[AMBER] Fwd: simulation terminates for no apparent reason

From: Gabriel Urquiza <urquizagabes.gmail.com>
Date: Fri, 10 Dec 2010 10:14:22 -0300

Greetings amberists,

I am having some problems running PMEMD simulations of a protein in a water
box. The system has around 60.000 atoms and I'm running it CUDA on a GeForce
GTX 480 1.4Ghz board with a global memory size of 1535 MB. I am running
several short dynamics with this system and it turns out that when I check
at the human-readable output files I notice that some of them just
abnormally terminated. The step in which the simulations finish doesn't
follow any apparent pattern, some terminate near the end, others right at
the beginning. Most of the simulations runs through though but if I remove
every file, restart the machine and resubmit all the simulations, using the
same script, in the same order, it is almost certain that the simulations
that crashed earlier won't be exactly the ones that will crash now. It seems
a very random thing and I find it very weird. I am placing my bets on the
narrow memory size of the board I'm using, but I've decided to ask for some
light on the matter.

The machine is running on double precision and it has an i7 processor. The
nohup pops one out of two error messages down below, whenever a dynamic

Error: the launch timed out and was terminated launching kernel
Error: the launch timed out and was terminated launching kernel

I hope you can assist me with this.

Gabriel Urquiza


Universidade Federal da Paraíba - UFPB
Departamento de Química - Programa de Pós-Graduação
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Received on Fri Dec 10 2010 - 05:30:04 PST
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