[AMBER] problem with pmemd.cuda

From: Giovanni Pavan <giovanni.pavan.supsi.ch>
Date: Wed, 9 Nov 2011 10:07:57 +0100

Dear all,

I am running a simulation on a single C2050 GPU.

The system is quite unconventional and composed by 9 single strand DNAs
attached with a short tiol onto a surface of gold

The system is created in order to have an equal spacing between each ssDNA
(also in terms of periodic images).

To do so the water box is created with 0 buffer in X and Y directions, and
with opportune spacing along Z.


The system seems to pass successfully the heating to 300K

After that, I run NVT MD simulation in order to maintain the box dimensions

The simulation is divided into 1ns stages and here the gold surface is
restrained with ntr=1 and a constant of 10.0.

The 1st part of simulation (1ns - but this is true independently on the
length of each stage) passes without problems , but when it goes to step 2

Starting from RST1 I obtain the following message:


Error: unspecified launch failure launching kernel kReduceForces
cudaFree GpuBuffer::Deallocate failed unspecified launch failure


My input file is below. (# indicates a comment just to make it clear).


equil SAM










  ntb=2, #the run is actually an NVT,

  ntp=1, #this trick is used to monitor

  taup=999999999999999999999999999, #pressure and density











fix surface


RES 1 5445





I need your help, since I don't understand if the problem is related to the
system or to some problem with the GPU.

(it seems more the 2nd case as from
http://dev-archive.ambermd.org/201103/0019.html ).

Maybe a problem due to a too short cutoff?

I eagerly look forward to receive any comment from you.




Dr. Giovanni Maria Pavan


SUPSI - Laboratory of Applied Mathematics and Physics (LaMFI)

Centro Galleria 2, Manno 6928, Switzerland.

e-mail: giovanni.pavan.supsi.ch

skype: giovanni_pavan

phone: +41 58 666 65 60


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Received on Wed Nov 09 2011 - 01:30:03 PST
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