Hi Adrian,
Sorry for the late reply. This is exactly the error message. The error
occurs during the production step of the simulation.
[sayu1995.bernal Tassmod4_HdeA_Explicit_CpHMD_7]$
HdeA_Exp_pH_phase2_ravi.bash
+ pmemd.cuda -O -i HdeA_Exp_pH_step3_equi.in -o HdeA_Exp_pH_step3_equi.out
-c HdeA_Exp_pH_step2.rst -p HdeA_Exp_pH_md.prmtop -r HdeA_Exp_pH_step3.rst
-x HdeA_Exp_pH_step3.nc -ref HdeA_Exp_pH_step2.rst -cpin HdeA_Exp_pH.cpin
+ pmemd.cuda -O -i HdeA_Exp_pH_step4_prod.in -o HdeA_Exp_pH_step4_prod.out
-c HdeA_Exp_pH_step3.rst -p HdeA_Exp_pH_md.prmtop -r HdeA_Exp_pH_step4.rst
-x HdeA_Exp_pH_step4.nc -ref HdeA_Exp_pH_step3.rst -cpin HdeA_Exp_pH.cpin
cudaMemcpy GpuBuffer::Upload failed an illegal memory access was encountered
I will also attach the mdout
| PMEMD implementation of SANDER, Release 16
| Run on 10/24/2017 at 21:48:04
| Executable path: pmemd.cuda
| Working directory: /home/sayu1995/Tasser_Model4/
Tassmod4_HdeA_Explicit_CpHMD_7
| Hostname: bernal.abrol.csun.edu
[-O]verwriting output
File Assignments:
| MDIN: HdeA_Exp_pH_step4_prod.in
| MDOUT: HdeA_Exp_pH_step4_prod.out
| INPCRD: HdeA_Exp_pH_step3.rst
| PARM: HdeA_Exp_pH_md.prmtop
| RESTRT: HdeA_Exp_pH_step4.rst
| REFC: HdeA_Exp_pH_step3.rst
| MDVEL: mdvel
| MDEN: mden
| MDCRD: HdeA_Exp_pH_step4.nc
| MDINFO: mdinfo
| MDFRC: mdfrc
Here is the input file:
Explicit solvent constant pH MD
&cntrl
imin=0, irest=1, ntx=5, ntxo=2,
ntpr=1000, ntwx=1000, nstlim= 5000000,
dt=0.002, ntt=3, tempi=300,
temp0=300, gamma_ln=5.0, ig=-1,
ntc=2, ntf=2, cut=8, iwrap=1,
ioutfm=1, icnstph=2, ntcnstph=200,
solvph= 7.0, ntrelax=100, saltcon=0.1,
/
Note: ig = -1. Setting random seed to 873475 based on wallclock time in
microseconds.
|--------------------- 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
|
| When publishing work that utilized the CUDA version
| of Constant pH please cite the following in addition
| to the regular AMBER GPU citations:
|
| - Ross C. Walker; Perri Needham; Adrian E. Roitberg
| "GPU Accelerated Constant pH Simulations"
| J. Phys Chem. B., 2016, in review.
|
|
|--------------------------------------------------------
|------------------- GPU DEVICE INFO --------------------
|
| CUDA_VISIBLE_DEVICES: not set
| CUDA Capable Devices Detected: 2
| CUDA Device ID in use: 1
| CUDA Device Name: GeForce GTX 1080
| CUDA Device Global Mem Size: 8114 MB
| CUDA Device Num Multiprocessors: 20
| CUDA Device Core Freq: 1.73 GHz
|
|--------------------------------------------------------
| Conditional Compilation Defines Used:
| PUBFFT
| BINTRAJ
| CUDA
| EMIL
| Largest sphere to fit in unit cell has radius = 37.672
| New format PARM file being parsed.
| Version = 1.000 Date = 09/29/17 Time = 14:34:33
| 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.
| INFO: Reading atomic numbers from topology file.
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
------------------------------------------------------------
--------------------
1. RESOURCE USE:
------------------------------------------------------------
--------------------
getting box info from netcdf restart file
NATOM = 35532 NTYPES = 15 NBONH = 34164 MBONA = 1392
NTHETH = 3276 MTHETA = 1886 NPHIH = 6352 MPHIA = 4796
NHPARM = 0 NPARM = 0 NNB = 59218 NRES = 11078
NBONA = 1392 NTHETA = 1886 NPHIA = 4796 NUMBND = 38
NUMANG = 84 NPTRA = 39 NATYP = 24 NPHB = 1
IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0
NCOPY = 0
Implicit solvent radii are H(N)-modified Bondi radii (mbondi2)
|reading charge increments from file: HdeA_Exp_pH.cpin
| Coordinate Index Table dimensions: 16 16 17
| Direct force subcell size = 4.7198 4.7090 4.5697
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 =
5000000
iwrap = 1, ntwx = 1000, ntwv = 0, ntwe =
0
ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat=
0
Potential function:
ntf = 2, ntb = 1, igb = 0, nsnb =
25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 8.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 5000000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = -1.00000
Langevin dynamics temperature regulation:
ig = 873475
temp0 = 300.00000, tempi = 300.00000, gamma_ln= 5.00000
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
Constant pH options:
icnstph = 2
ntcnstph = 200
solvph = 7.00000
ntrelax = 100 mccycles = 1
| Intermolecular bonds treatment:
| no_intermolecular_bonds = 1
| Energy averages sample interval:
| ene_avg_sampling = 1000
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme =
1
vdwmeth = 1, eedmeth = 1, netfrc = 1
Box X = 75.516 Box Y = 75.345 Box Z = 77.685
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 80 NFFT2 = 80 NFFT3 = 80
Cutoff= 8.000 Tol =0.100E-04
Ewald Coefficient = 0.34864
Interpolation order = 4
------------------------------------------------------------
--------------------
3. ATOMIC COORDINATES AND VELOCITIES
------------------------------------------------------------
--------------------
default_name
begin time read from input coords = 400.000 ps
Number of triangulated 3-point waters found: 10900
On Mon, Oct 16, 2017 at 8:31 AM, Adrian Roitberg <roitberg.ufl.edu> wrote:
>
>
> On 10/16/17 11:26 AM, Pacheco, Sayuri wrote:
> > Dear All,
> >
> > I have been trying to run a constant pH explicit solvent MD using
> > pmemd.cuda and while running the production step I get the following
> error
> > c*udaMemcpy** GpuBuffer:: Upload failed an illegal memory access was
> > encountered*. When I tried running the MD with pmemd the simulation ran
> > without a problem for a few minutes and then it crashed (icnstph=2) . Do
> > you know what might cause this error message?
> >
> > P.S I ran the simulation with no problem when I set icnstph= 0 with pmemd
> > and pmemd.cuda. When I changed icnstph to 2 the simulations crashed with
> > both pmemd and pmemd.cuda.
>
> What is the error in pmemd with cpus ?
> Can you quantify 'ran without a problem fir a few minutes'
> Time does not help us, we need to know number of steps, if the system
> tried and succeeded to make at least one protonation change, etc.
>
> Maybe print to mdout and mdcrd more often to see whaty is happening ?
>
> thanks
> adrian
> >
> > Sincerely,
> > Sayuri Pacheco
> > _______________________________________________
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> > AMBER.ambermd.org
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> --
> Dr. Adrian E. Roitberg
> University of Florida Research Foundation Professor
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
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--
Sayuri Pacheco
California State University, Northridge
Biochemistry Major
Undergraduate Biomedical Researcher
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Received on Tue Oct 24 2017 - 22:00:03 PDT
