Hi Parker
It's pretty easy to roll your own which is what I recommend. Just make sure yiu have mvapich, gnu and cuda 5 modules loaded and the amber12 one unloaded and you should be able to compile your own pretty essily. Just build -cuda and -cuda -mpi and you wont have to worry about all the extra stuff needed for ambertools.
All the best
Ross
-------- Original message --------
From: Parker de Waal <Parker.deWaal09.kzoo.edu>
Date: 07/17/2013 12:28 (GMT-08:00)
To: AMBER Mailing List <amber.ambermd.org>
Cc: Laura Furge <Laura.Furge.kzoo.edu>
Subject: Re: [AMBER] pmemd.cuda.MPI NPT Issues
Thank you for the reply Ross,
Unfortunately I'm currently working on a XSEDE allocation on TACC's
Stampede server and do not have control over which software is installed.
I will however put in a ticket request to upgrade AMBER to 12.3
Best,
Parker
On Wed, Jul 17, 2013 at 2:29 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Parker,
>
> |--------------------- INFORMATION ----------------------
> | GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
> | Version 12.2
> |
> | 01/10/2013
>
>
> Update your AMBER installation. Version 12.3 (which is from bugfix.18)
> fixed an issue with NPT where systems start with a low initial density
> (like yours does).
>
> All the best
> Ross
>
>
> On 7/17/13 10:45 AM, "Parker de Waal" <Parker.deWaal09.kzoo.edu> wrote:
>
> >Hi Everyone,
> >
> >I'm currently trying to perform a 50 ns production run (NPT ensemble)
> >using
> >pmemd.cuda.MPI and am encountering a weird issue with my system density
> >continually going down. Interestingly, using the same settings I am able
> >to
> >run pmemd.cuda runs on a single card without error.
> >
> >While looking through the AMBER mailing list I found a previous thread
> >discussing this error -> http://archive.ambermd.org/201304/0313.html ,
> >Does
> >this error still persist or is there another reason why my system density
> >is constantly decreasing?
> >
> >An output of a 200 ps NPT using pmemd.cuda.MPI can be found here ->
> >https://gist.github.com/ParkerdeWaal/438e0d81e2570d097f0d
> >
> >Best,
> >Parker
> >_______________________________________________
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> >AMBER.ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
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Received on Wed Jul 17 2013 - 13:30:02 PDT
