AW: REMD on IBM iDataPlex DX360M3

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Jul 09 2014 - 02:24:27 CDT

 

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Francesco Pietra
Gesendet: Dienstag, 8. Juli 2014 19:14
An: Norman Geist
Cc: Namd Mailing List
Betreff: Re: namd-l: REMD on IBM iDataPlex DX360M3

 

 

enabling GBSA

I already use GB SASA

try the impact of “twoawayx yes” and if that helps try additionally “twoawayy yes”

 

Could you please redirect me to the pertinent literature?

What’s about the NAMD manual?

explicit water works much better anyway and the problem of exchange ratios can be overcome with the TIGER variant of REMD

 

Could you please redirect me to TIGER literature?

At any event, I already completed (on a longer peptide) a T-REMD (on a BlueGene/Q) under either explicit TIP3 water or GB SASA. Forgetting about ergodicity, which can not be achieved, starting from random, unfolded, I got substantially the same modeling. Should TIGER save money ...

What’s about google? A query like “TIGER2 REMD” will point you in the right direction. The main advantage of TIGER2 is, that you can freely choose the number of replicas as exchanges happen at baseline temperature. So you can use your computing resources more efficiently.

francesco pietra

 

On Tue, Jul 8, 2014 at 8:12 AM, Norman Geist <norman.geist_at_uni-greifswald.de> wrote:

You can raise the precision and work load for implicit solvent REMD by enabling GBSA and increased cutoff ;)

 

But seriously you may want to try the impact of “twoawayx yes” and if that helps try additionally “twoawayy yes”.

 

See also that explicit water works much better anyway and the problem of exchange ratios can be overcome with the TIGER variant of REMD.

 

Norman Geist.

 

Von: Francesco Pietra [mailto:chiendarret_at_gmail.com]
Gesendet: Dienstag, 8. Juli 2014 07:42
An: NAMD; Norman Geist
Betreff: Fwd: namd-l: REMD on IBM iDataPlex DX360M3

 

At CINECA it has been determined that my REMD, with a peptide of 19 aa under GB conditions, provided too less for the GPUs. In fact, under explicit water conditions, I could run REMD with also the GPUs. If anything, I expected more from the GPUs under these conditions: like with only CPUs, very many replicas are needed in order to have adequate exchange.

fp

 

---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Thu, Jul 3, 2014 at 4:42 PM
Subject: Re: namd-l: REMD on IBM iDataPlex DX360M3
To: Norman Geist <norman.geist_at_uni-greifswald.de>
Cc: Namd Mailing List <namd-l_at_ks.uiuc.edu>

We also have namd 2.10 compiled on the IBM machine. Hopefully someone more expert than me in hardware/software, and particularly on that IBM machine, will intervene from our side.

francesco

 

On Thu, Jul 3, 2014 at 12:42 PM, Norman Geist <norman.geist_at_uni-greifswald.de> wrote:

Forgot to mention that I’m working with an MPI based build of namd 2.10 nightly build which have native REMD support and might be required.

 

Norman Geist.

 

Von: Francesco Pietra [mailto:chiendarret_at_gmail.com]
Gesendet: Donnerstag, 3.

Juli 2014 11:54

An: Norman Geist
Cc: Namd Mailing List

Betreff: Re: namd-l: REMD on IBM iDataPlex DX360M3

 

I have no recent records. When we tried some months ago, it seemed that the problem is probably trying to make
sure that every replica has the same number of MPI tasks + GPUs. Probably the GPUs can not be shared between replicas. However, I am giving second hand information, probably as bad as any second hand information.

We had no problem on running the same jobs on a BlueGene/Q, except a lot of CPUs required. I hoped to save money through the GPUs (which perform excellently on the same iDataPlex DX360M3 for both normal MD and accelerated MD)

 

francesco pietra

 

On Thu, Jul 3, 2014 at 11:28 AM, Norman Geist < <mailto:norman.geist_at_uni-greifswald.de> norman.geist_at_uni-greifswald.de> wrote:

What happens if you try?

 

Norman Geist.

 

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Francesco Pietra
Gesendet: Donnerstag, 3. Juli 2014 08:15
An: NAMD
Betreff: namd-l: REMD on IBM iDataPlex DX360M3

 

Hello:

Any recent success in carrying out replica exchange molecular dynamics on

IBM iDataPlex DX360M3 by also utilizing the GPUs?
thanks
 
francesco pietra

 

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