Yambo Community Forum

Posted: **Mon Oct 28, 2024 2:13 pm**

Hi all,

I recently compiled yambo (I attached the config.log file). I tested it first calculating the screening on MoS2 and everything went well. However, while calculating the BSE part, I get these errors in my output file:

Code: Select all

[n111:1714943] *** Process received signal ***
[n111:1714943] Signal: Segmentation fault (11)
[n111:1714943] Signal code: Address not mapped (1)
[n111:1714943] Failing at address: 0x14e15adfc810
[n111:1714943] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x3c050)[0x14e0dd52c050]
[n111:1714943] [ 1] yambo[0x5ea510]
[n111:1714943] [ 2] yambo[0x5360fb]
[n111:1714943] [ 3] yambo[0x52e3fd]
[n111:1714943] [ 4] yambo[0x4199f4]
[n111:1714943] [ 5] yambo[0x41d171]
[n111:1714943] [ 6] yambo[0x411814]
[n111:1714943] [ 7] yambo[0x40b6a8]
[n111:1714943] [ 8] yambo[0x40a548]
[n111:1714943] [ 9] yambo[0x6eacfd]
[n111:1714943] [10] yambo[0x4088de]
[n111:1714943] [11] /lib/x86_64-linux-gnu/libc.so.6(+0x2724a)[0x14e0dd51724a]
[n111:1714943] [12] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x85)[0x14e0dd517305]
[n111:1714943] [13] yambo[0x408641]
[n111:1714943] *** End of error message ***

As I am new to Yambo, I returned to the tutorial examples and tried running the 3D hBN example to ensure I did not do anything wrong in setting up my calculations.
However, there I also saw a similar issue:

First time I run the BSE kernel calculation with:

Code: Select all

yambo -o b -k sex -F 02_3D_BSE_kernel.in -J 3D_BSE

and then

Code: Select all

yambo -F 02_3D_BSE_kernel.in -J 3D_BSE

I get this output:

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  __ __  ____ ___ ___ ____   ___
 |  |  |/    |   |   |    \ /   \
 |  |  |  o  | _   _ |  o  )     |
 |  ~  |     |  \_/  |     |  O  |
 |___, |  _  |   |   |  O  |     |
 |     |  |  |   |   |     |     |
 |____/|__|__|___|___|_____|\___/


 <---> [01] MPI/OPENMP structure, Files & I/O Directories
 <---> [02] CORE Variables Setup
 <---> [02.01] Unit cells
 <---> [02.02] Symmetries
 <---> [02.03] Reciprocal space
 <---> [02.04] K-grid lattice
 <---> Grid dimensions      :   6   6   2
 <---> [02.05] Energies & Occupations
 <---> [03] Transferred momenta grid and indexing
 <---> [04] Dipoles
 <---> [WARNING] [r,Vnl^pseudo] included in position and velocity dipoles.
 <---> [WARNING] In case H contains other non local terms, these are neglected
 <---> [05] Bethe Salpeter Equation driver
 <---> [05.01] Bethe Salpeter Equation @q1
 <---> [05.01.01] Transition pre-analysis @q1
 <---> [05.01.02] Transition Groups build-up @q1
 <---> [BSK] Size (resonant):   432
 <---> [BSK]         (total):   432
 <---> [BSK] N. of matrices :  1
 <---> [05.01.03] Loading Dipoles @q1
 <---> BSE dipoles |########################################| [100%] --(E) --(X)
 <---> [05.01.04] Independent Particles properties @q1
 <---> IP properties |########################################| [100%] --(E) --(X)
 <---> [05.01.05] BSE Kernel @q1 (Resonant CORRRELATION EXCHANGE)
 <---> [05.01.05.01] Screened interaction header I/O
 <---> [FFT-BSK] Mesh size:  12  12  27
 <---> [05.01.05.02] Wave-Function Phases
 <---> [05.01.05.03] Main kernel loop
 <---> Kernel |                                        | [000%] --(E) --(X)

[ERROR] STOP signal received while in[05.01.05.03] Main kernel loop
[ERROR] EMPTY WF index @ b10 k0 spin1 ID0

If I try to run it once more then I get:

Code: Select all

 __    __ ______           ____     _____
/\ \  /\ \\  _  \  /"\_/`\/\  _`\ /\  __`\
\ `\`\\/"/ \ \L\ \/\      \ \ \L\ \ \ \/\ \
 `\ `\ /" \ \  __ \ \ \__\ \ \  _ <" \ \ \ \
   `\ \ \  \ \ \/\ \ \ \_/\ \ \ \L\ \ \ \_\ \
     \ \_\  \ \_\ \_\ \_\\ \_\ \____/\ \_____\
      \/_/   \/_/\/_/\/_/ \/_/\/___/  \/_____/


 <---> [01] MPI/OPENMP structure, Files & I/O Directories
 <---> [02] CORE Variables Setup
 <---> [02.01] Unit cells
 <---> [02.02] Symmetries
 <---> [02.03] Reciprocal space
 <---> [02.04] K-grid lattice
 <---> Grid dimensions      :   6   6   2
 <---> [02.05] Energies & Occupations
 <---> [03] Transferred momenta grid and indexing
 <---> [04] Dipoles
 <---> [WARNING] [r,Vnl^pseudo] included in position and velocity dipoles.
 <---> [WARNING] In case H contains other non local terms, these are neglected
 <---> [05] Bethe Salpeter Equation driver
 <---> [05.01] Bethe Salpeter Equation @q1
 <---> [05.01.01] Transition pre-analysis @q1
 <---> [05.01.02] Transition Groups build-up @q1
 <---> [BSK] Size (resonant):   432
 <---> [BSK]         (total):   432
 <---> [BSK] N. of matrices :  1
 <---> [05.01.03] Loading Dipoles @q1
 <---> BSE dipoles |########################################| [100%] --(E) --(X)
 <---> [05.01.04] Independent Particles properties @q1
 <---> IP properties |########################################| [100%] --(E) --(X)
 <---> [05.01.05] BSE Kernel @q1 (Resonant CORRRELATION EXCHANGE)
 <---> Possible partial BSE file not accepted in reading mode : ./3D_BSE//ndb.BS_PAR_Q1
 <---> [05.01.05.01] Screened interaction header I/O
 <---> [FFT-BSK] Mesh size:  12  12  27
 <---> [05.01.05.02] Wave-Function Phases
 <---> [05.01.05.03] Main kernel loop
 <---> Partial BSE file found in ./3D_BSE//ndb.BS_PAR_Q1 used as restart.
 <---> Loading partial kernel |########################################| [100%] --(E) --(X)
 <---> Kernel loaded percentual :  0.000000 [%]
 <---> Kernel |                                        | [000%] --(E) --(X)[hummel2-front1:4064801] *** Process received signal ***
[hummel2-front1:4064801] Signal: Segmentation fault (11)
[hummel2-front1:4064801] Signal code: Invalid permissions (2)
[hummel2-front1:4064801] Failing at address: 0x14939c0b1010
[hummel2-front1:4064801] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x3c050)[0x1493a319b050]
[hummel2-front1:4064801] [ 1] yambo[0x5ea510]
[hummel2-front1:4064801] [ 2] yambo[0x5360fb]
[hummel2-front1:4064801] [ 3] yambo[0x52e3fd]
[hummel2-front1:4064801] [ 4] yambo[0x4199f4]
[hummel2-front1:4064801] [ 5] yambo[0x41d171]
[hummel2-front1:4064801] [ 6] yambo[0x411814]
[hummel2-front1:4064801] [ 7] yambo[0x40b6a8]
[hummel2-front1:4064801] [ 8] yambo[0x40a548]
[hummel2-front1:4064801] [ 9] yambo[0x6eacfd]
[hummel2-front1:4064801] [10] yambo[0x4088de]
[hummel2-front1:4064801] [11] /lib/x86_64-linux-gnu/libc.so.6(+0x2724a)[0x1493a318624a]
[hummel2-front1:4064801] [12] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x85)[0x1493a3186305]
[hummel2-front1:4064801] [13] yambo[0x408641]
[hummel2-front1:4064801] *** End of error message ***
Segmentation fault

Is this an issue with some libraries that Yambo does not have access to? I find it a little odd that the static screening worked just fine but then I get these errors in the BSE part for both examples.

Posted: **Mon Oct 28, 2024 2:16 pm**

Dear Miguel,
please sign your posts with your name and affiliation, this is a rule of the forum, and you can do once for all by filling your user profile.
Can you please attach your input and report file? You can use the attachment button and rename the file with an allowed suffix (e.g. .txt, or zip file).

Best,
Daniele

Posted: **Mon Oct 28, 2024 3:20 pm**

Dear Daniele,

got it!

here are the files. In case is useful, the commented lines in the input file regarding parallelization were previously uncommented and tested with different combinations.

Best,

Miguel

Posted: **Tue Oct 29, 2024 8:55 am**

Dear Miguel,

actually, it would be useful to have a look at the report file (r-40b_6Ry*).
In any case, from the log file I can see that this is a restart calculation with a screening calculated from a different QE calculation. It is possible (just wondering) that something went wrong with the restart. Can you try to perform a calculation from scratch (i.e. deleting the previous ndb.em1s and ndb.BS_PAR_Q1 files) and see if the problem persists?

Best,
Daniele

Posted: **Tue Oct 29, 2024 9:48 am**

Dear Daniele,

I indeed intentionally calculated the screening using another QE calculation. I prepared some QE calculations without SOC for the screening and some with SOC for further steps. The purpose is to get used to doing it this way, as I will do in the future more computationally demanding systems. I made sure that for the input file of the BSE I used twice as many bands compared to the screening so for instance, using:

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% BndsRnXs
 1 | 80 |

where for the screening I used:

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% BndsRnXs
 1 | 40 |

I reran the calculations from scratch, and I still get the same error at the same point. I have attached the r-40b_6Ry* file this time.

Best,

Miguel

Posted: **Mon Nov 04, 2024 2:27 pm**

Dear Miguel,
can you post the QE input files, the pseudos, and the yambo input file.

I'll try to see if I can reproduce the probem.

Best,
D.

Yambo Community Forum

Issues when calculating BSE kernel and diagonalization

Issues when calculating BSE kernel and diagonalization

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Re: Issues when calculating BSE kernel and diagonalization