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Re: Espressomd-users Digest, Vol 116, Issue 6


From: Peter Košovan
Subject: Re: Espressomd-users Digest, Vol 116, Issue 6
Date: Fri, 25 Sep 2020 09:38:47 +0200

Dear Chandra,

By construction, the simulation time is proportional to the number of steps. By using a parallel environment, you can reduce only the proportionality constant. If this is not sufficient, you need to use a lower number of steps. So, if you change the default 1e3 equilibration steps to 1e5, then your equilibration will run 100 times longer. This is what you would like to do in a non-interactive production run to achieve a good accuracy but not in an interactive tutorial session.

Please, note the remark in Tutorial 11:
Remark: The equilibration and sampling times used in this tutorial would be not sufficient for scientific purposes, but they are long enough to get at least a qualitative insight of the behaviour of ferrofluids. They have been shortened so we achieve reasonable computation times for the purpose of a tutorial.

With regards,

Peter

On Fri, Sep 25, 2020 at 7:17 AM chandra shekhar maurya <chandra15294@gmail.com> wrote:

If I want to run Jupyter-notebooks with Mpi, then how can I reduce the simulation time?


Thanks & Regards
Chandra Shekhar Maurya
Mechanical Eng. Dept.
Indian Institute of Technology Patna
Contact No:9793572837



On Thu, Sep 24, 2020 at 9:55 PM <espressomd-users-request@nongnu.org> wrote:
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Today's Topics:

   1. regarding reducing the simulation time (chandra shekhar maurya)
   2. Re: regarding reducing the simulation time (Rudolf Weeber)


----------------------------------------------------------------------

Message: 1
Date: Thu, 24 Sep 2020 19:45:04 +0530
From: chandra shekhar maurya <chandra15294@gmail.com>
To: espressomd-users-request@nongnu.org,
        espressomd-users-owner@nongnu.org
Cc: espressomd-users@nongnu.org
Subject: regarding reducing the simulation time
Message-ID:
        <CALf1gExvReh5qLFtFiUSgBud3Scs5eS+DXAt81nwOz1EGJ4FVQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Dear all,
I am simulating 11-ferrofluid_part1. When I increase equil_steps = 100000,
it is taking much time. How can I reduce the simulation time?
Please help. I will be highly obliged to you.



*Thanks & Regards*
Chandra Shekhar Maurya
Mechanical Eng. Dept.
Indian Institute of Technology Patna
Contact No:9793572837
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Message: 2
Date: Thu, 24 Sep 2020 17:31:24 +0200
From: Rudolf Weeber <weeber@icp.uni-stuttgart.de>
To: chandra shekhar maurya <chandra15294@gmail.com>
Cc: espressomd-users@nongnu.org
Subject: Re: regarding reducing the simulation time
Message-ID: <20200924153124.GB910401@icp.uni-stuttgart.de" target="_blank">20200924153124.GB910401@icp.uni-stuttgart.de>
Content-Type: text/plain; charset=us-ascii

Hi Chandra,
On Thu, Sep 24, 2020 at 07:45:04PM +0530, chandra shekhar maurya wrote:
> Dear all,
> I am simulating 11-ferrofluid_part1. When I increase equil_steps = 100000,
> it is taking much time. How can I reduce the simulation time?
> Please help. I will be highly obliged to you.
The algorithms used in the tutorial (in particular the dipolar P3M) are mpi-parallelized.
So, you can run the simulation on more than one core.
In theory, it is possible to run Jupyter-notebooks with Mpi, but the setup is likely non-trivial.
It is probably easier to save the tutorial as a Python file and run it using
mpirun -np 4 pypresso script.py

Regards, Rudolf




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End of Espressomd-users Digest, Vol 116, Issue 6
************************************************


--
Dr. Peter Košovan

Department of Physical and Macromolecular Chemistry
Faculty of Science, Charles University in Prague, Czech Republic

Katedra fyzikální a makromolekulární chemie
Přírodovědecká fakulta Univerzity Karlovy v Praze

www.natur.cuni.cz/chemistry/fyzchem/
Tel. +420221951029
Fax +420224919752

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