[Pw_forum] dos.x : segmentation fault occurred

B S Bhushan ecebhushan at gmail.com
Thu Nov 9 18:12:34 CET 2017 

The input scripts in support of the query raised in earlier reply are
attached here.

On Thu, Nov 9, 2017 at 10:37 PM, B S Bhushan <ecebhushan at gmail.com> wrote:

> Dear Dr. Andea Thank you so much.
>
> Dear Dr. Lorenzo, YES I read your mail, and I replied with thanks as well.
>
> I am facing a new problem with *QE-6.2* on my supercomputer account.
>
> I had run a SCF for doped graphene structure with 48 atoms, and then tried
> to run NSCF calculation (I wanted to calculate DOS ultimately).
> The NSCF calculation stopped in between because the calculation has already*
> consumed 80 GB* and the disk ran out of memory.
> I am a bit surprised... because I have never seen an NSCF calculation
> taking too much of memory before.
> I am not getting why this case has happened.
>
> Can any of u plz suggest.
>
> I am very thankful for your precious time and knowledge.
>
>
> Sincerely,
> B S Bhushan
> ABV-IIITM Gwalior, India.
>
>
>
> On Tue, Nov 7, 2017 at 4:10 PM, Lorenzo Paulatto <paulatz at gmail.com>
> wrote:
>
>> Dear BS,
>> Did you read my email? Was it not clear at some point?
>>
>> Kind regards
>>
>> --
>> Lorenzo Paulatto
>> Written on a virtual keyboard with real fingers
>>
>> On 7 Nov 2017 10:37 a.m., "B S Bhushan" <ecebhushan at gmail.com> wrote:
>>
>> Seems like the dos.x of QE-6.2 can not find xml data from NSCF produced
>> using QE-6.1.
>> The following error was shown,
>>
>> ------------------------------------------------------------
>> ------------------------------------------------------------
>> ------------------------------------------------------------
>>  Program DOS v.6.2 (svn rev. 13949:13950) starts on  7Nov2017 at 13:22:50
>>
>>      This program is part of the open-source Quantum ESPRESSO suite
>>      for quantum simulation of materials; please cite
>>          "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
>>          "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);
>>
>>           URL http://www.quantum-espresso.org",
>>      in publications or presentations arising from this work. More
>> details at
>>      http://www.quantum-espresso.org/quote
>>
>>      Parallel version (MPI), running on     1 processors
>>
>>      MPI processes distributed on     1 nodes
>>
>>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> %%%%%%%%%%%%%%%%%%%
>>      Error in routine pw_readschemafile (1):
>>      xml data file not found
>>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> %%%%%%%%%%%%%%%%%%%
>>
>>      stopping ...
>> ------------------------------------------------------------
>> --------------
>> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
>> with errorcode 1.
>>
>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>> You may or may not see output from other processes, depending on
>> exactly when Open MPI kills them.
>> ------------------------------------------------------------
>> --------------
>> ------------------------------------------------------------
>> ------------------------------------------------------------
>> -----------------------------------------------------------------------
>>
>>
>> *should I do the VC-relax and NSCF again using QE-6.2 ??????????????*
>>
>> Please Suggest...
>>
>> Thank you very much for your kind support.
>>
>> Sincerely,
>> B S Bhushan
>> Ph.D Scholar,
>> ABV-IIITM Gwalior, India.
>>
>>
>> On Tue, Nov 7, 2017 at 11:41 AM, B S Bhushan <ecebhushan at gmail.com>
>> wrote:
>>
>>> Thank you very very much Dr. Andrea.
>>>
>>> I have a question sir...
>>> If I install the QE-6.2 on my supercomputer and run dos.x directly on
>>> the NSCF outputs produced using QE-6.1 will it work properly.
>>> Or I have to do VC-relax and NSCF again using QE-6.2.
>>>
>>> Please suggest... Your answer will save a lot of time for time.
>>>
>>> Thank you so so much for your precious time and knowledge.
>>>
>>> Sincerely,
>>> B S Bhushan
>>>
>>> On Tue, Nov 7, 2017 at 3:45 AM, Vahid Askarpour <vh261281 at dal.ca> wrote:
>>>
>>>> I think the input to dos.x (I call it dos.in) looks like this:
>>>>
>>>>  &DOS
>>>>    outdir='./'
>>>>    prefix=‘graphene'
>>>>    fildos=‘graphene.dos',
>>>>    Emin=-10.0, Emax=16, DeltaE=0.002
>>>> /
>>>>
>>>> You run dos.x after the nscf run. I think the nscf.in should contain
>>>> the relaxed structure.
>>>>
>>>> For the definition of Emin, Emax and DeltaE, see the online dos.x
>>>> manual.
>>>>
>>>>
>>>> Cheers,
>>>>
>>>> Vahid
>>>>
>>>> Vahid Askarpour
>>>> Department of Physics and Atmospheric Science
>>>> Dalhousie University,
>>>> Halifax, NS, Canada
>>>>
>>>> On Nov 6, 2017, at 4:19 PM, B S Bhushan <ecebhushan at gmail.com> wrote:
>>>>
>>>> Dear Experts,
>>>>
>>>> I am trying to extract the DOS profiles for some graphene systems using
>>>> Supercomputing facility.
>>>>
>>>> First, I performed VC-relax and then NSCF (I have not manually updated
>>>> the relaxed coordinates in the nscf input file, since nscf automatically
>>>> reads them from previous scf run). Then I tried to execute dos.x, however I
>>>> am getting segmentation fault error as shown below.
>>>>
>>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>>>      Program DOS v.6.1 (svn rev. 13369) starts on  6Nov2017 at 23:32:32
>>>>
>>>>      This program is part of the open-source Quantum ESPRESSO suite
>>>>      for quantum simulation of materials; please cite
>>>>          "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502
>>>> (2009);
>>>>           URL http://www.quantum-espresso.org",
>>>>      in publications or presentations arising from this work. More
>>>> details at
>>>>      http://www.quantum-espresso.org/quote
>>>>
>>>>      Parallel version (MPI), running on    16 processors
>>>>      R & G space division:  proc/nbgrp/npool/nimage =      16
>>>>
>>>>    Info: using nr1, nr2, nr3 values from input
>>>>
>>>>    Info: using nr1, nr2, nr3 values from input
>>>> forrtl: severe (174): SIGSEGV, segmentation fault occurred
>>>> Image              PC                Routine            Line
>>>> Source
>>>> dos.x              000000000073A4B1  qexml_module_mp_q        3753
>>>> qexml.f90
>>>> dos.x              000000000055AD27  pw_restart_mp_rea        2101
>>>> pw_restart.f90
>>>> dos.x              00000000005579E4  pw_restart_mp_pw_        1057
>>>> pw_restart.f90
>>>> dos.x              000000000040A828  read_xml_file_            240
>>>> read_file.f90
>>>> dos.x              0000000000406331  MAIN__                     95
>>>> dos.f90
>>>> dos.x              000000000040621C  Unknown               Unknown
>>>> Unknown
>>>> libc.so.6          0000003FF541ECDD  Unknown               Unknown
>>>> Unknown
>>>> dos.x              0000000000406119  Unknown               Unknown
>>>> Unknown
>>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>>>
>>>>
>>>> I am not getting any error, if I run dos.x directly after vc-relax.
>>>> However, If I run dos.x after NSCF the error appears.
>>>>
>>>> The input script for vc-relax, nscf are attached with the mail here.
>>>>
>>>> I thank you very much for your precious time and knowledge.
>>>>
>>>>
>>>> Sincerely,
>>>> B S Bhushan
>>>> Ph.D Scholar,
>>>> ABV-IIITM Gwalior, India.
>>>>
>>>>
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>>>
>>>
>>
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