Bethe-Salpeter calculations (Segmentation fault)

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Bethe-Salpeter calculations (Segmentation fault)

Postby Janpreet Sidhu » Wed Oct 15, 2014 12:42 pm

Hello everyone
I am following tutorial http://www.abinit.org/documentation/helpfiles/for-v7.8/tutorial/lesson_bse.html to plot dielectric fuction. there are two input files i.e. tbs_1.in and tbs_2.in. i have already calculted these resutls using 9 atoms. Now i am calculating dielectric function for different structure using 27 atoms, when i run first file tbs_1.in everything ok but at last display some error in log file.
Code: Select all
 using density-functional theory.
 M. Fuchs, M. Scheffler, Comput. Phys. Commun. 119, 67 (1999).
 Comment : Some pseudopotential generated using the FHI code were used.

 [2] ABINIT : First-principles approach of materials and nanosystem properties.
 X. Gonze, B. Amadon, P.-M. Anglade, J.-M. Beuken, F. Bottin, P. Boulanger, F. Bruneval,
 D. Caliste, R. Caracas, M. Cote, T. Deutsch, L. Genovese, Ph. Ghosez, M. Giantomassi
 S. Goedecker, D.R. Hamann, P. Hermet, F. Jollet, G. Jomard, S. Leroux, M. Mancini, S. Mazevet,
 M.J.T. Oliveira, G. Onida, Y. Pouillon, T. Rangel, G.-M. Rignanese, D. Sangalli, R. Shaltaf,
 M. Torrent, M.J. Verstraete, G. Zerah, J.W. Zwanziger
 Computer Phys. Comm. 180, 2582-2615 (2009).
 Comment : the third generic paper describing the ABINIT project.
 Note that a version of this paper, that is not formatted for Computer Phys. Comm.
 is available at http://www.abinit.org/about/ABINIT_CPC_v10.pdf .
 The licence allows the authors to put it on the Web.

 [3] A brief introduction to the ABINIT software package.
 X. Gonze, G.-M. Rignanese, M. Verstraete, J.-M. Beuken, Y. Pouillon, R. Caracas, F. Jollet,
 M. Torrent, G. Zerah, M. Mikami, Ph. Ghosez, M. Veithen, J.-Y. Raty, V. Olevano, F. Bruneval,
 L. Reining, R. Godby, G. Onida, D.R. Hamann, and D.C. Allan.
 Z. Kristallogr. 220, 558-562 (2005).
 Comment : the second generic paper describing the ABINIT project. Note that this paper
 should be cited especially if you are using the GW part of ABINIT, as several authors
 of this part are not in the list of authors of the first or third paper.
 The .pdf of the latter paper is available at http://www.abinit.org/about/zfk_0505-06_558-562.pdf.
 Note that it should not redistributed (Copyright by Oldenburg Wissenshaftverlag,
 the licence allows the authors to put it on the Web).


 And optionally :

 [4] First-principles computation of material properties : the ABINIT software project.
 X. Gonze, J.-M. Beuken, R. Caracas, F. Detraux, M. Fuchs, G.-M. Rignanese, L. Sindic,
 M. Verstraete, G. Zerah, F. Jollet, M. Torrent, A. Roy, M. Mikami, Ph. Ghosez, J.-Y. Raty, D.C. Allan.
 Computational Materials Science 25, 478-492 (2002). http://dx.doi.org/10.1016/S0927-0256(02)00325-7
 Comment : the original paper describing the ABINIT project.

 [5] Fast radix 2, 3, 4 and 5 kernels for Fast Fourier Transformations
 on computers with overlapping multiply-add instructions.
 S. Goedecker, SIAM J. on Scientific Computing 18, 1605 (1997).
 Proc.   0 individual time (sec): cpu=      47437.2  wall=      47741.2

 Calculation completed.
.Delivered    0 WARNINGs and   0 COMMENTs to log file.
--- !FinalSummary
start_date: Tue Oct 14 11:37:53 2014
end_date: Wed Oct 15  0:53:34 2014
overall_cpu_time:      190116.0
overall_wall_time:      190964.4
...
[itlab-HP-Compaq-Elite-8300-SFF:2440] Local abort after MPI_FINALIZE completed successfully; not able to aggregate error messages, and not able to guarantee that all other processes were killed!
[itlab-HP-Compaq-Elite-8300-SFF:2441] Local abort after MPI_FINALIZE completed successfully; not able to aggregate error messages, and not able to guarantee that all other processes were killed!
[itlab-HP-Compaq-Elite-8300-SFF:2442] Local abort after MPI_FINALIZE completed successfully; not able to aggregate error messages, and not able to guarantee that all other processes were killed!
[itlab-HP-Compaq-Elite-8300-SFF:2439] Local abort after MPI_FINALIZE completed successfully; not able to aggregate error messages, and not able to guarantee that all other processes were killed!
-------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

  Process name: [[14027,1],0]
  Exit code:    65
--------------------------------------------------------------------------


Abinit generate _SUS and _SCR files of size 3.4 Gb each. Then i run the second file named tbs_2.in then i got error:

Code: Select all
 ==== FFT mesh for wavefunctions ====
  FFT mesh divisions ........................    15   15  180
  Augmented FFT divisions ...................    15   15  180
  FFT algorithm .............................   112
  FFT cache size ............................    16
 wfd_read_wfk: about to read tbs_2i_WFK
wfd_read_wfk: will read 5120 (b,k,s) states
 about to read ik_ibz:            1 , spin:            1
 about to read ik_ibz:            2 , spin:            1
 about to read ik_ibz:            3 , spin:            1
 about to read ik_ibz:            4 , spin:            1
 about to read ik_ibz:            5 , spin:            1
 about to read ik_ibz:            6 , spin:            1
 about to read ik_ibz:            7 , spin:            1
 about to read ik_ibz:            8 , spin:            1
 about to read ik_ibz:            9 , spin:            1
 about to read ik_ibz:           10 , spin:            1
 about to read ik_ibz:           11 , spin:            1
 about to read ik_ibz:           12 , spin:            1
 about to read ik_ibz:           13 , spin:            1
 about to read ik_ibz:           14 , spin:            1
 about to read ik_ibz:           15 , spin:            1
 about to read ik_ibz:           16 , spin:            1
 about to read ik_ibz:           17 , spin:            1
 about to read ik_ibz:           18 , spin:            1
 about to read ik_ibz:           19 , spin:            1
 about to read ik_ibz:           20 , spin:            1
 about to read ik_ibz:           21 , spin:            1
 about to read ik_ibz:           22 , spin:            1
 about to read ik_ibz:           23 , spin:            1
 about to read ik_ibz:           24 , spin:            1
 about to read ik_ibz:           25 , spin:            1
 about to read ik_ibz:           26 , spin:            1
 about to read ik_ibz:           27 , spin:            1
 about to read ik_ibz:           28 , spin:            1
 about to read ik_ibz:           29 , spin:            1
 about to read ik_ibz:           30 , spin:            1
 about to read ik_ibz:           31 , spin:            1
 about to read ik_ibz:           32 , spin:            1
 about to read ik_ibz:           33 , spin:            1
 about to read ik_ibz:           34 , spin:            1
 about to read ik_ibz:           35 , spin:            1
 about to read ik_ibz:           36 , spin:            1
 about to read ik_ibz:           37 , spin:            1
 about to read ik_ibz:           38 , spin:            1
 about to read ik_ibz:           39 , spin:            1
 about to read ik_ibz:           40 , spin:            1
 about to read ik_ibz:           41 , spin:            1
 about to read ik_ibz:           42 , spin:            1
 about to read ik_ibz:           43 , spin:            1
 about to read ik_ibz:           44 , spin:            1
 about to read ik_ibz:           45 , spin:            1
 about to read ik_ibz:           46 , spin:            1
 about to read ik_ibz:           47 , spin:            1
 about to read ik_ibz:           48 , spin:            1
 about to read ik_ibz:           49 , spin:            1
 about to read ik_ibz:           50 , spin:            1
 about to read ik_ibz:           51 , spin:            1
 about to read ik_ibz:           52 , spin:            1
 about to read ik_ibz:           53 , spin:            1
 about to read ik_ibz:           54 , spin:            1
 about to read ik_ibz:           55 , spin:            1
 about to read ik_ibz:           56 , spin:            1
 about to read ik_ibz:           57 , spin:            1
 about to read ik_ibz:           58 , spin:            1
 about to read ik_ibz:           59 , spin:            1
 about to read ik_ibz:           60 , spin:            1
 about to read ik_ibz:           61 , spin:            1
 about to read ik_ibz:           62 , spin:            1
 about to read ik_ibz:           63 , spin:            1
 about to read ik_ibz:           64 , spin:            1
cpu_time =     23.90, wall_time =     38.25
[itlab-HP-Compaq-Elite-8300-SFF:04263] *** Process received signal ***
[itlab-HP-Compaq-Elite-8300-SFF:04263] Signal: Segmentation fault (11)
[itlab-HP-Compaq-Elite-8300-SFF:04263] Signal code: Address not mapped (1)
[itlab-HP-Compaq-Elite-8300-SFF:04263] Failing at address: (nil)
[itlab-HP-Compaq-Elite-8300-SFF:04263] [ 0] [0xb774b40c]
[itlab-HP-Compaq-Elite-8300-SFF:04263] [ 1] abinit[0x8a308c7]
[itlab-HP-Compaq-Elite-8300-SFF:04263] [ 2] abinit[0x8a32544]
[itlab-HP-Compaq-Elite-8300-SFF:04263] [ 3] abinit[0x8a0158e]
[itlab-HP-Compaq-Elite-8300-SFF:04263] [ 4] abinit[0x843d57e]
[itlab-HP-Compaq-Elite-8300-SFF:04263] [ 5] abinit[0x846f89a]
[itlab-HP-Compaq-Elite-8300-SFF:04263] [ 6] abinit[0x80d5709]
[itlab-HP-Compaq-Elite-8300-SFF:04263] [ 7] abinit[0x805890e]
[itlab-HP-Compaq-Elite-8300-SFF:04263] [ 8] abinit[0x804cb27]
[itlab-HP-Compaq-Elite-8300-SFF:04263] [ 9] abinit[0x804bdd4]
[itlab-HP-Compaq-Elite-8300-SFF:04263] [10] /lib/i386-linux-gnu/libc.so.6(__libc_start_main+0xf3)[0xb6a244d3]
[itlab-HP-Compaq-Elite-8300-SFF:04263] [11] abinit[0x804bdf9]
[itlab-HP-Compaq-Elite-8300-SFF:04263] *** End of error message ***
[itlab-HP-Compaq-Elite-8300-SFF:04265] *** Process received signal ***
[itlab-HP-Compaq-Elite-8300-SFF:04262] *** Process received signal ***
[itlab-HP-Compaq-Elite-8300-SFF:04262] Signal: Segmentation fault (11)
[itlab-HP-Compaq-Elite-8300-SFF:04262] Signal code: Address not mapped (1)
[itlab-HP-Compaq-Elite-8300-SFF:04262] Failing at address: (nil)
[itlab-HP-Compaq-Elite-8300-SFF:04262] [ 0] [0xb770840c]
[itlab-HP-Compaq-Elite-8300-SFF:04262] [ 1] abinit[0x8a308c7]
[itlab-HP-Compaq-Elite-8300-SFF:04262] [ 2] abinit[0x8a32544]
[itlab-HP-Compaq-Elite-8300-SFF:04262] [ 3] abinit[0x8a0158e]
[itlab-HP-Compaq-Elite-8300-SFF:04262] [ 4] abinit[0x843d57e]
[itlab-HP-Compaq-Elite-8300-SFF:04262] [ 5] abinit[0x846f89a]
[itlab-HP-Compaq-Elite-8300-SFF:04262] [ 6] abinit[0x80d5709]
[itlab-HP-Compaq-Elite-8300-SFF:04262] [ 7] abinit[0x805890e]
[itlab-HP-Compaq-Elite-8300-SFF:04262] [ 8] abinit[0x804cb27]
[itlab-HP-Compaq-Elite-8300-SFF:04262] [ 9] abinit[0x804bdd4]
[itlab-HP-Compaq-Elite-8300-SFF:04262] [10] /lib/i386-linux-gnu/libc.so.6(__libc_start_main+0xf3)[0xb69e14d3]
[itlab-HP-Compaq-Elite-8300-SFF:04262] [11] abinit[0x804bdf9]
[itlab-HP-Compaq-Elite-8300-SFF:04262] *** End of error message ***
[itlab-HP-Compaq-Elite-8300-SFF:04264] *** Process received signal ***
[itlab-HP-Compaq-Elite-8300-SFF:04264] Signal: Segmentation fault (11)
[itlab-HP-Compaq-Elite-8300-SFF:04264] Signal code: Address not mapped (1)
[itlab-HP-Compaq-Elite-8300-SFF:04264] Failing at address: (nil)
[itlab-HP-Compaq-Elite-8300-SFF:04264] [ 0] [0xb77dc40c]
[itlab-HP-Compaq-Elite-8300-SFF:04264] [ 1] abinit[0x8a308c7]
[itlab-HP-Compaq-Elite-8300-SFF:04264] [ 2] abinit[0x8a32544]
[itlab-HP-Compaq-Elite-8300-SFF:04264] [ 3] abinit[0x8a0158e]
[itlab-HP-Compaq-Elite-8300-SFF:04264] [ 4] abinit[0x843d57e]
[itlab-HP-Compaq-Elite-8300-SFF:04264] [ 5] abinit[0x846f89a]
[itlab-HP-Compaq-Elite-8300-SFF:04264] [ 6] abinit[0x80d5709]
[itlab-HP-Compaq-Elite-8300-SFF:04264] [ 7] abinit[0x805890e]
[itlab-HP-Compaq-Elite-8300-SFF:04264] [ 8] abinit[0x804cb27]
[itlab-HP-Compaq-Elite-8300-SFF:04264] [ 9] abinit[0x804bdd4]
[itlab-HP-Compaq-Elite-8300-SFF:04264] [10] /lib/i386-linux-gnu/libc.so.6(__libc_start_main+0xf3)[0xb6ab54d3]
[itlab-HP-Compaq-Elite-8300-SFF:04264] [11] abinit[0x804bdf9]
[itlab-HP-Compaq-Elite-8300-SFF:04264] *** End of error message ***
[itlab-HP-Compaq-Elite-8300-SFF:04265] Signal: Segmentation fault (11)
[itlab-HP-Compaq-Elite-8300-SFF:04265] Signal code: Address not mapped (1)
[itlab-HP-Compaq-Elite-8300-SFF:04265] Failing at address: (nil)
[itlab-HP-Compaq-Elite-8300-SFF:04265] [ 0] [0xb76f440c]
[itlab-HP-Compaq-Elite-8300-SFF:04265] [ 1] abinit[0x8a308c7]
[itlab-HP-Compaq-Elite-8300-SFF:04265] [ 2] abinit[0x8a32544]
[itlab-HP-Compaq-Elite-8300-SFF:04265] [ 3] abinit[0x8a0158e]
[itlab-HP-Compaq-Elite-8300-SFF:04265] [ 4] abinit[0x843d57e]
[itlab-HP-Compaq-Elite-8300-SFF:04265] [ 5] abinit[0x846f89a]
[itlab-HP-Compaq-Elite-8300-SFF:04265] [ 6] abinit[0x80d5709]
[itlab-HP-Compaq-Elite-8300-SFF:04265] [ 7] abinit[0x805890e]
[itlab-HP-Compaq-Elite-8300-SFF:04265] [ 8] abinit[0x804cb27]
[itlab-HP-Compaq-Elite-8300-SFF:04265] [ 9] abinit[0x804bdd4]
[itlab-HP-Compaq-Elite-8300-SFF:04265] [10] /lib/i386-linux-gnu/libc.so.6(__libc_start_main+0xf3)[0xb69cd4d3]
[itlab-HP-Compaq-Elite-8300-SFF:04265] [11] abinit[0x804bdf9]
[itlab-HP-Compaq-Elite-8300-SFF:04265] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 4262 on node itlab-HP-Compaq-Elite-8300-SFF exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------


i thought it was error from mpi, so reinstalled code using openmpi. And also see http://forum.abinit.org/viewtopic.php?f=11&t=2294 , added variable fftgw 11 , still getting same error.

Janpreet
Janpreet Sidhu
 
Posts: 16
Joined: Thu Apr 04, 2013 1:09 pm
Location: India

Re: Bethe-Salpeter calculations (Segmentation fault)

Postby shalom » Tue Sep 04, 2018 4:33 pm

Hello dear friends abniter. I have a small problem. I have redone the BS test with silicon. In point 3, we should get 5 files tbs_3o_DS but I get only 2, the DS1 and DS2 but not the others. I do not understand, help me please.
shalom
 
Posts: 12
Joined: Wed Mar 01, 2017 6:00 pm


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