GW calculation using 5.0 fails with segmentation fault (signal 11)

You can post here problems arising when using the latest 5.0 reslease of Yambo. Issues as parallelization strategy, performance issues and other technical aspects realted to the new release.

Moderators: Davide Sangalli, Daniele Varsano, andrea.ferretti, andrea marini, Conor Hogan, myrta gruning

Bramhachari Khamari
Posts: 49
Joined: Wed Oct 23, 2019 5:52 am

Re: GW calculation using 5.0 fails with segmentation fault (signal 11)

Post by Bramhachari Khamari » Tue Jan 12, 2021 2:05 pm

Dear Sir,
Thanks a lot for helping me to solve the segmentation fault issue. By following your suggestions for the configurations options, I remove all the linking to other linear algebra libraries as
--with-blas-libs --with-lapack-libs after adding --enable-int-linalg (internal linear algebra). It compiles the code without any problem.

I did a test calculation using GW approaximation on hBN and got no error like segmentation fault that I was getting earlier. Now, I proceed further to see the qp band interpolation using ypp. I followed following procedure,

i) ypp -s b

ii) ypp -y # to remove TR symmetry, this produces the input

fixsyms # [R] Remove symmetries not consistent with an external perturbation
% Efield1
0.000000 | 0.000000 | 0.000000 | # First external Electric Field
%
% Efield2
0.000000 | 0.000000 | 0.000000 | # Additional external Electric Field
%
BField= 0.000000 T # [MAG] Magnetic field modulus
Bpsi= 0.000000 deg # [MAG] Magnetic field psi angle [degree]
Btheta= 0.000000 deg # [MAG] Magnetic field theta angle [degree]
#RmAllSymm # Remove all symmetries
RmTimeRev # Remove Time Reversal
#RmSpaceInv # Remove Spatial Inversion

When I run ypp after that FIxSymm folder is created. However, the SAVE folder is empty. following output for ypp.

<---> [01] MPI/OPENMP structure, Files & I/O Directories
<---> [02] Y(ambo) P(ost)/(re) P(rocessor)
<---> [03] Core DB
<---> :: Electrons :: 16.00000
<---> :: Temperature [ev]:: 0.000000
<---> :: Lattice factors [a.u.]:: 4.71774 4.08568 12.29080
<---> :: K points :: 50
<---> :: Bands :: 100
<---> :: Symmetries :: 12
<---> :: RL vectors :: 8101
<---> [04] K-point grid
<---> :: Q-points (IBZ):: 50
<---> :: X K-points (IBZ):: 50
<---> [05] CORE Variables Setup
<---> [05.01] Unit cells
<---> [05.02] Symmetries
<---> [05.03] Reciprocal space
<---> [05.04] K-grid lattice
<---> Grid dimensions : 10 10 4
<---> [05.05] Energies & Occupations
<---> Symmetries-respecting SAVE written to./FixSymm
<---> BZ -> IBZ reduction |########################################| [100%] --(E) --(X)
<---> Symmetries did not change. Program terminaned.
<---> [06] Timing Overview
<---> [07] Game Over & Game summary
The output says "Symmetries did not change. Program terminated", although, I remove TR symmetry (in ypp.in). In the earlier version (yambo-4.4.0) post processing using ypp was fine. I don't know what went wrong. Any help will be appreciated.

Regards,
Bramhachari Khamari
Post Doctoral Fellow
Department of Physics
IIT Kanpur, India.

User avatar
Daniele Varsano
Posts: 2604
Joined: Tue Mar 17, 2009 2:23 pm
Contact:

Re: GW calculation using 5.0 fails with segmentation fault (signal 11)

Post by Daniele Varsano » Tue Jan 12, 2021 2:22 pm

Dear Bramhachari,
I think the removal of the time-reversal symmetry it is not need anymore.
Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/

Bramhachari Khamari
Posts: 49
Joined: Wed Oct 23, 2019 5:52 am

Re: GW calculation using 5.0 fails with segmentation fault (signal 11)

Post by Bramhachari Khamari » Wed Jan 13, 2021 7:31 am

Dear Sir,
Thank you for the reply. I have couple of doubts for real time simulation. If the removal of TR symmetry is not needed then can we skip this steps while doing the calculation for real time simulation (yambo_rt). I followed the instruction from the Lumen tutorial (http://www.attaccalite.com/lumen/linear_response.html) it is mentioned that steps (5) and (6) are to remove TR symmetry.

i) By removing the TR symmetry by applying electric field (as instructed in steps 5 of Lumen tutorials), ypp run says

<---> WFs comp. reduction i_sp_pol= 1 |########################################| [100%] --(E) --(X)
<06s> WFs rotation i_sp_pol= 1 |########################################| [100%] 04s(E) 04s(X)
<06s> [ERROR] Allocation of qp%table failed with code 151

[ERROR] STOP signal received while in[06.05] QP energies
[ERROR]allocatable array is already allocated

ii) When I generate the input for collision using yambo_rt -b -e v hsex -V qp the input was not generated and it says "yambo_rt: unrecognized option '-b'. In 5.0 version what should I run to get the input for collision.
Any suggestion regarding above issue will be highly appreciated.

Regards,
Bramhachari Khamari
Post Doctoral Fellow
Department of Physics
IIT Kanpur, India.

User avatar
claudio
Posts: 284
Joined: Tue Mar 31, 2009 11:33 pm
Contact:

Re: GW calculation using 5.0 fails with segmentation fault (signal 11)

Post by claudio » Wed Jan 13, 2021 9:25 am

Dear Bramhachari

please follow the tutorial on the wik webpage becuase they are more upated

http://www.yambo-code.org/wiki/index.ph ... =Tutorials

and in particular

http://www.yambo-code.org/wiki/index.ph ... imulations

then I will try to reproduce your calculations with Yambo 5.0 and let you know

best
Claudio
Claudio Attaccalite
[CNRS/ Aix-Marseille Université/ CINaM laborarory / TSN department
Campus de Luminy – Case 913
13288 MARSEILLE Cedex 09
web site: http://www.attaccalite.com
Freely download scientific books from: http://www.freescience.info

User avatar
claudio
Posts: 284
Joined: Tue Mar 31, 2009 11:33 pm
Contact:

Re: GW calculation using 5.0 fails with segmentation fault (signal 11)

Post by claudio » Wed Jan 13, 2021 9:55 am

Dear Bramhachari

I checked the code, and there was a bug in the 5.0, I fixed it in the github,
you can update your code and it will work

best
Claudio
Claudio Attaccalite
[CNRS/ Aix-Marseille Université/ CINaM laborarory / TSN department
Campus de Luminy – Case 913
13288 MARSEILLE Cedex 09
web site: http://www.attaccalite.com
Freely download scientific books from: http://www.freescience.info

Bramhachari Khamari
Posts: 49
Joined: Wed Oct 23, 2019 5:52 am

Re: GW calculation using 5.0 fails with segmentation fault (signal 11)

Post by Bramhachari Khamari » Wed Jan 13, 2021 11:25 am

Dear Sir,
Thanks a lot for the quick reply. I have downloaded it and trying for the compilation. I will do the test calculation and consult you further.



Regards,
Bramhachari Khamari
Post Doctoral Fellow
Department of Physics
IIT Kanpur, India.

Bramhachari Khamari
Posts: 49
Joined: Wed Oct 23, 2019 5:52 am

Re: GW calculation using 5.0 fails with segmentation fault (signal 11)

Post by Bramhachari Khamari » Thu Jan 14, 2021 5:45 am

Dear Sir,
I compiled the code as per your suggestions. Now, prerequisites for real time was done correctly. However, this time I faced the problem in generating the input for real time collision part. I run the command

yambo_rt -b -e -v hsex

It says yambo_rt: unrecognized option '-b'. Any suggestion will be appreciated.

Regards,
Bramhachari Khamari
Post Doctoral Fellow
Department of Physics
IIT Kanpur, India.

User avatar
claudio
Posts: 284
Joined: Tue Mar 31, 2009 11:33 pm
Contact:

Re: GW calculation using 5.0 fails with segmentation fault (signal 11)

Post by claudio » Thu Jan 14, 2021 9:21 am

Dear Bramhachari

in yambo 5.0 the command changed in

Code: Select all

yambo_rt  -X s -e -v hsex
I updated the tutorial

best
Claudio
Claudio Attaccalite
[CNRS/ Aix-Marseille Université/ CINaM laborarory / TSN department
Campus de Luminy – Case 913
13288 MARSEILLE Cedex 09
web site: http://www.attaccalite.com
Freely download scientific books from: http://www.freescience.info

Bramhachari Khamari
Posts: 49
Joined: Wed Oct 23, 2019 5:52 am

Re: GW calculation using 5.0 fails with segmentation fault (signal 11)

Post by Bramhachari Khamari » Thu Jan 14, 2021 12:08 pm

Dear Sir,
Thanks a lot for the reply.

Regards
Bramhachari Khamari
Post Doctoral Fellow
Department of Physics
IIT Kanpur, India.

Post Reply