[DFTB-Plus-User] RE Ben: Error message of "severe (174): SIGSEGV, segmentation fault occurred"

Ben Hourahine benjamin.hourahine at strath.ac.uk
Tue Dec 2 12:49:40 CET 2008

Hello Wu Xing,

I would very strongly suggest you start by using a serial run. If you
are using the standard 1.01 DFTB+ code, then this can use shared memory
processors via openMP, but not distributed memory parallel machines as
you have.

So probably you should be using

#PBS -l nodes=1:ppn=1
#PBS -l ncpus=1

initially, and once this is working then contact your local systems
administrator about running with openMP using more cpus on the same node.

Regarding the basis set for the calculations, you should use

  O = "p"
  Si = "d"

with the SK files all coming from the pbc-01 parameter set.
The d-states on the oxygen are not parameterized (set to 0 in the SK
files) so should not be included, however the d states on the Si should
be used to model SiO2.



#WU XING# wrote:
> Dear Ben Hourahine,
> Thank for your suggestion.
> Yes I am using MPI run, and the code is as the following:
> #!/bin/sh
> #PBS -N geo_3rdNanocluster
> #PBS -l nodes=2:ppn=2
> #PBS -l ncpus=4
> #PBS -l walltime=72:00:00
> #PBS -V
> #PBS -m bea
> #PBS -M wu0008ng at ntu.edu.sg
> #PBS -o output_geo_3rdNanocluster.out
> #PBS -e err_geo_3rdNanocluster.log
> cd dftb/dftb+_1.0.1_src/prg_dftb/_obj_x86_64-linux-ifort
> # Run the program
> ./dftb+
> According to your suggestion, I should change 'nodes=2:ppn=2' to
> 'nodes=1:ppn=1'? Or not necessary since it is MPI?
> Also, I am trying to calculate SiO2 cluster, so is it appropriate to set
> like the following?
> MaxAngularMomentum = {
>     O = "d"
>     Si = "d"
> }
> I am very new to the quantum chemistry area, so your suggestion would be
> very helpful to me.
> Thank you.
> Best regards.
> Wu Xing
> ------------------------------
> Message: 2
> Date: Mon, 01 Dec 2008 18:39:55 +0000
> From: Ben Hourahine <benjamin.hourahine at strath.ac.uk>
> Subject: Re: [DFTB-Plus-User] Error message of "severe (174): SIGSEGV,
>         segmentation fault occurred"
> To: User list for DFTB+ related questions
>         <dftb-plus-user at dftb-plus.info>
> Message-ID: <49342F7B.2070301 at strath.ac.uk>
> Content-Type: text/plain; charset=ISO-8859-1
> Hello WU Xing,
> I would like to add to B?lint's comment, that you also appear to be
> running in parallel (there is some message about 'nodes=2:ppn=2' in part
> of the error stream). Is this a shared memory machine, or are you using
> something like mpirun?
> In either case, I would suggest you try using a serial run with only a
> single processor as a first attempt. 300 atoms is quite a small system
> (unless you have many d or f electron atomic species), so you may even
> be able to be run completely in serial.
> Regards
> Ben
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     Dr. B. Hourahine, 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 University of Strathclyde is a charitable body,
registered in Scotland, with registration number SC015263

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