[Pw_forum] error in charge density difference (chden.f90)
Paolo Giannozzi
p.giannozzi at gmail.com
Wed Sep 23 15:15:06 CEST 2015
The segmentation violation happens at line 84 of flib/plot_io.f90, which
should be this one:
read (iunplot, * ) (plot (ir), ir = 1, nr1x * nr2x * nr3)
Likely it is an out-of-bound error. Use pp.x in serial execution,
especially whne you produce files containing intermediate results (I think
the code crashes when reading one of those)
Paolo
On Wed, Sep 23, 2015 at 2:38 PM, Juliana Mendes <
mendesjuliana.juli at gmail.com> wrote:
> Dear Pwscf users,
>
> I am trying to do a charge density difference plot of my system (an
> organic molecule adsorbed on iron (001)), but I'm finding the following
> problem when I run the pp.x code.
>
>
> Currently Loaded Modulefiles:
> 1) softwares/intel/11.0/schrodinger/2012-04
> 2) compiladores/intel/2011
> 3) bibliotecas/intel/2011/openmpi/1.4.5
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image PC Routine Line
> Source
> pp.x 00000000008A56F4 Unknown Unknown Unknown
> pp.x 00000000008A02C2 Unknown Unknown Unknown
> pp.x 000000000084A766 Unknown Unknown Unknown
> pp.x 00000000008499D7 Unknown Unknown Unknown
> pp.x 0000000000761932 plot_io_ 84
> plot_io.f90
> pp.x 0000000000433D35 chdens_ 258
> chdens.f90
> pp.x 000000000043233B MAIN__ 44
> postproc.f90
> pp.x 0000000000431B5C Unknown Unknown Unknown
> libc.so.6 000000356B41D994 Unknown Unknown Unknown
> pp.x 0000000000431A69 Unknown Unknown Unknown
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image PC Routine Line
> Source
> pp.x 00000000008A56F4 Unknown Unknown Unknown
> pp.x 00000000008A02C2 Unknown Unknown Unknown
> pp.x 000000000084A766 Unknown Unknown Unknown
> pp.x 00000000008499D7 Unknown Unknown Unknown
> pp.x 0000000000761932 plot_io_ 84
> plot_io.f90
> pp.x 0000000000433D35 chdens_ 258
> chdens.f90
> pp.x 000000000043233B MAIN__ 44
> postproc.f90
> pp.x 0000000000431B5C Unknown Unknown Unknown
> libc.so.6 000000356B41D994 Unknown Unknown Unknown
> pp.x 0000000000431A69 Unknown Unknown Unknown
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image PC Routine Line
> Source
> pp.x 00000000008A56F4 Unknown Unknown Unknown
> pp.x 00000000008A02C2 Unknown Unknown Unknown
> pp.x 000000000084A766 Unknown Unknown Unknown
> pp.x 00000000008499D7 Unknown Unknown Unknown
> pp.x 0000000000761932 plot_io_ 84
> plot_io.f90
> pp.x 0000000000433D35 chdens_ 258
> chdens.f90
> pp.x 000000000043233B MAIN__ 44
> postproc.f90
> pp.x 0000000000431B5C Unknown Unknown Unknown
> libc.so.6 000000356B41D994 Unknown Unknown Unknown
> pp.x 0000000000431A69 Unknown Unknown Unknown
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image PC Routine Line
> Source
> pp.x 00000000008A56F4 Unknown Unknown Unknown
> pp.x 00000000008A02C2 Unknown Unknown Unknown
> pp.x 000000000084A766 Unknown Unknown Unknown
> pp.x 00000000008499D7 Unknown Unknown Unknown
> pp.x 0000000000761932 plot_io_ 84
> plot_io.f90
> pp.x 0000000000433D35 chdens_ 258
> chdens.f90
> pp.x 000000000043233B MAIN__ 44
> postproc.f90
> pp.x 0000000000431B5C Unknown Unknown Unknown
> libc.so.6 000000356B41D994 Unknown Unknown Unknown
> pp.x 0000000000431A69 Unknown Unknown Unknown
> --------------------------------------------------------------------------
> mpirun has exited due to process rank 0 with PID 5390 on
> node compute-3-1.local exiting without calling "finalize". This may
> have caused other processes in the application to be
> terminated by signals sent by mpirun (as reported here).
> --------------------------------------------------------------------------
>
> I am working with 4 processors (all calculations) and my version of
> quantum espresso is 5.0. I tried in different machines to check if the
> problem was in my machine, but I still have the same problem.
> I don't know if the problem is in my machines, in the QE version or if it
> is a compilation problem.
>
> Below is attached my input:
>
> &inputpp
> /
> &plot
> nfile=3
> filepp(1)='imidza.perp.hollow.mag141.charge', weight(1)=1.0
> filepp(2)='sup63.opt.mag141.charge', weight(2)=-1.0
> filepp(3)='imidza.perp.hollow.charge', weight(3)=-1.0
> iflag=3
> output_format=5
> fileout='sup.imidza.cdd.xsf'
> /
>
> *Does anyone have an idea of what is happening? *
>
> Thanks in advance for the help!
>
> Regards,
>
> Juliana Mendes.
>
>
> --
>
> Juliana de O. Mendes
>
> Postdoctoral in Chemistry
>
> Physical Chemistry Department
> Chemistry Institute
> Federal University of Rio de Janeiro
> Cidade Universitária, CT Bloco A sala 412
> Rio de Janeiro, RJ 21949-900
> Brazil
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
--
Paolo Giannozzi, Dept. Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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