[Pw_forum] dos.x : segmentation fault occurred

B S Bhushan ecebhushan at gmail.com
Sat Nov 18 18:46:31 CET 2017 

Ok... Then the problem might be with the environment or something.

I will contact my HPC admin.

Thank you so much Dr. Andrea.

On Mon, Nov 13, 2017 at 5:06 PM, Andrea Ferretti <andrea.ferretti at unimore.it
> wrote:

>
> Dear Bhushan,
>
> I've re-run your scf+nscf using both qe-6.0 and 6.2 and both result in the
> same amount of disk usage (about 1GB for scf and 23 GB for nscf), which
> sounds reasonable given the size of the problem you are running (you have
> relatively large cell*nkpt parameters)
>
> take care
> Andrea
>
>
> 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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> --
> Andrea Ferretti, PhD
> S3 Center, Istituto Nanoscienze, CNR
> via Campi 213/A, 41125, Modena, Italy
> Tel: +39 059 2055322;  Skype: andrea_ferretti
> URL: http://www.nano.cnr.it
>
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