Segmentation Fault in p2y, QE6.5, YAMBO4.5

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Segmentation Fault in p2y, QE6.5, YAMBO4.5

Post by manasakani » Fri Jul 17, 2020 8:53 pm

Dear Developers and Users,

I'm encountering a Segmentation Fault while executing p2y. This is the error:

<---> DBs path set to .
<---> detected QE data format: qexsd
<---> == PWscf v.6.x generated data (QEXSD fmt) ==
<---> Header/K-points/Energies... done
<---> Cell data...
<---> [WARNING]Two or more crystal structures fit the given cell done
<---> Atomic data... done
<---> Symmetries...[SI no]......[-I no]...[TR yes]
<---> XC functional...Perdew, Burke & Ernzerhof(X)+Perdew, Burke & Ernzerhof(C)
<---> EXX fraction... 0.000000
<---> EXX screening... 0.000000
<---> K-points mesh... done
<---> RL vectors... done
<---> IGK arrays...[gra-login1:31172:0] Caught signal 11 (Segmentation fault)
==== backtrace ====
2 0x000000000005723c mxm_handle_error() /tmp/mxm_local_copy/mxm-3.5.3094/src/mxm/util/debug/debug.c:641
3 0x00000000000573ac mxm_error_signal_handler() /tmp/mxm_local_copy/mxm-3.5.3094/src/mxm/util/debug/debug.c:616
4 0x0000000000033280 killpg() ??:0
5 0x0000000000076d45 malloc_printerr() ??:0
6 0x00000000000775de _int_free() ??:0
7 0x00000000007f7d46 for__free_vm() ??:0
8 0x00000000007b3c7c for__close_proc() ??:0
9 0x00000000007b2fa2 for_close() ??:0
10 0x00000000004281cd qexsd_read_rhog() /project/6004669/mkanisel/q-e/yambo-stable/interfaces/p2y/qexsd_p2y.f90:2157
11 0x000000000044277f get_r_vectors() /project/6004669/mkanisel/q-e/yambo-stable/interfaces/p2y/mod_p2y.f90:726
12 0x0000000000463425 p2y_db1() /project/6004669/mkanisel/q-e/yambo-stable/interfaces/p2y/p2y_db1.f90:108
13 0x00000000004671a4 p2y_i() /project/6004669/mkanisel/q-e/yambo-stable/interfaces/p2y/p2y_i.f90:120
14 0x000000000040c2eb main() ??:0
15 0x00000000000202e0 __libc_start_main() ??:0
16 0x000000000040b22a _start() /tmp/nix-build-glibc-2.24.drv-0/glibc-2.24/csu/../sysdeps/x86_64/start.S:120
Segmentation fault

My system is monolayer MoS2, and I've manually changed the lattice constant with cell_parameters. The warning in the p2y run ([WARNING]Two or more crystal structures fit the given cell done) appears in all my successful runs as well, I'm assuming that's a consequence of using ibrav=0. This error only appears when I use this specific set of atomic locations, so though I don't think it's a bug, I'm at a loss for how to fix it. Any advice is appreciated.

I've attached the scf and nscf files I'm using (and the pseudo potentials):
Edit: The error can be reproduced at 2x2x1 k-grid (for faster checking)
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Last edited by manasakani on Sun Jul 19, 2020 7:10 pm, edited 1 time in total.
Manasa Kaniselvan
University of Waterloo, Waterloo, ON, Canada

Posts: 132
Joined: Fri Jan 31, 2014 11:13 am

Re: Segmentation Fault in p2y, QE6.5, YAMBO4.5

Post by andrea.ferretti » Sun Jul 19, 2020 6:05 pm

Dear Manasa,

thanks for porting.
I'll have a look and come back to you.
take care
Andrea Ferretti, PhD
CNR-NANO-S3 and MaX Centre
via Campi 213/A, 41125, Modena, Italy
Tel: +39 059 2055322; Skype: andrea_ferretti

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