Re: [AMBER-Developers] infinite ptraj.MPI, was: First AmberTools release candidate

From: Lachele Foley <lfoley.ccrc.uga.edu>
Date: Wed, 17 Mar 2010 09:10:11 -0400

> ??? Neither sander nor pmemd do parallel i/o, as far as I can see.

Exacty... That was one of my first questions to Bob D: do the file writes do anything fancy like leave pointers hanging mid-file, etc.? He said "just dumb-bunny appends," which is what makes sense to do.

> Does your problem exist with netcdf trajectories?

Haven't tried netcdf. I guess I have a job now for the grad student who just offered to help... I doubt it will matter a lot, because I've also seen issues, for example, in my min.o file. But, all information helps.

Regarding Ross's comment, since the filesystem I had the problem on is Lustre, "a real parallel filesystem", then the ptraj.MPI should be good there (better, even?), not hung forever. Right?


:-) Lachele 
--
B. Lachele Foley, PhD '92,'02
Assistant Research Scientist
Complex Carbohydrate Research Center, UGA
706-542-0263
lfoley.ccrc.uga.edu
----- Original Message -----
From: case
[mailto:case.biomaps.rutgers.edu]
To: AMBER Developers Mailing List
[mailto:amber-developers.ambermd.org]
Sent: Wed, 17 Mar 2010 07:43:57
-0400
Subject: Re: [AMBER-Developers] infinite ptraj.MPI,	was: First
AmberTools 	release candidate
> On Tue, Mar 16, 2010, Lachele Foley wrote:
> > 
> > > I wouldn't be surprised if it did turn out to be a FS issue - even
> simple
> > > NFS mount points can get really wacky sometimes (same file has different
> > > contents/attributes on different computers etc). For now I would say
> avoid
> > > using ptraj over any network filesystem in parallel.
> > 
> > ...or sander, pmemd...
> 
> ??? Neither sander nor pmemd do parallel i/o, as far as I can see.
> 
> Does your problem exist with netcdf trajectories?
> 
> ...dac
> 
> 
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