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DLPOLY  August 2017

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Subject:

Re: DLPOLY 4.08 Low Efficiency Mode + HISTORY print formatting

From:

Michael Ferguson <[log in to unmask]>

Reply-To:

DL_POLY Mailing List <[log in to unmask]>

Date:

Thu, 24 Aug 2017 14:53:53 +0000

Content-Type:

text/plain

Parts/Attachments:

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text/plain (105 lines)

Dear Ilian,

Thank you for your reply, I will look into the prospect of a larger system as I cannot reduce my intermolecular interaction cutoffs by a great deal.

I have encountered a small bug today regarding the HISTORY output.  It appears that when I have a large RMSD for a particle the is no white space separation between the particle's charge and RMSD values in the output.

for example;

HW            2045    1.008000    0.42380046373.548781

If separated this line should read;

HW            2045    1.008000    0.423800   46373.548781

Could you please instruct me how to edit the HISTORY printing format so that I may force this white space between the two values?  I would like to use the charge and RMSD values separately for analysis purposes.

Kind regards

Michael

________________________________________
From: DL_POLY Mailing List [[log in to unmask]] on behalf of Ilian Todorov [[log in to unmask]]
Sent: 23 August 2017 08:32
To: [log in to unmask]
Subject: Re: DLPOLY 4.08 Low Efficiency Mode

Dear Michael,

I doubt you can do anything much to help you as given your input that is the best you can get out as speed form the DL_POLY machinery.

The low-efficiency warning is just a warning.  Take a look at the user manual about performance and what are the engineering limitations on performance if you'd like to find out more.

The only way to get better performance is to load more - larger system or the same one but with much shorter ranged interactions.

Regards,

Ilian
-----Original Message-----
From: DL_POLY Mailing List [mailto:[log in to unmask]] On Behalf Of Michael Ferguson
Sent: 18 August 2017 16:13
To: [log in to unmask]
Subject: DLPOLY 4.08 Low Efficiency Mode

Dear Developers,

I am currently studying a liquid system of approximately 40,000 atoms in a 50x50x200 cell using DLPOLY v4.08.

The computer to which I have access has nodes of 8, 16 or 32 processor cores.  I have therefore attempted some scaling tests on each node to evaluate my most efficient option.

However, in the OUTPUT file of each simulation, I receive the following message;

8 CORE:

node/domain decomposition (x,y,z):      1     1     8

 cutoffs driven limit on largest possible decomposition:   144 nodes/domains (3,3,16)

 cutoffs driven limit on largest balanced decomposition:     8 nodes/domains (1,1,8)

 link-cell decomposition 1 (x,y,z):      3     3     2

 warning issued    100

 *** warning - primary link cell algorithm has a link cell dimension that is < 3 !!! ***
 *** DL_POLY_4 RUNNING IN LOW EFFICIENCY MODE !!! ***



16 CORE:

node/domain decomposition (x,y,z):      1     2     8

 cutoffs driven limit on largest possible decomposition:   144 nodes/domains (3,3,16)

 cutoffs driven limit on largest balanced decomposition:     8 nodes/domains (1,1,8)

 link-cell decomposition 1 (x,y,z):      3     1     2

 warning issued    100

 *** warning - primary link cell algorithm has a link cell dimension that is < 3 !!! ***
 *** DL_POLY_4 RUNNING IN LOW EFFICIENCY MODE !!! ***


32 CORE:

 node/domain decomposition (x,y,z):      2     2     8

 cutoffs driven limit on largest possible decomposition:   144 nodes/domains (3,3,16)

 cutoffs driven limit on largest balanced decomposition:     8 nodes/domains (1,1,8)

 link-cell decomposition 1 (x,y,z):      1     1     2

 warning issued    100

 *** warning - primary link cell algorithm has a link cell dimension that is < 3 !!! ***
 *** DL_POLY_4 RUNNING IN LOW EFFICIENCY MODE !!! ***

Could you please explain to what I can do to increase the efficiency of the DLPOLY simulation.

Kind Regards

Michael

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