[DFTB-Plus-User] DFTB-Plus-User Digest, Vol 78, Issue 3
Cristian Sanchez
cristian.g.sanchez at gmail.com
Tue Feb 9 15:34:57 CET 2021
Dear Raghavendra,
I see. The code will use as much RAM as it needs, if that is more that the physical RAM it’ll start to swap and that’s usually bad.
One option to accellerate electron dynamics runs is to compile the code with OpenMP enables and the set the proper environment variables OPM_NUM_THREADS, and MKL_NUM_THREADS to the number of PHYSICAL cores.
Without more specifics, that’s all that comes to mind.
Best,
C.
--
Dr. Cristián G. Sánchez
Investigador Principal
Instituto Interdisciplinario de Ciencias Básicas (ICB)
Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)
Profesor Asociado
Facultad de Ciencias Exactas Físicas y Naturales (FCEN)
Universidad Nacional de Cuyo (UNCuyo)
Padre Jorge Contreras 1300, Parque General San Martín
M5502JMA, Mendoza, Argentina
http://www.cgsanchez.net/
cristian.g.sanchez at gmail.com
csanchez at mendoza-conicet.gob.ar
--
> On 6 Feb 2021, at 13:36, Raghavendra V <raghav011986 at gmail.com> wrote:
>
> Dear Prof. Cristian Sacnhez,
>
> Thanks for your reply. I am not getting any error message. I just want to speed up the process by increasing the amount of RAM the calculation is going to use. Is there any specific keyword that we can
> input in the input file so that the program chooses to use the specified RAM while running a job.
>
> Thank you for your time sir.
>
> On Wed, Feb 3, 2021 at 2:36 PM <dftb-plus-user-request at mailman.zfn.uni-bremen.de <mailto:dftb-plus-user-request at mailman.zfn.uni-bremen.de>> wrote:
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> Today's Topics:
>
> 1. Re: How to allot RAM memory (Cristian Sanchez)
> 2. Re: issues on waveplot (toufik esssakhri)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 2 Feb 2021 13:16:49 -0300
> From: Cristian Sanchez <cristian.g.sanchez at gmail.com <mailto:cristian.g.sanchez at gmail.com>>
> To: User list for DFTB+ related questions
> <dftb-plus-user at mailman.zfn.uni-bremen.de <mailto:dftb-plus-user at mailman.zfn.uni-bremen.de>>
> Subject: Re: [DFTB-Plus-User] How to allot RAM memory
> Message-ID: <1EB81A29-5814-4575-8958-B1C19E84F64E at gmail.com <mailto:1EB81A29-5814-4575-8958-B1C19E84F64E at gmail.com>>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Raghavendra,
>
> Can you please show what kid of error message are you getting?
>
> Cheers,
>
> C.
>
> --
> Dr. Cristián G. Sánchez
>
> Investigador Principal
> Instituto Interdisciplinario de Ciencias Básicas (ICB)
> Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)
>
> Profesor Asociado
> Facultad de Ciencias Exactas Físicas y Naturales (FCEN)
> Universidad Nacional de Cuyo (UNCuyo)
>
> Padre Jorge Contreras 1300, Parque General San Martín
> M5502JMA, Mendoza, Argentina
>
> http://www.cgsanchez.net/ <http://www.cgsanchez.net/>
> cristian.g.sanchez at gmail.com <mailto:cristian.g.sanchez at gmail.com>
> csanchez at mendoza-conicet.gob.ar <mailto:csanchez at mendoza-conicet.gob.ar>
> --
>
> > On 29 Jan 2021, at 16:39, Raghavendra V <raghav011986 at gmail.com <mailto:raghav011986 at gmail.com>> wrote:
> >
> > Dear All,
> >
> > I am a new to DFTB+. How can I allot RAM memory in general or electron dynamics calculation to be specific. Kind suggest if there is anything more to memory.
> >
> > Thank you.
> >
> > Sincerely,
> >
> > V. Raghavendra
> > Research Scholar
> > C/O Dr. V. Subramanian
> > Inorganic and Physical Chemistry Division
> > Central Leather Research Institute (CSIR-CLRI)
> > Adyar, Chennai - 600 020
> > Tamil Nadu, India
> > http://clri.res.in/subramanian/index.html <http://clri.res.in/subramanian/index.html> <http://clri.res.in/subramanian/group.html <http://clri.res.in/subramanian/group.html>>
> > Mobile - +91 9962 559 388
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> ------------------------------
>
> Message: 2
> Date: Wed, 3 Feb 2021 09:05:54 +0000
> From: toufik esssakhri <tousak at hotmail.fr <mailto:tousak at hotmail.fr>>
> To: Mat Toliday <djlets2004 at yahoo.co.uk <mailto:djlets2004 at yahoo.co.uk>>, User list for DFTB+ related
> questions <dftb-plus-user at mailman.zfn.uni-bremen.de <mailto:dftb-plus-user at mailman.zfn.uni-bremen.de>>
> Subject: Re: [DFTB-Plus-User] issues on waveplot
> Message-ID:
> <AM4PR0302MB2819AA2D7FFD54D835AB0149ADB49 at AM4PR0302MB2819.eurprd03.prod.outlook.com <mailto:AM4PR0302MB2819AA2D7FFD54D835AB0149ADB49 at AM4PR0302MB2819.eurprd03.prod.outlook.com>>
>
> Content-Type: text/plain; charset="windows-1252"
>
> Dear Mat,
> Thank you for your help, but unfortunately I am still getting the same warning.
>
> Regards
> Toufik
>
> ________________________________
> De : DFTB-Plus-User <dftb-plus-user-bounces at mailman.zfn.uni-bremen.de <mailto:dftb-plus-user-bounces at mailman.zfn.uni-bremen.de>> de la part de Mat Toliday via DFTB-Plus-User <dftb-plus-user at mailman.zfn.uni-bremen.de <mailto:dftb-plus-user at mailman.zfn.uni-bremen.de>>
> Envoyé : mardi 2 février 2021 10:16
> À : User list for DFTB+ related questions <dftb-plus-user at mailman.zfn.uni-bremen.de <mailto:dftb-plus-user at mailman.zfn.uni-bremen.de>>
> Cc : Mat Toliday <djlets2004 at yahoo.co.uk <mailto:djlets2004 at yahoo.co.uk>>
> Objet : Re: [DFTB-Plus-User] issues on waveplot
>
> Hello,
> The warnings occur because the wfc file has the basis for all the atoms, but you are only using a subset of them. In your input file you should add:
> ParserOptions {
> IgnoreUnprocessedNodes = yes
> }
> I think this will do it.
> Yours
> Mat
>
>
> Sent from Yahoo Mail on Android<https://go.onelink.me/107872968?pid=InProduct&c=Global_Internal_YGrowth_AndroidEmailSig__AndroidUsers&af_wl=ym&af_sub1=Internal&af_sub2=Global_YGrowth&af_sub3=EmailSignature <https://go.onelink.me/107872968?pid=InProduct&c=Global_Internal_YGrowth_AndroidEmailSig__AndroidUsers&af_wl=ym&af_sub1=Internal&af_sub2=Global_YGrowth&af_sub3=EmailSignature>>
>
> On Tue, 2 Feb 2021 at 9:45, toufik esssakhri
> <tousak at hotmail.fr <mailto:tousak at hotmail.fr>> wrote:
>
>
> Dear all,
>
>
> I wanted to produce the spin density using waveplot, I got a Warning and I can’t get the cube file.
>
> ____________________
>
> WARNING!
>
> -> The following 7 node(s) have been ignored by the parser:
>
> (1)
>
> Path: waveplot/Basis/B
>
> Line: 63-103 (File: wfc.matsci-0-3.hsd)
>
> (2)
>
> Path: waveplot/Basis/N
>
> Line: 105-145 (File: wfc.matsci-0-3.hsd)
>
> (3)
>
> Path: waveplot/Basis/Na
>
> Line: 189-229 (File: wfc.matsci-0-3.hsd)
>
> (4)
>
> Path: waveplot/Basis/Al
>
> Line: 231-290 (File: wfc.matsci-0-3.hsd)
>
> (5)
>
> Path: waveplot/Basis/Si
>
> Line: 292-351 (File: wfc.matsci-0-3.hsd)
>
> (6)
>
> Path: waveplot/Basis/P
>
> Line: 353-412 (File: wfc.matsci-0-3.hsd)
>
> (7)
>
> Path: waveplot/Basis/Cu
>
> Line: 484-552 (File: wfc.matsci-0-3.hsd)
>
> ____________________
>
>
> I am using matsci dataset:
>
>
> # Definition of the basis
>
> Basis {
>
> Resolution = 0.01
>
> <<+ "wfc.matsci-0-3.hsd"
>
> }
>
>
> Best regards,
>
> Toufik
>
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