[Pw_forum] Error optmizing doped graphene

Tue Oct 24 13:44:22 CEST 2017

First, I optimized the structure using LCAO code (ATK) on my local machine.
Then I submitted the same for optimization on HPC.

It worked fine. HPC shown No error.

On Tue, Oct 24, 2017 at 4:09 PM, Paolo Giannozzi <p.giannozzi at gmail.com>
wrote:

> It might also be a problem of tiny numerical differences, due to different
> parallelization/compiler/libraries/phases of the moon, leading the code
> to different execution patterns. It has always been hard to pinpoint the
> origin of those errors.
>
> Paolo
>
> On Tue, Oct 24, 2017 at 10:45 AM, Giuseppe Mattioli <
> giuseppe.mattioli at ism.cnr.it> wrote:
>
>>
>> Dear Bhushan
>>
>> > The calculation has successfully completed on my local server without
>> any
>> > error.
>>
>> On mine too.
>>
>> It is likely an issue arising from a compiler or a library error, and
>> it is of course *very difficult* to correct, because we have no access
>> to your hpc facility and such kind of debug is a really time-consuming
>> task. I can only suggest you to ask the hpc system administrator, to
>> tell him that an application is running fine on your local cluster
>> when compiled with a given compiler and linked against a given set of
>> libraries, and it is not on the hpc cluster.
>>
>> HTH
>> Giuseppe
>>
>> Quoting B S Bhushan <ecebhushan at gmail.com>:
>>
>> > Dear Dr.Giuseppe and Dr. Lorenzo,
>> >
>> > The calculation has successfully completed on my local server without
>> any
>> > error.
>> > However, I am not yet sure why I am getting the error on Supercomputer,
>> and
>> > how to get rid of it.
>> >
>> > Thank you.
>> >
>> >
>> > On Mon, Oct 23, 2017 at 9:54 PM, B S Bhushan <ecebhushan at gmail.com>
>> wrote:
>> >
>> >> Dear Dr. Giuseppe,
>> >>
>> >> I have already submitted the same job on a different machine (my local
>> >> server) and awaiting the result. So far I have not seen any error, yet
>> I am
>> >> awaiting the final result.
>> >>
>> >> The error I posted was actually received when I tried to perform it
>> using
>> >> a High Performance computing facility.
>> >>
>> >> I will let you know of the result from my local server.
>> >>
>> >>
>> >> On Mon, Oct 23, 2017 at 9:48 PM, B S Bhushan <ecebhushan at gmail.com>
>> wrote:
>> >>
>> >>> Thank you very much for your support Dr. Lorenzo.
>> >>>
>> >>> I will try these and let you know the result.
>> >>>
>> >>> On Mon, Oct 23, 2017 at 9:07 PM, Lorenzo/Eric Paulatto <
>> >>> ericpaulatto at gmail.com> wrote:
>> >>>
>> >>>> Dear B S,
>> >>>>
>> >>>> I've had a look at your input, I see that the C-N distance is already
>> >>>> quite small at the beginning, and become even smaller after a couple
>> of
>> >>>> iteration; definitely smaller that the core radius of the two
>> >>>> pseudopotentials used, which is a typical cause of
>> >>>> diagonalisation problems.
>> >>>>
>> >>>> You should try using some harder pseudopotentials, I've attached two
>> >>>> hard pseudopotential fro mthe pslibrary of Andrea Dal Corso (do not
>> forget
>> >>>> to cite), which should do the trick. Take care of converging the
>> cutoff.
>> >>>> UPDATE: I'm not attaching the pseudos because they don't pass in the
>> list,
>> >>>> I'm sending them privately in a minute
>> >>>>
>> >>>> Please let us know if this solves your problem!
>> >>>>
>> >>>> kind regards
>> >>>>
>> >>>> On 23/10/17 15:08, B S Bhushan wrote:
>> >>>>
>> >>>> Dear Dr. Lorenzo,
>> >>>>
>> >>>> I think the error is occurring in the 4th optimization step.
>> >>>> I have attached the output file for your reference.
>> >>>>
>> >>>>
>> >>>> Awaiting your kind response.
>> >>>> B S Bhushan
>> >>>> Ph.D Scholar,
>> >>>> ABV-IIITM Gwalior, India.
>> >>>>
>> >>>>
>> >>>>
>> >>>> On Mon, Oct 23, 2017 at 4:44 PM, Lorenzo Paulatto <paulatz at gmail.com
>> >
>> >>>> wrote:
>> >>>>
>> >>>>> is it at the first structural relaxation step or later? I'm afraid
>> that
>> >>>>> doing a vc-relax of a small supercell with a defect could cause an
>> >>>>> unphysical crunch
>> >>>>>
>> >>>>> On 21/10/17 18:52, B S Bhushan wrote:
>> >>>>>
>> >>>>> Dear Expert,
>> >>>>>
>> >>>>> I was getting the below error while trying to vc-relax a doped
>> graphene.
>> >>>>> can you please suggest why is it occurring??
>> >>>>>
>> >>>>>
>> >>>>>      iteration #  9     ecut=    30.00 Ry     beta=0.70
>> >>>>>      Davidson diagonalization with overlap
>> >>>>>
>> >>>>>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> >>>>> %%%%%%%%%%%%%%%%%%%
>> >>>>>      Error in routine  cdiaghg (261):
>> >>>>>       problems computing cholesky
>> >>>>>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> >>>>> %%%%%%%%%%%%%%%%%%%
>> >>>>>
>> >>>>>      stopping ...
>> >>>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 22
>> >>>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 20
>> >>>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4
>> >>>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>> Sincerely,
>> >>>>>
>> >>>>> B S Bhushan,
>> >>>>> Ph.D scholar,
>> >>>>> ABV-IIITM Gwalior, India.
>> >>>>>
>> >>>>>
>> >>>>> _______________________________________________
>> >>>>> Pw_forum mailing
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>> >>>>>
>> >>>>>
>> >>>>> --
>> >>>>> Lorenzo Paulatto - Paris
>> >>>>>
>> >>>>>
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>> >>>>
>> >>>>
>> >>>>
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>>
>>
>>
>> GIUSEPPE MATTIOLI
>> CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
>> Via Salaria Km 29,300 - C.P. 10
>> I-00015 - Monterotondo Scalo (RM)
>> Mob (*preferred*) +39 373 7305625
>> Tel + 39 06 90672342 - Fax +39 06 90672316
>> E-mail: <giuseppe.mattioli at ism.cnr.it>
>>
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>
>
>
> --
> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
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