| Scott Le Grand (nVIDIA)
|
| Version 18 performance extensions by:
| David Cerutti (Rutgers)
|
| Precision model in use:
| [SPFP] - Single Precision Forces, 64-bit Fixed Point
| Conditional Compilation Defines Used:
| PUBFFT
| BINTRAJ
| CUDA
| EMIL
| Largest sphere to fit in unit cell has radius = 34.029
| New format PARM file being parsed.
| Version = 1.000 Date = 10/22/19 Time = 10:45:11
| 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 box info from netcdf restart file
NATOM = 43837 NTYPES = 17 NBONH = 41515 MBONA = 2367
NTHETH = 5150 MTHETA = 3201 NPHIH = 10365 MPHIA = 10049
NHPARM = 0 NPARM = 0 NNB = 77578 NRES = 13385
NBONA = 2367 NTHETA = 3201 NPHIA = 10049 NUMBND = 71
NUMANG = 159 NPTRA = 201 NATYP = 39 NPHB = 1
IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Coordinate Index Table dimensions: 12 15 13
| Direct force subcell size = 5.6714 5.7317 5.7556
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
default_name
General flags:
imin = 0, nmropt = 0
Nature and format of input:
ntx = 5, irest = 1, ntrx = 1
Nature and format of output:
ntxo = 2, ntpr = 1000, ntrx = 1, ntwr = 1000
iwrap = 1, ntwx = 1000, ntwv = 0, ntwe = 0
ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 1, 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 = 1
restraint_wt = 100.00000
Molecular dynamics:
nstlim = 5000000, nscm = 0, nrespa = 1
t = 0.00000, dt = 0.00100, vlimit = -1.00000
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
vdwmeth = 1, eedmeth = 1, netfrc = 1
Box X = 68.057 Box Y = 85.975 Box Z = 74.823
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 72 NFFT2 = 96 NFFT3 = 80
Cutoff= 10.000 Tol =0.100E-04
Ewald Coefficient = 0.27511
Interpolation order = 4
LOADING THE CONSTRAINED ATOMS AS GROUPS
5. REFERENCE ATOM COORDINATES
default_name
Mask :287; matches 6 atoms
TI Mask 1 :C3N; matches 6 atoms
TI Mask 2 matches 0 atoms
TI region 1: 43837 atoms
TI region 2: 43831 atoms
SC Mask 1 :C3N; matches 6 atoms
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
default_name
begin time read from input coords = 2010.000 ps
Molecule 2 is completely softcore and skipped for C.O.M..
Number of triangulated 3-point waters found: 13086
Number of shake restraints removed in TI region 1 : 0
Number of shake restraints removed in TI region 2 : 0
Sum of charges for TI region 1 = -0.00000013
Forcing neutrality...
Sum of charges for TI region 2 = -0.00000013
Forcing neutrality...
| Dynamic Memory, Types Used:
| Reals 2537180
| Integers 2301103
| Nonbonded Pairs Initial Allocation: 13259596
| GPU memory information (estimate):
| KB of GPU memory in use: 0
| KB of CPU memory in use: 0
--------------------------------------------------------------------------------
4. RESULTS
That’s it.. why I don’t see anything beyond results??
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Received on Mon Dec 16 2019 - 13:30:02 PST
