[CP2K-user] [CP2K:17116] CPASSERT failed when trying to restart AIMD with periodic efield

Rajorshi Chattopadhyay rajorshichat at gmail.com
Fri Jun 10 10:26:20 UTC 2022
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Hello,

Yes, the simulation restarts, runs several steps and terminates with this
error.

On Fri, 10 Jun 2022 at 10:23, Matt Watkins <mattwatkinsuk at gmail.com> wrote:

> It could be directly related to CP2K but looks suspiciously like a memory
> leak in the MPI stack.
> Just checking - it restarted OK and ran several steps before that error?
> If there are no better ideas suggested, I'd check if there was a newer
> executable available and check reproducibility / report to your helpdesk.
> Matt
> On Friday, 10 June 2022 at 09:02:02 UTC+1 rajors... at gmail.com wrote:
>
>> Hi,
>>
>> I face another problem while trying to restart calculations with periodic
>> electric fields. After running for some steps, I get the following error :
>>
>> [1654828609.897841] [jwc01n044:28373:0]          ib_md.c:329  UCX  ERROR
>> ibv_reg_mr(address=0x134e71de0, length=5664, access=0xf) failed: Cannot
>> allocate memory
>> [1654828609.897897] [jwc01n044:28373:0]         ucp_mm.c:137  UCX  ERROR
>> failed to register address 0x134e71de0 mem_type bit 0x1 length 5664 on
>> md[5]=mlx5_0: Input/output error (md reg_mem_types 0x15)
>> [1654828609.897902] [jwc01n044:28373:0]    ucp_request.c:280  UCX  ERROR
>> failed to register user buffer datatype 0x8 address 0x134e71de0 len 5664:
>> Input/output error
>>
>>
>>
>>  *******************************************************************************
>>  *   ___
>>       *
>>  *  /   \
>>      *
>>  * [ABORT]
>>       *
>>  *  \___/      MPI error 17 in mpi_waitall @ mp_waitall_1 : See the
>> MPI_ERROR  *
>>  *    |                   field in MPI_Status for the error code
>>       *
>>
>>  *  O/|
>>      *
>>  * /| |
>>      *
>>  * / \
>>  dbcsr_mpiwrap.F:1022 *
>>
>>  *******************************************************************************
>>
>> But when I restart the calculation again from this point, it runs well
>> for a few steps and again gives the same error. Also, I have not noticed
>> this error in simulations which do not involve periodic electric fields. I
>> run my calculations in JUWELS HPC with CP2K version 7.1. I have attached
>> the input file for your reference.
>>
>> Thank you in advance.
>>
>> On Fri, 27 May 2022 at 12:49, Rajorshi Chattopadhyay <rajors... at gmail.com>
>> wrote:
>>
>>> Hi,
>>> Thanks a lot for your suggestion. Making &RESTART_RTP FALSE under
>>> &EXT_HISTORY solved the problem.
>>>
>>> On Thu, 26 May 2022 at 12:27, Jürg Hutter <hut... at chem.uzh.ch> wrote:
>>>
>>>> Hi
>>>>
>>>> this is the reason why your job stops:
>>>>
>>>>          ! periodic fields don't work with RTP
>>>>          CPASSERT(.NOT. do_rtp)
>>>>
>>>> If you don't activate RTP, please send your input to further
>>>> investigate.
>>>> If you want to use RTP, you can have periodic efields with the current
>>>> version of
>>>> the code.
>>>>
>>>> regards
>>>>
>>>> Juerg Hutter
>>>>
>>>> ________________________________________
>>>> From: cp... at googlegroups.com <cp... at googlegroups.com> on behalf of
>>>> Rajorshi Chattopadhyay <rajors... at gmail.com>
>>>> Sent: Wednesday, May 25, 2022 3:05 PM
>>>> To: cp... at googlegroups.com
>>>> Subject: Re: [CP2K:17034] CPASSERT failed when trying to restart AIMD
>>>> with periodic efield
>>>>
>>>> Hello,
>>>> Sorry for missing out on this important information. Here is the full
>>>> error:
>>>>
>>>>
>>>> *******************************************************************************
>>>>  *   ___
>>>>        *
>>>>  *  /   \
>>>>         *
>>>>  * [ABORT]
>>>>        *
>>>>  *  \___/                             CPASSERT failed
>>>>         *
>>>>  *    |
>>>>         *
>>>>  *  O/|
>>>>         *
>>>>  * /| |
>>>>         *
>>>>  * / \
>>>> cp_control_utils.F:431 *
>>>>
>>>>  *******************************************************************************
>>>>
>>>>
>>>>  ===== Routine Calling Stack =====
>>>>
>>>>             2 qs_init_subsys
>>>>             1 CP2K
>>>>
>>>> On Wed, 25 May 2022 at 14:04, Jürg Hutter <hut... at chem.uzh.ch<mailto:
>>>> hut... at chem.uzh.ch>> wrote:
>>>> Hi
>>>>
>>>> there should be important information printed together with the
>>>> CPASSERT failure.
>>>> Can you provide this, so we get a hint on the source of the problem?
>>>>
>>>> regards
>>>>
>>>> Juerg Hutter
>>>>
>>>> ________________________________________
>>>> From: cp... at googlegroups.com<mailto:cp... at googlegroups.com> <
>>>> cp... at googlegroups.com<mailto:cp... at googlegroups.com>> on behalf of
>>>> Rajorshi Chattopadhyay <rajors... at gmail.com<mailto:rajors... at gmail.com
>>>> >>
>>>> Sent: Wednesday, May 25, 2022 10:58 AM
>>>> To: cp... at googlegroups.com<mailto:cp... at googlegroups.com>
>>>> Subject: [CP2K:17027] CPASSERT failed when trying to restart AIMD with
>>>> periodic efield
>>>>
>>>> Hello all,
>>>>
>>>> I am trying to run an AIMD simulation to calculate wannier centers in
>>>> the presence of an external electric field (cp2k version 9.1.0). I
>>>> equilibrate the system (in the presence of the efield) and then use the
>>>> .restart and .wfn files to run a production simulation. However, during the
>>>> production run, I encounter the 'CPASSERT failed' error. Here are the
>>>> important sections of the input file for production simulation:
>>>>
>>>> &EXT_RESTART
>>>>   RESTART_FILE_NAME Water_amb_Bulk_efield-1.restart
>>>> &END EXT_RESTART
>>>>
>>>> &DFT
>>>>       BASIS_SET_FILE_NAME ./BASIS_MOLOPT
>>>>       POTENTIAL_FILE_NAME ./GTH_POTENTIALS
>>>>   &MGRID
>>>>       CUTOFF 280
>>>>       REL_CUTOFF 40
>>>>       NGRIDS 5
>>>>   &END MGRID
>>>>   &SCF
>>>>      SCF_GUESS RESTART
>>>>      MAX_SCF 1000
>>>>      &OT
>>>>         MINIMIZER DIIS
>>>>         PRECONDITIONER FULL_SINGLE_INVERSE
>>>>      &END OT
>>>>   &END SCF
>>>>
>>>>   &PERIODIC_EFIELD
>>>>      INTENSITY 5.0E-3
>>>>      POLARISATION 1.0 0.0 0.0
>>>>   &END PERIODIC_EFIELD
>>>>   &LOCALIZE
>>>>      METHOD CRAZY
>>>>      EPS_LOCALIZATION 1.0E-8
>>>>      MAX_ITER 2000
>>>> &PRINT
>>>>         &MOLECULAR_DIPOLES
>>>>          PERIODIC TRUE
>>>>          &EACH
>>>>           MD 2
>>>>          &END EACH
>>>>         &END MOLECULAR_DIPOLES
>>>>        &WANNIER_CENTERS
>>>>             IONS+CENTERS
>>>>             FILENAME =water_wannier.xyz<http://water_wannier.xyz><
>>>> http://water_wannier.xyz>
>>>>             &EACH
>>>>                MD 2
>>>>             &END EACH
>>>>        &END WANNIER_CENTERS
>>>>      &END PRINT
>>>>   &END LOCALIZE
>>>>   &XC
>>>>      &XC_FUNCTIONAL BLYP
>>>>      &END XC_FUNCTIONAL
>>>>      &XC_GRID
>>>>        XC_DERIV NN10_SMOOTH
>>>>        XC_SMOOTH_RHO NN10
>>>>      &END XC_GRID
>>>>      &VDW_POTENTIAL
>>>>          DISPERSION_FUNCTIONAL PAIR_POTENTIAL
>>>>          &PAIR_POTENTIAL
>>>>               TYPE DFTD3
>>>>               PARAMETER_FILE_NAME dftd3.dat
>>>>              REFERENCE_FUNCTIONAL BLYP
>>>>          &END PAIR_POTENTIAL
>>>>      &END VDW_POTENTIAL
>>>>     &END XC
>>>>     &PRINT
>>>>      &MOMENTS
>>>>       PERIODIC TRUE
>>>>       FILENAME = moment.out
>>>>       &EACH
>>>>         MD 2
>>>>       &END EACH
>>>>      &END MOMENTS
>>>>     &END PRINT
>>>>    &END DFT
>>>>
>>>> When I use the same script but without the &PERIODIC EFIELD part, this
>>>> problem is solved. Can you give some suggestions to get over this issue ?
>>>>
>>>> Thanking you in advance
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> With Regards,
>>>> Rajorshi Chattopadhyay,
>>>> PhD Researcher in Mineralogy/Crystallography,
>>>> Institut für Geologie und Mineralogie,
>>>> Universität zu Köln, Germany
>>>>
>>>>
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>>>> .
>>>>
>>>>
>>>> --
>>>> With Regards,
>>>> Rajorshi Chattopadhyay,
>>>> PhD Researcher in Mineralogy/Crystallography,
>>>> Institut für Geologie und Mineralogie,
>>>> Universität zu Köln, Germany
>>>>
>>>> 
>>>>
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>>>> .
>>>>
>>>
>>>
>>> --
>>> With Regards,
>>> Rajorshi Chattopadhyay,
>>> PhD Researcher in Mineralogy/Crystallography,
>>> Institut für Geologie und Mineralogie,
>>> Universität zu Köln, Germany
>>>
>>> 
>>>
>>
>>
>> --
>> With Regards,
>> Rajorshi Chattopadhyay,
>> PhD Researcher in Mineralogy/Crystallography,
>> Institut für Geologie und Mineralogie,
>> Universität zu Köln, Germany
>>
>> 
>>
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>


-- 
With Regards,
Rajorshi Chattopadhyay,
PhD Researcher in Mineralogy/Crystallography,
Institut für Geologie und Mineralogie,
Universität zu Köln, Germany



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