[AMBER] cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered

From: Andreas Tosstorff <andreas.tosstorff.cup.uni-muenchen.de>
Date: Thu, 3 Nov 2016 13:15:47 +0100

I am receiving the following error message when running a simulation with
pmemd.cuda:

 

cudaMemcpy GpuBuffer::Download failed an illegal memory access was
encountered

 

 

The output file sometimes reads:

 

ERROR: nfft2 must be in the range of 6 to 512

ERROR: nfft3 must be in the range of 6 to 512

 

 

Input errors occurred. Terminating execution.

 

I attached another complete output file below.

 

I am running a series of simulations here, where the input files are
basically the same. The error however occurs only for some of the runs. So I
am not sure if the problem comes from my input files or something else.

 

 

When I run the simulation with pmemd instead of pmemd.cuda I receive the
following error:

 

Program received signal SIGSEGV: Segmentation fault - invalid memory
reference.

Backtrace for this error:
#0 0x7F3C1522D467
#1 0x7F3C1522DAAE
#2 0x7F3C1473366F
#3 0x4808C9 in __pme_slab_recip_mod_MOD_do_slab_pmesh_kspace
#4 0x4930CF in __pme_force_mod_MOD_pme_force
#5 0x4B2791 in __runmd_mod_MOD_runmd
#6 0x4E39D6 in MAIN__ at pmemd.F90:?

 

 

 

Is there anything that can be done about it?

 

 

Best,


Andreas

 

 

 

          -------------------------------------------------------

          Amber 16 PMEMD 2016

          -------------------------------------------------------

 

| PMEMD implementation of SANDER, Release 16

 

| Run on 11/03/2016 at 11:04:19

 

| Executable path: pmemd.cuda

| Working directory:
/home/WIN/andtos/Dropbox/PhD/Trastuzumab/Her_Modeller_2_FabHer/TRZ_2016_91

| Hostname: kemi-steno-2-0.win.dtu.dk

 

  [-O]verwriting output

 

File Assignments:

| MDIN: mdin_eq.57.5


| MDOUT: TRZ_2016_91_eq_57.5.out


| INPCRD: TRZ_2016_91_min_57.5.rst


| PARM: TRZ_2016_91.parm7


| RESTRT: TRZ_2016_91_eq_57.5.rst


| REFC: refc


| MDVEL: mdvel


| MDEN: mden


| MDCRD: TRZ_2016_91_eq_57.5.nc


| MDINFO: mdinfo


| MDFRC: mdfrc


 

 

Here is the input file:

 

100 ps NPT equilibration for 57.5 A


Constant pressure constant temperature production run


 &cntrl


  nstlim=500000, dt=0.002, ntx=1, irest=0, ntpr=5000, ntwr=5000, ntwx=0,


  tempi=0.0, temp0=300.0, ntt=3, gamma_ln=5.0, tautp=2.0,


 


  ntb=2, ntp=1,


 


  ntc=2, ntf=2,


 


  nmropt = 1, ioutfm = 1,


 


&end


 


&wt


  type='END',


 &end


DISANG=disang.57.5


 

 

Note: ig = -1. Setting random seed to 240918 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

|

|--------------------------------------------------------

|------------------- GPU DEVICE INFO --------------------

|

| CUDA_VISIBLE_DEVICES: 1

| CUDA Capable Devices Detected: 1

| CUDA Device ID in use: 0

| CUDA Device Name: GeForce GTX TITAN X

| CUDA Device Global Mem Size: 12206 MB

| CUDA Device Num Multiprocessors: 24

| CUDA Device Core Freq: 1.22 GHz

|

|--------------------------------------------------------

 

| Conditional Compilation Defines Used:

| PUBFFT

| BINTRAJ

| CUDA

| EMIL

 

| Largest sphere to fit in unit cell has radius = 44.588

 

| New format PARM file being parsed.

| Version = 1.000 Date = 11/03/16 Time = 10:24:51

 

| 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  =  238553 NTYPES =      19 NBONH =  231813 MBONA  =    6906
NTHETH =   14792 MTHETA =    9416 NPHIH =   30808 MPHIA  =   29876
NHPARM =       0 NPARM  =       0 NNB   =  373736 NRES   =   75985
NBONA  =    6906 NTHETA =    9416 NPHIA =   29876 NUMBND =      83
NUMANG =     180 NPTRA  =     206 NATYP =      47 NPHB   =       1
IFBOX  =       1 NMXRS  =      66 IFCAP =       0 NEXTRA =       0
NCOPY  =       0
 
| Coordinate Index Table dimensions:    19   38   39
| Direct force subcell size =     4.6935    4.5396    4.5327
 
     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    =    5000, ntrx    =       1, ntwr    =
5000
     iwrap   =       0, ntwx    =       0, ntwv    =       0, ntwe    =
0
     ioutfm  =       1, 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     =   8.00000, intdiel =   1.00000
 
Frozen or restrained atoms:
     ibelly  =       0, ntr     =       0
 
Molecular dynamics:
     nstlim  =    500000, nscm    =      1000, nrespa  =         1
     t       =   0.00000, dt      =   0.00200, vlimit  =  -1.00000
 
Langevin dynamics temperature regulation:
     ig      =  240918
     temp0   = 300.00000, tempi   =   0.00000, gamma_ln=   5.00000
 
Pressure regulation:
     ntp     =       1
     pres0   =   1.00000, comp    =  44.60000, taup    =   1.00000
 
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 =    5000
 
Ewald parameters:
     verbose =       0, ew_type =       0, nbflag  =       1, use_pme =
1
     vdwmeth =       1, eedmeth =       1, netfrc  =       1
     Box X =   89.176   Box Y =  172.506   Box Z =  176.777
     Alpha =   90.000   Beta  =   90.000   Gamma =   90.000
     NFFT1 =   96       NFFT2 =  180       NFFT3 =  180
     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 =     0.000 ps
 
 
 
           Begin reading energy term weight changes/NMR restraints
WEIGHT CHANGES:
                         ** No weight changes given **
 
RESTRAINTS:
Requested file redirections:
  DISANG    = disang.57.5
Restraints will be read from file: disang.57.5
Here are comments from the DISANG input file:
 
                       Number of restraints read =     1
 
                  Done reading weight changes/NMR restraints
 
 
 Number of triangulated 3-point waters found:    75095
 
     Sum of charges from parm topology file =   0.00299838
     Forcing neutrality...
 
| Dynamic Memory, Types Used:
| Reals             9370003
| Integers          7010189
 
| Nonbonded Pairs Initial Allocation:    39844314
 
| GPU memory information (estimate):
| KB of GPU memory in use:    925850
| KB of CPU memory in use:    260980
 
----------------------------------------------------------------------------
----
   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 =   0.8332E-11   at   2.782960
---------------------------------------------------
|---------------------------------------------------
| APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
|  with   50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt.   2.47
| APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
|  with   50.0 points per unit in tabled values
| Relative Error Limit not exceeded for r .gt.   2.89
|---------------------------------------------------
 
NSTEP =        0   TIME(PS) =       0.000  TEMP(K) =     0.00  PRESS =
33843.8
Etot   = 799268359.5628  EKtot   =         0.0000  EPtot      =
799268359.5628
BOND   =       438.8129  ANGLE   =      1759.1345  DIHED      =
9997.8663
1-4 NB =      2615.8612  1-4 EEL =     37243.5935  VDWAALS    =
800538966.9396
EELEC  =  -1322662.6453  EHBOND  =         0.0000  RESTRAINT  =
0.0001
EAMBER (non-restraint)  = 799268359.5627
EKCMT  =         0.0000  VIRIAL  =  -1987167.2492  VOLUME     =
2719428.9129
                                                    Density    =
0.8847
----------------------------------------------------------------------------
--
 
NMR restraints: Bond =    0.000   Angle =     0.000   Torsion =     0.000
============================================================================
===
 
 
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Received on Thu Nov 03 2016 - 05:30:04 PDT
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