Re: [gmx-users] Replica Exchange MD on more than 64 processors

2010-02-03 Thread Sebastian Breuers
Subject: RE: [gmx-users] Replica Exchange MD on more than 64 processors To: Discussion list for GROMACS users --- | Hi, One issue could be MPI memory usage. I have noticed that many MPI implementations use an amount of memory per

Re: RE: [gmx-users] Replica Exchange MD on more than 64 processors

2010-02-02 Thread Mark Abraham
- Original Message - From: Berk Hess Date: Wednesday, February 3, 2010 5:13 Subject: RE: [gmx-users] Replica Exchange MD on more than 64 processors To: Discussion list for GROMACS users --- | > Hi, > > One issue

RE: [gmx-users] Replica Exchange MD on more than 64 processors

2010-02-02 Thread Berk Hess
Hi, One issue could be MPI memory usage. I have noticed that many MPI implementations use an amount of memory per process that is quadratic (!) in the number of processes involved. This can quickly get out of hand. But 28 GB is a lot of memory. One thing that might help slightly is to not use do

Re: [gmx-users] Replica Exchange MD on more than 64 processors

2009-12-28 Thread Mark Abraham
bharat v. adkar wrote: On Mon, 28 Dec 2009, David van der Spoel wrote: bharat v. adkar wrote: On Mon, 28 Dec 2009, Mark Abraham wrote: > bharat v. adkar wrote: > > On Sun, 27 Dec 2009, Mark Abraham wrote: > > > > > bharat v. adkar wrote: > > > >On Sun, 27 Dec 2009, Mark Abraham wrot

Re: [gmx-users] Replica Exchange MD on more than 64 processors

2009-12-28 Thread bharat v. adkar
On Mon, 28 Dec 2009, David van der Spoel wrote: bharat v. adkar wrote: On Mon, 28 Dec 2009, Mark Abraham wrote: > bharat v. adkar wrote: > > On Sun, 27 Dec 2009, Mark Abraham wrote: > > > > > bharat v. adkar wrote: > > > >On Sun, 27 Dec 2009, Mark Abraham wrote: > > > > > > >bh

Re: [gmx-users] Replica Exchange MD on more than 64 processors

2009-12-27 Thread David van der Spoel
bharat v. adkar wrote: On Mon, 28 Dec 2009, Mark Abraham wrote: bharat v. adkar wrote: On Sun, 27 Dec 2009, Mark Abraham wrote: > bharat v. adkar wrote: > > On Sun, 27 Dec 2009, Mark Abraham wrote: > > > > > bharat v. adkar wrote: > > > > > >Dear all, > > > > I am trying to per

Re: [gmx-users] Replica Exchange MD on more than 64 processors

2009-12-27 Thread bharat v. adkar
On Mon, 28 Dec 2009, Mark Abraham wrote: bharat v. adkar wrote: On Sun, 27 Dec 2009, Mark Abraham wrote: > bharat v. adkar wrote: > > On Sun, 27 Dec 2009, Mark Abraham wrote: > > > > > bharat v. adkar wrote: > > > > > >Dear all, > > > > I am trying to perform replica exchange

Re: [gmx-users] Replica Exchange MD on more than 64 processors

2009-12-27 Thread Mark Abraham
bharat v. adkar wrote: On Sun, 27 Dec 2009, Mark Abraham wrote: bharat v. adkar wrote: On Sun, 27 Dec 2009, Mark Abraham wrote: > bharat v. adkar wrote: > > > > Dear all, > > I am trying to perform replica exchange MD (REMD) on a 'protein in > > water' system. I am following instru

Re: [gmx-users] Replica Exchange MD on more than 64 processors

2009-12-27 Thread bharat v. adkar
On Sun, 27 Dec 2009, Mark Abraham wrote: bharat v. adkar wrote: On Sun, 27 Dec 2009, Mark Abraham wrote: > bharat v. adkar wrote: > > > > Dear all, > > I am trying to perform replica exchange MD (REMD) on a 'protein in > > water' system. I am following instructions given on wiki (H

Re: [gmx-users] Replica Exchange MD on more than 64 processors

2009-12-27 Thread Mark Abraham
bharat v. adkar wrote: On Sun, 27 Dec 2009, Mark Abraham wrote: bharat v. adkar wrote: Dear all, I am trying to perform replica exchange MD (REMD) on a 'protein in water' system. I am following instructions given on wiki (How-Tos -> REMD). I have to perform the REMD simulation with 35 d

Re: [gmx-users] Replica Exchange MD on more than 64 processors

2009-12-27 Thread bharat v. adkar
On Sun, 27 Dec 2009, Mark Abraham wrote: bharat v. adkar wrote: Dear all, I am trying to perform replica exchange MD (REMD) on a 'protein in water' system. I am following instructions given on wiki (How-Tos -> REMD). I have to perform the REMD simulation with 35 different temperatures.

Re: [gmx-users] Replica Exchange MD on more than 64 processors

2009-12-26 Thread Mark Abraham
bharat v. adkar wrote: Dear all, I am trying to perform replica exchange MD (REMD) on a 'protein in water' system. I am following instructions given on wiki (How-Tos -> REMD). I have to perform the REMD simulation with 35 different temperatures. As per advise on wiki, I equilibrated the sys