Dear David,
Thanks for the reply. I tried both. The error occurs before the first
energy calculation(Before the first step output was written to the file).
And when I ran the simulation with sander.MPI, I get the following error.
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 0 24998 49727 49728
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 0 14844 29626 29627
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
Just to put to your notice, I also ran a short 20ps, NVT and NPT
simulations each before running production on the system with HMR.
Moreover, diff prmtop hmr.prmtop shows many lines of differences.
Thank you,
Aravind R
Junior Research Fellow
Ranabir Das lab
NCBS, GKVK
Bellary Road
Bengaluru 560065
On Mon, September 24, 2018 5:09 pm, David A Case wrote:
> On Mon, Sep 24, 2018, Aravind Ravichandran wrote:
>
>
>> I wanted to run my production MD with HMR. So, after preparing my
>> simulation, running minimization and equilibration steps, I used parmed
>> to change the H-mass. {
>> parmed prmtop HMassRepartition
>> outparm hmr.prmtop }
>> After this I ran my production where I got the following error:
>>
>>
>> cudaMemcpy GpuBuffer::Download failed an illegal memory access was
>> encountered
>
> Usual debugging strategy: run a short simulation with ntpr=1. Do you
> see anything that helps? Does the above error occur before the first energy
> calcualation or somewhere later on?
>
> Second strategy: run the same short simluation with the CPU version. Is
> there any difference?
>
> You may also want to try a constant volume simulation, to see if the
> instability in your system is related to pressure or density changes.
>
> ...good luck...dac
>
>
>
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Received on Mon Sep 24 2018 - 06:30:03 PDT
