AMBER Archive (2008)

Subject: Re: AMBER: Amber9 with MPICH2 failure at runtime

From: Sasha Buzko (obuzko_at_ucla.edu)
Date: Wed Apr 16 2008 - 19:40:09 CDT

Thank you for your reply, David.
make test.pmemd passed all tests. I also changed the number of
processors to 8 and started another mpd on an additional node - I had 8
concurrent processes running. With that, it doesn't seem to be a problem
with the pmemd executable.
I'll test it with a larger system, since apparently pmemd doesn't like
the small 10-bp DNA fragment from an amber tutorial.

Thanks

Sasha

On Wed, 2008-04-16 at 17:26 -0700, David A. Case wrote:

> On Wed, Apr 16, 2008, Sasha Buzko wrote:
> >
> > Speaking of pmemd, I did compile it and tried to run it on the same
> > example from the tutorial. For some reason, I only get one pmemd process
> > on one node and it just hangs there using up 100% of the cpu/core but
> > not writing any output.
>
> Did your pmemd pass the test suite? That would help narrow down the problem.
>
> There doesn't need to be much pmemd documentation, since it should be a
> drop-in replacement for sander (for the subset of sander tasks it can handle.)
>
> ...dac
>
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