AMBER Archive (2008)

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

From: Dirar Homouz (dirar_at_hotmail.com)
Date: Thu May 22 2008 - 10:58:27 CDT


Hi David,

Thanks for responding to my email. I tried narrowing it down. Regular MD works fine on the same cluster. The number of cpus doesn't
seem to make a difference. I ran the same simulation (SGLD) on 16 cpus then 14 cpus, I still have the same error.

Dirar

> Date: Thu, 22 May 2008 03:16:23 -0700
> From: case_at_scripps.edu
> To: amber_at_scripps.edu
> Subject: Re: AMBER: Parallel Self-guided Langevin simulation
>
> 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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