AMBER Archive (2008)

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

From: Dirar Homouz (dirar_at_hotmail.com)
Date: Wed May 28 2008 - 01:31:03 CDT


Hi dac,

Thanks again. Both systems (serial and parallel) passed the tests. I got it to work now by setting igb=1. I'm not sure why is that so.
The same input file without igb work serially.

Dirar

> Date: Sun, 25 May 2008 23:06:03 -0700
> From: case_at_scripps.edu
> To: amber_at_scripps.edu
> Subject: Re: AMBER: Parallel Self-guided Langevin simulation
>
> On Thu, May 22, 2008, Dirar Homouz wrote:
> >
> >
> > 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.
>
> Does your system pass the self-guided Langevin tests in the gb_rna and
> gact_ips directories (under $AMBERHOME/test)? Look for the tests with "sgld"
> in the name. You can run those in serial and in parallel. If those work, you
> should look for differences between what you are doing and those examples.
> If the tests fail, post that here, and remind us what compiler and OS you are
> using.
>
> ...dac
>
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