[DFTB-Plus-User] Cannot calculate transport

Nick Papior Andersen nickpapior at gmail.com
Wed Apr 15 20:53:43 CEST 2015


To clarify your mail

2015-04-15 18:57 GMT+02:00 Alessandro Pirrotta <
alessandro.pirrotta at chem.ku.dk>:

> Dear Argo,
>
> Thank you very much for your email and your tips but none of those fixed
> the problem.
>
> Dear Gabriele,
>
> Thank you for your email.
> The second paragraph of the trouble shooting (executing "ulimit -t
> unlimited" right before running dftb+)
> fixes the problem. Now the program runs. Is that something that should not
> happen on a correctly compiled dftb+?
>
You meant ulimit -s unlimited, right?
ulimit -t is related to execution time.

>
> I tried to compiling again using these flags ( -ipo -O3 -no-prec-div -xP )
> as suggested on the intel forum but I could not compile it correctly. I got
> an extremely long list of : ipo_out4.f:(.text.hot000d3+0x33df): undefined
> reference to ..... "
>
> 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
> MOB +45 52 81 23 41
>
> alessandro.pirrotta at chem.ku.dk
>
> alessandro.pirrotta at gmail.com
>
> www.ki.ku.dk
>
> On 15 April 2015 at 14:33, Gabriele Penazzi <penazzi at uni-bremen.de> wrote:
>
>>  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
>> MOB +45 52 81 23 41
>>
>>  alessandro.pirrotta at chem.ku.dk
>>
>> alessandro.pirrotta at gmail.com
>>
>> www.ki.ku.dk
>>
>>
>> _______________________________________________
>> DFTB-Plus-User mailing listDFTB-Plus-User at mailman.zfn.uni-bremen.dehttps://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
>>
>>
>> _______________________________________________
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>>
>>
>
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>


-- 
Kind regards Nick
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