Segm. Fault when running Bethe-Salpeter kernel for bulk-BN

Deals with issues related to computation of optical spectra, in RPA (-o c) or by solving the Bethe-Salpeter equation (-o b). Includes local field effects, excitons, etc.

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plasmon
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Joined: Thu Aug 23, 2018 9:18 am
Location: Fudan University, Shanghai, China
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Segm. Fault when running Bethe-Salpeter kernel for bulk-BN

Post by plasmon » Fri Aug 31, 2018 2:28 pm

Dear Developers,

I am trying to follow the BSE calculations for bulk-BN (http://www.yambo-code.org/wiki/index.ph ... step_guide). But I failed at the second step with the error information as follows,

<---> [01] CPU structure, Files & I/O Directories
<---> [02] CORE Variables Setup
<---> [02.01] Unit cells
<---> [02.02] Symmetries
<---> [02.03] RL shells
<---> [02.04] K-grid lattice
<---> [02.05] Energies [ev] & Occupations
<---> [03] Transferred momenta grid
<---> [04] Dynamic Dielectric Matrix (PPA)
<---> [05] Response Functions in Transition space[admin:01621] *** Process received signal ***
[admin:01621] Signal: Segmentation fault (11)
[admin:01621] Signal code: Address not mapped (1)
[admin:01621] Failing at address: 0x100
[admin:01621] [ 0] /lib64/libpthread.so.0[0x370b60f7e0]
[admin:01621] [ 1] yambo[0x589f0d]
[admin:01621] [ 2] yambo[0x40ce07]
[admin:01621] [ 3] yambo[0x40c6bd]
[admin:01621] [ 4] yambo[0x4076bd]
[admin:01621] [ 5] /lib64/libc.so.6(__libc_start_main+0xfd)[0x370ae1ed1d]
[admin:01621] [ 6] yambo[0x4064d9]
[admin:01621] *** End of error message ***
Segmentation fault (core dumped)

Could you please tell me how to fix this problem? Thank you very much!

Hao Zhang
Dr. Hao Zhang
Department of Optical Science and Engineering, Fudan University,Shanghai 200433, China
http://homepage.fudan.edu.cn/zhanghao/

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Daniele Varsano
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Re: Segm. Fault when running Bethe-Salpeter kernel for bulk-

Post by Daniele Varsano » Fri Aug 31, 2018 2:50 pm

Dear Hao,
can you please post your input/report and logs file or any other information useful to spot the problem?

Thanks,
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/

plasmon
Posts: 28
Joined: Thu Aug 23, 2018 9:18 am
Location: Fudan University, Shanghai, China
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Re: Segm. Fault when running Bethe-Salpeter kernel for bulk-

Post by plasmon » Sat Sep 01, 2018 12:57 pm

Daniele Varsano wrote:Dear Hao,
can you please post your input/report and logs file or any other information useful to spot the problem?

Thanks,
Daniele
Dear Daniele,

The calculations include four .in files, two of them are for QE DFT calculations, the other two are for Yambo BSE calculations.

1) scf file
&control
calculation='scf',
prefix='hBN',
restart_mode='from_scratch'
pseudo_dir = './Pseudos'
wf_collect=.true.
nstep = 200
verbosity = 'high'
/
&system
ibrav = 4,
celldm(1) = 4.716
celldm(3) = 2.582
nat= 4,
ntyp= 2,
force_symmorphic=.true.
ecutwfc = 40,
/
&electrons
electron_maxstep = 100
conv_thr = 1.0e-8
/
ATOMIC_SPECIES
B 10 B.pz-vbc.UPF
N 14 N.pz-vbc.UPF
ATOMIC_POSITIONS {crystal}
B 0.6666667 0.3333333 0.0000000
N -0.6666667 -0.3333333 0.0000000
B -0.6666667 -0.3333333 0.5000000
N 0.6666667 0.3333333 0.5000000
K_POINTS {automatic}
6 6 2 1 1 1

2)nscf file
&control
calculation='nscf',
prefix='hBN',
pseudo_dir = './Pseudos'
nstep = 200
verbosity = 'high'
wf_collect=.true.
/
&system
ibrav = 4,
celldm(1) = 4.716
celldm(3) = 2.582
nat= 4,
ntyp= 2,
force_symmorphic=.true.
ecutwfc = 40,nbnd = 100
/
&electrons
diago_thr_init=5.0e-6,
diago_full_acc=.true.
electron_maxstep = 100,
diagonalization='david'
mixing_mode = 'plain'
mixing_beta = 0.6
conv_thr = 1.0e-8
/
ATOMIC_SPECIES
B 10 B.pz-vbc.UPF
N 14 N.pz-vbc.UPF
ATOMIC_POSITIONS {crystal}
B 0.6666667 0.3333333 0.0000000
N -0.6666667 -0.3333333 0.0000000
B -0.6666667 -0.3333333 0.5000000
N 0.6666667 0.3333333 0.5000000
K_POINTS {automatic}
6 6 2 0 0 0

3) .in file for static screening by YAMBO,
em1s # [R Xs] Static Inverse Dielectric Matrix
Chimod= "hartree" # [X] IP/Hartree/ALDA/LRC/PF/BSfxc
% BndsRnXs
1 | 40 | # [Xs] Polarization function bands
%
NGsBlkXs= 4 Ry # [Xs] Response block size
% DmRngeXs
0.10000 | 0.10000 | eV # [Xs] Damping range
%
% LongDrXs
1.000000 | 1.000000 | 1.000000 | # [Xs] [cc] Electric Field
%


4) .in file for BSE calculations for YAMBO
optics # [R OPT] Optics
bse # [R BSE] Bethe Salpeter Equation.
bsk # [R BSK] Bethe Salpeter Equation kernel
em1d # [R Xd] Dynamical Inverse Dielectric Matrix
ppa # [R Xp] Plasmon Pole Approximation
Chimod= "Hartree" # [X] IP/Hartree/ALDA/LRC/PF/BSfxc
BSEmod= "retarded" # [BSE] resonant/retarded/coupling
BSKmod= "SEX" # [BSE] IP/Hartree/HF/ALDA/SEX
BSENGexx= 30 Ry # [BSK] Exchange components
BSENGBlk= 4 Ry # [BSK] Screened interaction block size
#WehCpl # [BSK] eh interaction included also in coupling
KfnQPdb= "none" # [EXTQP BSK BSS] Database
KfnQP_N= 1 # [EXTQP BSK BSS] Interpolation neighbours
% KfnQP_E
0.000000 | 1.000000 | 1.000000 | # [EXTQP BSK BSS] E parameters (c/v) eV|adim|adim
%
KfnQP_Z= ( 1.000000 , 0.000000 ) # [EXTQP BSK BSS] Z factor (c/v)
KfnQP_Wv_E= 0.000000 eV # [EXTQP BSK BSS] W Energy reference (valence)
% KfnQP_Wv
0.00 | 0.00 | 0.00 | # [EXTQP BSK BSS] W parameters (valence) eV| 1|eV^-1
%
KfnQP_Wv_dos= 0.000000 eV # [EXTQP BSK BSS] W dos pre-factor (valence)
KfnQP_Wc_E= 0.000000 eV # [EXTQP BSK BSS] W Energy reference (conduction)
% KfnQP_Wc
0.00 | 0.00 | 0.00 | # [EXTQP BSK BSS] W parameters (conduction) eV| 1 |eV^-1
%
KfnQP_Wc_dos= 0.000000 eV # [EXTQP BSK BSS] W dos pre-factor (conduction)
% BEnRange
0.00000 | 10.00000 | eV # [BSS] Energy range
%
% BDmRange
0.10000 | 0.10000 | eV # [BSS] Damping range
%
BEnSteps=0 # [BSS] Energy steps
% BLongDir
1.000000 | 0.000000 | 0.000000 | # [BSS] [cc] Electric Field
%
% BSEBands
6 | 10 | # [BSK] Bands range
%
XfnQPdb= "none" # [EXTQP Xd] Database
XfnQP_N= 1 # [EXTQP Xd] Interpolation neighbours
% XfnQP_E
0.000000 | 1.000000 | 1.000000 | # [EXTQP Xd] E parameters (c/v) eV|adim|adim
%
XfnQP_Z= ( 1.000000 , 0.000000 ) # [EXTQP Xd] Z factor (c/v)
XfnQP_Wv_E= 0.000000 eV # [EXTQP Xd] W Energy reference (valence)
% XfnQP_Wv
0.00 | 0.00 | 0.00 | # [EXTQP Xd] W parameters (valence) eV| 1|eV^-1
%
XfnQP_Wv_dos= 0.000000 eV # [EXTQP Xd] W dos pre-factor (valence)
XfnQP_Wc_E= 0.000000 eV # [EXTQP Xd] W Energy reference (conduction)
% XfnQP_Wc
0.00 | 0.00 | 0.00 | # [EXTQP Xd] W parameters (conduction) eV| 1 |eV^-1
%
XfnQP_Wc_dos= 0.000000 eV # [EXTQP Xd] W dos pre-factor (conduction)
% BndsRnXp
1 | 30 | # [Xp] Polarization function bands
%
NGsBlkXp= 37 RL # [Xp] Response block size
% LongDrXp
0.5774E-5 |0.5774E-5 |0.5774E-5 | # [Xp] [cc] Electric Field
%
PPAPntXp= 27.21138 eV # [Xp] PPA imaginary energy
Dr. Hao Zhang
Department of Optical Science and Engineering, Fudan University,Shanghai 200433, China
http://homepage.fudan.edu.cn/zhanghao/

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Daniele Varsano
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Re: Segm. Fault when running Bethe-Salpeter kernel for bulk-

Post by Daniele Varsano » Sat Sep 01, 2018 3:23 pm

Dear Hao,
can you please upload them as an attachment?
If it complaints just renaim them as .txt
Please post also the report file.

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/

plasmon
Posts: 28
Joined: Thu Aug 23, 2018 9:18 am
Location: Fudan University, Shanghai, China
Contact:

Re: Segm. Fault when running Bethe-Salpeter kernel for bulk-

Post by plasmon » Sun Sep 02, 2018 1:45 am

Daniele Varsano wrote:Dear Hao,
can you please upload them as an attachment?
If it complaints just renaim them as .txt
Please post also the report file.

Best,

Daniele
Dear Daniele,

I have tried to upload a .txt file but failed with the error message,
'Sorry, the board attachment quota has been reached.'

Hao
Dr. Hao Zhang
Department of Optical Science and Engineering, Fudan University,Shanghai 200433, China
http://homepage.fudan.edu.cn/zhanghao/

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Daniele Varsano
Posts: 2655
Joined: Tue Mar 17, 2009 2:23 pm
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Re: Segm. Fault when running Bethe-Salpeter kernel for bulk-

Post by Daniele Varsano » Sun Sep 02, 2018 7:11 am

Dear Hao,
thanks for reporting,
I've just changed the setting and now it should be possible to attach files.
Please post your inputs and reports: I will look to your problem in the next days.

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/

plasmon
Posts: 28
Joined: Thu Aug 23, 2018 9:18 am
Location: Fudan University, Shanghai, China
Contact:

Re: Segm. Fault when running Bethe-Salpeter kernel for bulk-

Post by plasmon » Mon Sep 03, 2018 2:07 am

Daniele Varsano wrote:Dear Hao,
thanks for reporting,
I've just changed the setting and now it should be possible to attach files.
Please post your inputs and reports: I will look to your problem in the next days.

Best,
Daniele
Dear Daniele,

Thank you very much for the help. I have uploaded the files here.

Hao Zhang
You do not have the required permissions to view the files attached to this post.
Dr. Hao Zhang
Department of Optical Science and Engineering, Fudan University,Shanghai 200433, China
http://homepage.fudan.edu.cn/zhanghao/

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Daniele Varsano
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Re: Segm. Fault when running Bethe-Salpeter kernel for bulk-

Post by Daniele Varsano » Thu Sep 06, 2018 4:24 pm

Dear Hao,
I have been out for a conference and only now I had the time to have a look at your files.
I was not able to reproduce your error, nevertheless I realized there is an inconsistency in your input file:
You first calculate the *static* screening including 4 Ry which correspond to 1491 Gvectors:

Code: Select all

[WR./SAVE//ndb.em1s]----------------------------------------
  Brillouin Zone Q/K grids (IBZ/BZ):  14   72   14   72
  RL vectors                   (WF): 1491
This should then be used in your BSE calcualtion, but in your input file you ask for dynamical screening calculation:

Code: Select all

optics                         # [R OPT] Optics
bse                            # [R BSE] Bethe Salpeter Equation.
bsk                            # [R BSK] Bethe Salpeter Equation kernel
em1d                           # [R Xd] Dynamical Inverse Dielectric Matrix
ppa                            # [R Xp] Plasmon Pole Approximation
as you include the "ppa" keyword. In youn input file then you ask for 37 G vectors:

Code: Select all

NGsBlkXp=  37          RL      # [Xp] Response block size
but you ask for 4Ry in the kernel:

Code: Select all

BSENGBlk=  4          Ry      # [BSK] Screened interaction block size
so Yambo has not enough G vector to calculate the kernel. If I run your input anyway yambo complains but do not crash.

Usually, the pp option in the BSE calculation is added if you have already calculated the *dynamical* screening for GW calculation and you want to use the omega=0 (static) components.
I suggest you start a new calculation from scratch setting a consistent value in the calculation of the screening and the building of the kernel.
Note that the static screening (as well the dynamical) can be included in the same input file of the BSE:

Code: Select all

yambo -b -o b -k sex -y d 
Hop it helps,

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/

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