[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
>>
>>
>> _______________________________________________
>> DFTB-Plus-User mailing list
>> DFTB-Plus-User at mailman.zfn.uni-bremen.de
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>>
>>
>
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>
--
Kind regards Nick
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