AMBER Archive (2008)

Subject: Re: AMBER: Parallel Self-guided Langevin simulation

From: David A. Case (case_at_scripps.edu)
Date: Thu May 22 2008 - 05:16:23 CDT

On Wed, May 21, 2008, Dirar Homouz wrote:
>
> I used the following input file to run a self-guided Langevin dynamics
> simulation:
>
> Self-guided Langevin dynamics run
> &cntrl
> ntb=0,
> imin=0, irest=0, ntx=1,
> ntt=3, tempi=300,temp0=300.0,gamma_ln=10.0
> ntc=1, ntf=1,
> nstlim=50000000,
> ntwe=100, ntwx=100, ntpr=200,
> isgld=1, tsgavg=0.2,tempsg=1.
> cut=999.,rgbmax=999.,
> /
>
> This simulation works fine when I run it serially on my machine. However
> when I tried to run it in parallel on a TeraGrid NCSA cluster, it crashed.

Have you tried to narrow this down? For example, does it depend on running
self-guided dynamics? Does it depend on the number of nodes you used? etc.

Just seeing a segfault is not much help. But finding out which input
parameters are correlated with crashes would be a good start.

...dac

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