[DFTB-Plus-User] large-scale calculations

Hafid KHALFOUN h.khalfoun at univ-chlef.dz
Fri May 8 16:43:35 CEST 2020


thanks ,
Regards,
Hafid

Le ven. 8 mai 2020 à 16:52, Ben Hourahine via DFTB-Plus-User <
dftb-plus-user at mailman.zfn.uni-bremen.de> a écrit :

> Hello Hafid,
>
> In your script, can you try replacing
>
> dftb+
>
> with
>
> mpirun dftb+
>
> as you seem to have the binary started only on one process.
>
> At the moment you are using 1 processor per k-point, which depending on
> system size may not be enough. for ELSI solvers you may have to change the
> number of k-points and processor groups, as you should use at least as many
> groups as k-points for those solvers (and hence that number of processors).
> The default scalapack solvers allow multiple k-points in a group if you do
> not have sufficiently many processors.
>
> Regards
>
> Ben
>
>
> On 08/05/2020 15:38, khalfoun hafid via DFTB-Plus-User wrote:
>
> Dear Ben ,
> I try using  DFTB+ with the  ELPA ( mode = 2) solver
> (this is a part of my dftb_in.hsd input file)
> ....
> ....
> Hamiltonian = DFTB {
>   solver = ELPA {
>   mode = 2
> }
> ....
> .....
>   KPointsAndWeights = SupercellFolding {
>     1 0 0
>     0 1 0
>     0 0 38
>     0.0 0.0 0.0
>   }
> .....
> .....
>   Parallel {
>   Groups =4
>    Blacs {
>      BlockSize=64
> }
>  }
>
> Howover , after the submission of this script
>
> This is the script file
> #!/bin/bash
> # Submission script for Lemaitre3
> #SBATCH --job-name=essai
> #SBATCH --time=01:00:00 # hh:mm:ss
> #
> #SBATCH --ntasks=4
> #SBATCH --nodes=1
> #SBATCH --mem-per-cpu=500 # megabytes
> #SBATCH --partition=batch,debug
> #
> #SBATCH --mail-user=h_khalfoun at yahoo.com
> #SBATCH --mail-type=ALL
> #ulimit -s unlimited
>
> module load releases/2019b
> module load DFTB+/19.1-intel-2019b-Python-2.7.16
> dftb+
>
>
> I get  this ERROR message:
> --- >  in the run.sh.o (job ID) file :
>
>
> |===============================================================================
> |
> |  DFTB+ release 19.1
> |
> |  Copyright (C) 2006 - 2019  DFTB+ developers group
> |
>
> |===============================================================================
> |
> |  When publishing results obtained with DFTB+, please cite the following
> |  reference:
> |
> |  * B. Aradi, B. Hourahine and T. Frauenheim,
> |    DFTB+, a Sparse Matrix-Based Implementation of the DFTB Method,
> |    J. Phys. Chem. A, 111 5678 (2007).  [doi: 10.1021/jp070186p]
> |
> |  You should also cite additional publications crediting the
> parametrization
> |  data you use. Please consult the documentation of the SK-files for the
> |  references.
> |
>
> |===============================================================================
>
> Reading input file 'dftb_in.hsd'
> Parser version: 7
>
>
> --------------------------------------------------------------------------------
> ***  Converting input from version  6 to version  7 ...
> ***  Done.
>
> Reading SK-files:
> Done.
>
>
> Processed input in HSD format written to 'dftb_pin.hsd'
>
> Starting initialization...
>
> --------------------------------------------------------------------------------
>
> *ERROR! -> Number of groups (4) not compatible with number of processes
> (1)*
>
> and  this comment in
> in the run.e (job ID ) file
>
> The following have been reloaded with a version change:
>   1) releases/2018b => releases/2019b
>
>
>
>
> *application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 [unset]:
> write_line error; fd=-1 buf=:cmd=abort exitcode=1 : system msg for
> write_line failure : Bad file descriptor*
>
>
> I have tried some combination with the MPI parameters.
> Can you tell me what is wrong , please ?
> thanks
> Hafid
>
>
>
> Le mardi 7 avril 2020 à 16:30:27 UTC+2, Ben Hourahine via DFTB-Plus-User
> <dftb-plus-user at mailman.zfn.uni-bremen.de>
> <dftb-plus-user at mailman.zfn.uni-bremen.de> a écrit :
>
>
> Hello Hafid,
>
> unless there is something special about the electronic structure of your
> system. then the ELPA solver is probably the best choice for around 1E3 -
> 1E4 atoms. This will requires a binary compiled with MPI parallelism and
> both the ELSI and scalapack libraries.
>
> Regards
>
> Ben
> On 07/04/2020 15:19, khalfoun hafid via DFTB-Plus-User wrote:
>
> Dear Ben ,
> I would like to calculate band structure of carbon-based structure and
> plot de the DOS .
> By large-scale , I mean structures with great number of atoms ( .i.e.
> about thousands of atoms )
>
> I have MPI in my computational resourses .
>
> *Thanks*
>
> *Hafid *
>
>
> Le mardi 7 avril 2020 à 16:03:15 UTC+2, Ben Hourahine via DFTB-Plus-User
> <dftb-plus-user at mailman.zfn.uni-bremen.de>
> <dftb-plus-user at mailman.zfn.uni-bremen.de> a écrit :
>
>
> Hello Hafid,
>
> Can you supply some more information (and what do you mean by
> large-scale?):
>
> 1) What are your computational resources (serial/shared memory or MPI
> parallel)?
>
> 2) Do you have a GPU?
>
> 3) Is your system suitable for low order scaling parallel solvers
> (HOMO-LUMO gap or low spatial dimension)?
>
> Regards
>
> Ben
>
> On 07/04/2020 09:45, khalfoun hafid via DFTB-Plus-User wrote:
> > Dear Users
> > Which solver is suitable for large-scale calculations ?
> >
> > thanks
> >
> > Hafid
>
>
> --
>         Dr.  B.  Hourahine,  Senior  lecturer
>             SUPA, Department  of  Physics,
>             University  of  Strathclyde,
>               John  Anderson  Building,
>           107 Rottenrow, Glasgow G4 0NG, UK.
>   +44 141 548 2325, benjamin.hourahine at strath.ac.uk
>
> The  Department is  a partner  in SUPA,  the Scottish
>             Universities Physics Alliance
>
> The University  of Strathclyde  is a  charitable body,
>       registered in Scotland, number SC015263
>
>
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>
> --
>         Dr.  B.  Hourahine,  Senior  lecturer
>             SUPA, Department  of  Physics,
>              University  of  Strathclyde,
>               John  Anderson  Building,
>           107 Rottenrow, Glasgow G4 0NG, UK.
>   +44 141 548 2325, benjamin.hourahine at strath.ac.uk
>
> The  Department is  a partner  in SUPA,  the Scottish
>             Universities Physics Alliance
>
> The University  of Strathclyde  is a  charitable body,
>        registered in Scotland, number SC015263
>
> _______________________________________________
> DFTB-Plus-User mailing list
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>
> --
>         Dr.  B.  Hourahine,  Senior  lecturer
>             SUPA, Department  of  Physics,
>              University  of  Strathclyde,
>               John  Anderson  Building,
>           107 Rottenrow, Glasgow G4 0NG, UK.
>   +44 141 548 2325, benjamin.hourahine at strath.ac.uk
>
> The  Department is  a partner  in SUPA,  the Scottish
>             Universities Physics Alliance
>
> The University  of Strathclyde  is a  charitable body,
>        registered in Scotland, number SC015263
>
> _______________________________________________
> DFTB-Plus-User mailing list
> DFTB-Plus-User at mailman.zfn.uni-bremen.de
> https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
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