[DFTB-Plus-User] Cannot calculate transport

[Gabriele Penazzi]

Hi Alessandro,

have you checked if the system stack setting is responsible for this?
(see troubleshooting section in the manual and this link
https://software.intel.com/en-us/articles/intel-fortran-compiler-increased-stack-usage-of-80-or-higher-compilers-causes-segmentation-fault)?


Gabriele


On 04/15/2015 01:47 PM, Alessandro Pirrotta wrote:
> Dear DFTB+ users,
>
> I have compiled and successfully tested (with autotest) dftb+mpi-negf.
>
> I have then run a drain, source and device calculation.
> Drain and source run fine, but then the device calculation crashes
> giving this output:
>
> Reading SKF file
> ....
> .....
> Done.
>
> Processed input in HSD format written to 'dftb_pin.hsd'
>
> Starting initialization...
> --------------------------------------------------------------------------------
> PGRID:ALLPROC: 1 x 1
> PGRID:ATOM: 1 x 1
> Poisson parallelized on 1 nodes
>  Atomic density tolerance:   1.000000000000000E-005
>  Atomic density cutoff:    9.39669825812203      a.u.
>  Input PoissonBox=   30.0000   30.0000   30.0000  A
>  PoissAcc=  1.000000000000000E-007
>  Bulk Boundary Potential:    No
>  Atomic cutoff radius=   4.97251893391611      A
>
> CENTRAL REGION
>  Atom start - end =      1    22
>
> CONTACT #  1
>  Atom start - end =     23   118
>  direction:  3
>  Fermi Level=  -4.70500000000000      eV
>  mu=  0.136056922500000      V
>
> CONTACT #  2
>  Atom start - end =    119   214
>  direction: -3
>  Fermi Level=  -4.70500000000000      eV
>  mu= -0.136056922500000      V
>
> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>  INIT MPI-NEGF ON           1 NODES
>  CPU           0 READY
>  PRINTING CPU: T
> Mode:                        Static calculation
> Contact upload:              Yes
> Contact calculation:         No
> Use Poisson solver:          Yes
> Self consistent charges:     Yes
> SCC-tolerance:                 0.100000E-06
> Max. scc iterations:                   2000
> Ewald alpha parameter:         0.000000E+00
> Spin polarisation:           No
> Nr. of up electrons:          1091.000000
> Nr. of down electrons:        1091.000000
> Periodic boundaries:         No
> Diagonalizer:                Green's Functions (density matrix)
> Maximal SCC-cycles:                    2000
> Electronic temperature:        0.100000E-07
> Initial charges:             Set automatically (system chrg:   0.000E+00)
> Included shells:              S:  s, p, d
>                               C:  s, p
>                               O:  s, p
>                               H:  s
>                              Au:  s, p, d
> Extra options:
> --------------------------------------------------------------------------------
>
> ********************************************************************************
> ** Geometry step: 0
> ********************************************************************************
>
> MAXNEIGHBORS: 161
>   Structure info:
>   Number of PLs:           1
>   Interacting PLs:           1           1
>
>   iSCC Total electronic   Diff electronic      SCC error
> =========================================================================
>                     SOLVING POISSON EQUATION
> =========================================================================
> -------------------------------------------------------------------------
>  Poisson Box internally adjusted:
>  x range=   -14.93910    15.06090; Periodic:  F
>  y range=   -15.02760    14.97240; Periodic:  F
>  z range=    -3.14441    15.18553; Periodic:  F
>  Mesh details:
>  Lx=    30.000  nx= 129   dlx=  0.23437
>  Ly=    30.000  ny= 129   dly=  0.23437
>  Lz=    18.330  nz=  65   dlz=  0.28641
> -------------------------------------------------------------------------
>  -------------------------------------------------------------------------
>  Relative Poisson Error =  1.952627165542703E-008
>  Number of cycles executed =  8/ 60
>  -------------------------------------------------------------------------
> *************************************************************************
> =========================================================================
>                      COMPUTING DENSITY MATRIX
> =========================================================================
> CONTOUR INTEGRATION:*** 70 points
> srun: error: node244: task 0: Segmentation fault (core dumped)
> srun: Terminating job step 615175.0
>
> I have compiled it with mpif90, ifort 13.0.1, and openmpi-1.6.5-i4
> Any idea why the tests run fine and this does not?
>
> Kind regards,
> Alessandro
>
> *Alessandro Pirrotta*
> PhD student
>
>  
>
> *Faculty of Science**
> *Department of Chemistry &
> Nano-Science Center
> University of Copenhagen
> Universitetsparken 5, C321
> 2100 Copenhagen Ø
> Denmark
>
> DIR +45 21 18 11 90 <tel:%2B45%2021%2018%2011%2090>
> MOB +45 52 81 23 41 <tel:%2B45%2052%2081%2023%2041>
>
> alessandro.pirrotta at chem.ku.dk <mailto:alessandro.pirrotta at chem.ku.dk>
>
> alessandro.pirrotta at gmail.com <mailto:alessandro.pirrotta at gmail.com>
>
> www.ki.ku.dk <http://www.ki.ku.dk/>
>
>
>
> _______________________________________________
> 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

-- 
--
Dr. Gabriele Penazzi
BCCMS - University of Bremen

http://www.bccms.uni-bremen.de/
http://sites.google.com/site/gabrielepenazzi/
phone: +49 (0) 421 218 62337
mobile: +49 (0) 151 19650383

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.zfn.uni-bremen.de/pipermail/dftb-plus-user/attachments/20150415/78b36f7f/attachment.htm>