[DFTB-Plus-User] Max Number of Atoms
Marcelo Zimmer
mzsflores at gmail.com
Wed Oct 8 23:48:21 CEST 2008
Hello Ben,
Thank you for your response. I'm not sure about the stack size issue, since
I'm not familiar with it. In principle I can set the stack size to
unlimited, but I'm not sure how it will affect my calculations. After
setting it to unlimited, do I have to recompile dftb+? Also, when I set this
new limit, it gets back to its original value (8192KB) by the time I
reconnect to the machine. For now, I have too many doubts on how to work
(and workaraound) on this stack size issue. However, since my system was
made of a molecule over a surface (which is remained frozen during the
calculation) I could workaround my initial problem on calculating this
structure by dramatically reducing the number of atoms pertaining to the
surface (which was taken very big in order to check the limits of our
hardware available).
Regarding the eigensolver, as I new user of DFTB+, I have a question: is the
standard eigensolver the same as divide and conquer? The manual mentions
three flags for eigensolvers:
Standard {}
DivideAndConquer {}
RelativelyRobust {}
I've been using the Standard one so far, but I tested all these three flags
in a similar system having 1336 (but only 314 were free to move) atoms and
all of the flags used used 2.7 - 3.0 % of a total of 16Gb memory, so I
couldn't notice any difference between those eigensolvers related to memory
usage, however I haven't tested them by comparing total simulation time,
yet.
Best regards,
Marcelo Zimmer
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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