[DFTB-Plus-User] large-scale calculations

khalfoun hafid h_khalfoun at yahoo.com
Fri May 8 16:38:43 CEST 2020


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 ?thanksHafid



    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> 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> 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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