Re: AMBER: Amber9 with MPICH2 failure at runtime

From: Sasha Buzko <obuzko.ucla.edu>
Date: Wed, 16 Apr 2008 17:40:09 -0700

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
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Fri Apr 18 2008 - 21:19:56 PDT
Custom Search