[Pw_forum] dos.x : segmentation fault occurred
Andrea Ferretti
andrea.ferretti at unimore.it
Mon Nov 13 12:36:19 CET 2017
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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