[AMBER] Replica Exchange: an illegal memory access was encountered launching kernel kClearForces

From: Jason Ku Wang <jwang198.stanford.edu>
Date: Thu, 5 Apr 2018 13:58:35 -0700

Hi AMBER community,

I'm currently running temperature-based replica exchange on AMBER for a
soluble protein system using an explicit solvent.

In certain instances, after the replica exchange simulation has been
running smoothly for a good number of steps and exchanges, I suddenly hit a
GPU error:
*Error: an illegal memory access was encountered launching kernel
kClearForces*
*cudaFree GpuBuffer::Deallocate failed an illegal memory access was
encountered*

It seems that this error has been observed in the past, but is the
source/cause known?

For your reference, I use the following input parameters for my t-REMD
simulation:

 &cntrl
  imin=0, ! Molecular dynamics
  ntx=5, ! Positions and velocities read formatted
  irest=1, ! Restart calculation
  ntc=2, ! SHAKE on for bonds with hydrogen
  ntf=2, ! No force evaluation for bonds with hydrogen
  WATNAM='TIP3',
  OWTNM='OH2',
  tol=0.0000001, ! SHAKE tolerance
  ntt=3, ! Langevin dynamics
  gamma_ln=1.0, ! Collision frequency for Langevin dyn.
  temp0=XXXXX, ! Simulation temperature (K)
  ntpr=50000, ! Print to mdout every ntpr steps
  ntwr=50000, ! Write a restart file every ntwr steps
  ntwx=50000, ! Write to trajectory file every ntwc steps
  dt=0.004, ! Timestep (ps)
  ig=-1, ! Random seed for Langevin dynamics
  cut=9.0, ! Nonbonded cutoff (Angstroms)
  ioutfm=1, ! Write binary NetCDF trajectory
  ntxo=2, ! Write binary restart file
  barostat=2, ! Use Monte Carlo barostat (Amber 14)
  ntp=0, ! No pressure coupling, not supported by AMBER REMD
  ntb=1, ! Constant volume simulation, NVT
  nstlim=5000, ! Number of MD steps between each exchange attempt
  numexchg=1000, ! Number of exchange attempts during simulation
  nmropt=1, ! Read in chirality restraints
 /
 &wt TYPE='END'
 /
 DISANG=$RESTRAINTS_FILE

Many thanks once again,
Jason


-- 
Jason Wang
Stanford University, Class of 2018
jwang198.stanford.edu
ᐧ
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Received on Thu Apr 05 2018 - 14:00:03 PDT
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