Re: [AMBER] MMPBSA Job Parallel Running

From: Jason Swails <jason.swails.gmail.com>
Date: Thu, 14 Jan 2016 22:57:39 -0500

On Thu, Jan 14, 2016 at 11:47 AM, Guqin Shi <shi.293.osu.edu> wrote:

> Hi Jason,
>
> thanks for the help and file. The only problem is...the whole package is
> installed on a Super Computer Center and I have no access to either
> installation or update... I will contact them to see what I could do...
>

‚ÄčOK. Well I'm fairly confident that the change that I made will resolve
these problems. It really *should* have been calling MPI_Finalize, but
wasn't. Now that it is, there's no excuse for a working MPI implementation
to hang at the end of a MMPBSA.py job. (That doesn't mean it *won't*, it
just means that if it does, I will blame the MPI implementation instead of
MMPBSA.py.)

As this is more of an annoyance than a critical issue, I think we'll just
wait for AmberTools 16 to come out in a few months rather than trying to
push through an update to AmberTools 15. (By the way, the patch I sent
earlier was problematic -- it used MPI.Finalize() instead of
MPI.COMM_WORLD.Finalize()).

All the best,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jan 14 2016 - 20:00:03 PST
Custom Search