[DFTB-Plus-User] Max Number of Atoms
Marcelo Zimmer
mzsflores at gmail.com
Wed Oct 8 23:17:34 CEST 2008
Helo Ben,
I'm not sure the problem I was facing was related to the st
On Wed, Oct 8, 2008 at 05:59, Benjamin Hourahine <
benjamin.hourahine at strath.ac.uk> wrote:
> Hello Marcelo,
>
> Have you ruled out the stack size issue with ifort, which I also mailed
> you about?
>
> The probable reason for your discrepancy in estimating the memory is that
> both the Hamiltonian and overlap matrices have to be held in memory
> when using the LAPACK generalized eigensolvers. Incidentally, are you
> sure that you aren't using the divide and conquer eigensolver?
>
> Cheers
>
> Ben
>
> Dr. B. Hourahine, Department of Physics, SUPA, University of
> Strathclyde,
> John Anderson Building, 107 Rottenrow, Glasgow G4 0NG, United Kingdom
> Ph +44 141 548 2325 FAX +44 141 552 2891
> benjamin.hourahine at strath.ac.uk
>
> The University of Strathclyde is a Scottish registered charitable body,
> number SC015263
>
>
>
>
> -----Original Message-----
> From: dftb-plus-user-bounces at dftb-plus.info on behalf of Marcelo Zimmer
> Sent: Tue 07/10/2008 15:10
> To: User list for DFTB+ related questions
> Subject: Re: [DFTB-Plus-User] Max Number of Atoms
>
> Dr. B. Hourahine,
>
> Thank you for prompt answer. Actually, by "unexpected error" I meant: the
> job stoped without any error message. For this, I was wondering if the
> problem was caused by lack of memory or any limitation related to vector
> size allocation, which would limit the maximum number of atoms independent
> on hardware availability. Anyway, my calculations rely on the first case
> you've mentioned and I'm convinced the problem is lack of memory, although
> my expectations were that my calculations would require ~10Gb.
>
> Best regards,
>
> Marcelo Zimmer
>
> --
> ===================================================
> Marcelo Zimmer S. Flores
> (PhD Physics Student)
>
> Address:
> Universidade Estadual de Campinas - UNICAMP
> Instituto de Fisica Gleb Wataghin - IFGW
> Grupo de Solidos Organicos e Novos Materiais - GSONM
> Departamento de Fisica Aplicada (DFA) - Room 61
> Campinas - Sao Paulo - Brazil
> 13083-970
> Caixa Postal: 6165
> zimmer at ifi.unicamp.br
> ===================================================
>
> On Mon, Oct 6, 2008 at 19:26, Benjamin Hourahine <
> benjamin.hourahine at strath.ac.uk> wrote:
>
> > Hello Marcelo,
> >
> > I'll need some more information to give an accurate answer, but
> > if I assume all of the atoms have an SP basis, you have SCC
> > turned on, are using molecular boundary conditions (not periodic),
> > no spin polarization, and the 'standard' or 'relatively robust'
> > choice of eigensolvers then I'd estimate your memory requirements
> > at about 17 Gb for that system.
> >
> > If you use the default eigensolver (divide and conqer) this would rise
> > to a peak of about 28 Gb when it requires workspace. Similarly, changing
> > any of the above calculational conditions could also modify the memory
> use.
> >
> > This suggests you are running out of memory. What exactly is the
> > 'unexpected error'?
> >
> > Cheers
> >
> > Ben
> >
> > Dr. B. Hourahine, Department of Physics, SUPA, University of
> > Strathclyde,
> > John Anderson Building, 107 Rottenrow, Glasgow G4 0NG, United
> Kingdom
> > Ph +44 141 548 2325 FAX +44 141 552 2891
> > benjamin.hourahine at strath.ac.uk
> >
> > The University of Strathclyde is a Scottish registered charitable body,
> > number SC015263
> >
> >
> >
> >
> > -----Original Message-----
> > From: dftb-plus-user-bounces at dftb-plus.info on behalf of Marcelo Zimmer
> > Sent: Mon 06/10/2008 19:47
> > To: User list for DFTB+ related questions
> > Subject: [DFTB-Plus-User] Max Number of Atoms
> >
> > Hello all DFTB+ users,
> >
> > I`d like to know what is the maximum number of atoms that DFTB+ can carry
> > on
> > calculation for a molecule. I`m trying to compute approx. 8,000 atoms and
> > I`m having unexpected error during the first SCC cycle. I`m trying to run
> > this job under 8 Intel(R) Xeon(R) CPU E5420 @ 2.50GHz with 16Gb of RAM.
> >
> > Thank you in advance,
> >
> > Marcelo Zimmer
> >
> > --
> > ===================================================
> > Marcelo Zimmer S. Flores
> > (PhD Physics Student)
> >
> > Address:
> > Universidade Estadual de Campinas - UNICAMP
> > Instituto de Fisica Gleb Wataghin - IFGW
> > Grupo de Solidos Organicos e Novos Materiais - GSONM
> > Departamento de Fisica Aplicada (DFA) - Room 61
> > Campinas - Sao Paulo - Brazil
> > 13083-970
> > Caixa Postal: 6165
> > zimmer at ifi.unicamp.br
> > ===================================================
> >
> >
> > _______________________________________________
> > DFTB-Plus-User mailing list
> > DFTB-Plus-User at dftb-plus.info
> > http://www.dftb-plus.info/mailman/listinfo/dftb-plus-user
> >
>
>
>
> --
> ===================================================
> Marcelo Zimmer S. Flores
> (PhD Physics Student)
>
> Address:
> Universidade Estadual de Campinas - UNICAMP
> Instituto de Fisica Gleb Wataghin - IFGW
> Grupo de Solidos Organicos e Novos Materiais - GSONM
> Departamento de Fisica Aplicada (DFA) - Room 61
> Campinas - Sao Paulo - Brazil
> 13083-970
> Caixa Postal: 6165
> zimmer at ifi.unicamp.br
> ===================================================
>
>
> _______________________________________________
> DFTB-Plus-User mailing list
> DFTB-Plus-User at dftb-plus.info
> http://www.dftb-plus.info/mailman/listinfo/dftb-plus-user
>
--
===================================================
Marcelo Zimmer S. Flores
(PhD Physics Student)
Address:
Universidade Estadual de Campinas - UNICAMP
Instituto de Fisica Gleb Wataghin - IFGW
Grupo de Solidos Organicos e Novos Materiais - GSONM
Departamento de Fisica Aplicada (DFA) - Room 61
Campinas - Sao Paulo - Brazil
13083-970
Caixa Postal: 6165
zimmer at ifi.unicamp.br
===================================================
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