GW yambo error

Concerns issues with computing quasiparticle corrections to the DFT eigenvalues - i.e., the self-energy within the GW approximation (-g n), or considering the Hartree-Fock exchange only (-x)

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hammouri
Posts: 34
Joined: Fri Feb 09, 2018 11:25 pm

GW yambo error

Post by hammouri » Fri Apr 01, 2022 3:58 am

Hello,
I am doing GW by following the example in the tutorial. But I got the error below which I think related to memory so I increased it from 16GB to 96GB but still have the same error. Any advice?

Code: Select all

#                                                                     
#  __  __   ________   ___ __ __    _______   ______                  
# /_/\/_/\ /_______/\ /__//_//_/\ /_______/\ /_____/\                 
# \ \ \ \ \\::: _  \ \\::\| \| \ \\::: _  \ \\:::_ \ \                
#  \:\_\ \ \\::(_)  \ \\:.      \ \\::(_)  \/_\:\ \ \ \               
#   \::::_\/ \:: __  \ \\:.\-/\  \ \\::  _  \ \\:\ \ \ \              
#     \::\ \  \:.\ \  \ \\. \  \  \ \\::(_)  \ \\:\_\ \ \             
#      \__\/   \__\/\__\/ \__\/ \__\/ \_______\/ \_____\/             
#                                                                     
#                                                                     
#       Version 5.0.4 Revision 19595 Hash 896bffc02                   
#                        Branch is                                    
#                    MPI+HDF5_IO Build                                
#                http://www.yambo-code.org                            
#
HF_and_locXC                     # [R] Hartree-Fock
gw0                              # [R] GW approximation
ppa                              # [R][Xp] Plasmon Pole Approximation for the Screened Interaction                           
em1d                             # [R][X] Dynamically Screened Interaction
EXXRLvcs= 40           Ry    # [XX] Exchange    RL components
VXCRLvcs= 2019            RL    # [XC] XCpotential RL components
Chimod= "HARTREE"                # [X] IP/Hartree/ALDA/LRC/PF/BSfxc
% BndsRnXp
   1 |  10 |                         # [Xp] Polarization function bands
%
NGsBlkXp= 1                RL    # [Xp] Response block size
% LongDrXp
 1.000000 | 1.000000 | 1.000000 |        # [Xp] [cc] Electric Field
%
PPAPntXp= 27.21138         eV    # [Xp] PPA imaginary energy
XTermKind= "none"                # [X] X terminator ("none","BG" Bruneval-Gonze)
% GbndRnge
   1 |  44 |                         # [GW] G[W] bands range
%
GTermKind= "none"                # [GW] GW terminator ("none","BG" Bruneval-Gonze,"BRS" Berger-Reining-Sottile)
DysSolver= "n"                   # [GW] Dyson Equation solver ("n","s","g")
GWoIter=0                        # [GW] GWo self-consistent (evGWo) iterations on eigenvalues
GWIter=0                         # [GW] GW  self-consistent (evGW)  iterations on eigenvalues
%QPkrange                        # [GW] QP generalized Kpoint/Band indices
1|13|30|31|

Code: Select all

*** Error in `./yambo': free(): invalid next size (fast): 0x0000000006dbe190 ***
*** Error in `./yambo': free(): invalid next size (fast): 0x00000000063c2b60 ***
*** Error in `./yambo': free(): invalid next size (fast): 0x0000000006daaf80 ***
*** Error in `./yambo': free(): invalid next size (fast): 0x0000000005e83bc0 ***
*** Error in `./yambo': free(): invalid next size (fast): 0x0000000006f5b0f0 ***
*** Error in `./yambo': free(): invalid next size (fast): 0x0000000005581be0 ***
*** Error in `./yambo': free(): invalid next size (fast): 0x0000000006ef5fa0 ***
*** Error in `./yambo': free(): invalid next size (fast): 0x0000000006a6f8b0 ***
*** Error in `./yambo': free(): invalid next size (fast): 0x00000000057fdeb0 ***
*** Error in `./yambo': free(): invalid next size (fast): 0x0000000006272ab0 ***
*** Error in `./yambo': free(): invalid next size (fast): 0x0000000005e9ad60 ***
*** Error in `./yambo': free(): invalid next size (fast): 0x00000000070af6a0 ***
*** Error in `./yambo': free(): invalid next size (fast): 0x0000000006e4abd0 ***
*** Error in `./yambo': free(): invalid next size (fast): 0x00000000063eaac0 ***
*** Error in `./yambo': free(): invalid next size (fast): 0x000000000722ba40 ***
*** Error in `./yambo': free(): invalid next size (fast): 0x00000000062fa2b0 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81299)[0x1539cb369299]
./yambo[0x5d7958]
./yambo[0x5e1767]
./yambo[0x5d73d7]
./yambo[0x4a4b69]
./yambo[0x407c44]
./yambo[0x6717f8]
./yambo[0x405d46]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x1539cb30a555]
======= Backtrace: =========
/lib64/libc.so.6(+0x81299)[0x146c48f38299]
./yambo[0x5d7958]
./yambo[0x5e1767]
./yambo[0x5d73d7]
./yambo[0x4a4b69]
./yambo[0x407c44]
./yambo[0x6717f8]
./yambo[0x405d46]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x146c48ed9555]
./yambo[0x405dd7]
======= Memory map: ========
======= Backtrace: =========
/lib64/libc.so.6(+0x81299)[0x1500102be299]
./yambo[0x5d7958]
./yambo[0x5e1767]
./yambo[0x5d73d7]
./yambo[0x4a4b69]
./yambo[0x407c44]
./yambo[0x6717f8]
./yambo[0x405d46]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x15001025f555]
./yambo[0x405dd7]
======= Memory map: ========
======= Backtrace: =========
/lib64/libc.so.6(+0x81299)[0x147ff6435299]
./yambo[0x5d7958]
./yambo[0x5e1767]
./yambo[0x5d73d7]
./yambo[0x4a4b69]
./yambo[0x407c44]
./yambo[0x6717f8]
./yambo[0x405d46]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x147ff63d6555]
./yambo[0x405dd7]
======= Memory map: ========
======= Backtrace: =========
/lib64/libc.so.6(+0x81299)[0x14c2ded69299]
./yambo[0x5d7958]
./yambo[0x5e1767]
./yambo[0x5d73d7]
./yambo[0x4a4b69]
./yambo[0x407c44]
./yambo[0x6717f8]
./yambo[0x405d46]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x14c2ded0a555]
./yambo[0x405dd7]
======= Memory map: ========
======= Backtrace: =========
/lib64/libc.so.6(+0x81299)[0x147a45781299]
./yambo[0x5d7958]
./yambo[0x5e1767]
./yambo[0x5d73d7]
./yambo[0x4a4b69]
./yambo[0x407c44]
./yambo[0x6717f8]
./yambo[0x405d46]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x147a45722555]
./yambo[0x405dd7]
======= Memory map: ========
======= Backtrace: =========
/lib64/libc.so.6(+0x81299)[0x149193711299]
./yambo[0x5d7958]
./yambo[0x5e1767]
./yambo[0x5d73d7]
./yambo[0x4a4b69]
./yambo[0x407c44]
./yambo[0x6717f8]
./yambo[0x405d46]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x1491936b2555]
./yambo[0x405dd7]
======= Memory map: ========
======= Backtrace: =========
/lib64/libc.so.6(+0x81299)[0x15548b594299]
./yambo[0x5d7958]
./yambo[0x5e1767]
./yambo[0x5d73d7]
./yambo[0x4a4b69]
./yambo[0x407c44]
./yambo[0x6717f8]
./yambo[0x405d46]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x15548b535555]
./yambo[0x405dd7]
======= Memory map: ========
======= Backtrace: =========
/lib64/libc.so.6(+0x81299)[0x14921cfbc299]
./yambo[0x5d7958]
./yambo[0x5e1767]
./yambo[0x5d73d7]
./yambo[0x4a4b69]
./yambo[0x407c44]
./yambo[0x6717f8]
./yambo[0x405d46]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x14921cf5d555]
./yambo[0x405dd7]
======= Memory map: ========
======= Backtrace: =========
/lib64/libc.so.6(+0x81299)[0x145f51629299]
./yambo[0x5d7958]
./yambo[0x5e1767]
./yambo[0x5d73d7]
./yambo[0x4a4b69]
./yambo[0x407c44]
./yambo[0x6717f8]
./yambo[0x405d46]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x145f515ca555]
./yambo[0x405dd7]
======= Memory map: ========
======= Backtrace: =========
/lib64/libc.so.6(+0x81299)[0x14711c06c299]
./yambo[0x5d7958]
./yambo[0x5e1767]
./yambo[0x5d73d7]
./yambo[0x4a4b69]
./yambo[0x407c44]
./yambo[0x6717f8]
./yambo[0x405d46]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x14711c00d555]
./yambo[0x405dd7]
======= Memory map: ========
======= Backtrace: =========
/lib64/libc.so.6(+0x81299)[0x14e4aac47299]
./yambo[0x5d7958]
./yambo[0x5e1767]
./yambo[0x5d73d7]
./yambo[0x4a4b69]
./yambo[0x407c44]
./yambo[0x6717f8]
./yambo[0x405d46]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x14e4aabe8555]
./yambo[0x405dd7]
======= Memory map: ========
======= Backtrace: =========
/lib64/libc.so.6(+0x81299)[0x14722bc5a299]
./yambo[0x5d7958]
./yambo[0x5e1767]
./yambo[0x5d73d7]
./yambo[0x4a4b69]
./yambo[0x407c44]
./yambo[0x6717f8]
./yambo[0x405d46]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x14722bbfb555]
./yambo[0x405dd7]
======= Memory map: ========
00400000-00ee9000 r-xp 00000000 08:08 19136522                           /var/lib/condor/execute/slot1/dir_12336/yambo
00ee9000-00eea000 r--p 00ae8000 08:08 19136522                           /var/lib/condor/execute/slot1/dir_12336/yambo
00eea000-00f35000 rw-p 00ae9000 08:08 19136522                           /var/lib/condor/execute/slot1/dir_12336/yambo
00f35000-05209000 rw-p 00000000 00:00 0 
06e28000-075ef000 rw-p 00000000 00:00 0                                  [heap]
147218000000-147218021000 rw-p 00000000 00:00 0 
147218021000-14721c000000 ---p 00000000 00:00 0 
14721c000000-14721c021000 rw-p 00000000 00:00 0 
14721c021000-147220000000 ---p 00000000 00:00 0 
147220e80000-147221ff8000 rw-p 00000000 00:00 0 
147221ff8000-1472223f9000 rw-s 00000000 00:2c 1104764633                 /dev/shm/vader_segment.e2358.a5440001.15
1472223f9000-1472227fa000 rw-s 00000000 00:2c 1104746943                 /dev/shm/vader_segment.e2358.a5440001.14
1472227fa000-147222bfb000 rw-s 00000000 00:2c 1104768245                 ======= Backtrace: =========
/lib64/libc.so.6(+0x81299)[0x14573fe3b299]
./yambo[0x5d7958]
./yambo[0x5e1767]
./yambo[0x5d73d7]
./yambo[0x4a4b69]
./yambo[0x407c44]
./yambo[0x6717f8]
./yambo[0x405d46]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x14573fddc555]
./yambo[0x405dd7]
======= Memory map: ========
00400000-00ee9000 r-xp 00000000 08:08 19136522                           /var/lib/condor/execute/slot1/dir_12336/yambo
00ee9000-00eea000 r--p 00ae8000 08:08 19136522                           /var/lib/condor/execute/slot1/dir_12336/yambo
00eea000-00f35000 rw-p 00ae9000 08:08 19136522                           /var/lib/condor/execute/slot1/dir_12336/yambo
00f35000-05209000 rw-p 00000000 00:00 0 
06c2f000-073f6000 rw-p 00000000 00:00 0                                  [heap]
14572c000000-14572c021000 rw-p 00000000 00:00 0 
14572c021000-145730000000 ---p 00000000 00:00 0 
145730000000-145730021000 rw-p 00000000 00:00 0 
145730021000-145734000000 ---p 00000000 00:00 0 
145734f53000-145735ff8000 rw-p 00000000 00:00 0 
145735ff8000-1457363f9000 rw-s 00000000 00:2c 1104764633                 /dev/shm/vader_segment.e2358.a5440001.15
1457363f9000-1457367fa000 rw-s 00000000 00:2c 1104746943                 /dev/shm/vader_segment.e2358.a5440001.14
1457367fa000-145736bfb000 rw-s 00000000 00:2c 1104768245                 /dev/shm/vader_segment.e2358.a5440001.13
145736bfb000-145736ffc000 rw-s 00000000 00:2c 1104766688                 /dev/shm/vader_segment.e2358.a5440001.11
145736ffc000-1457373fd000 rw-s 00000000 00:2c 1104732937                 /dev/shm/vader_segment.e2358.a5440001.10
1457373fd000-1457377fe000 rw-s 00000000 00:2c 1104750526                 /dev/shm/vader_segment.e2358.a5440001.9
1457377fe000-145737bff000 rw-s 00000000 00:2c 1104729649                 /dev/shm/vader_segment.e2358.a5440001.8
145737bff000-145738000000 rw-s 00000000 00:2c 1104754519                 /dev/shm/vader_segment.e2358.a5440001.7
145738000000-145738021000 rw-p 00000000 00:00 0 
145738021000-14573c000000 ---p 00000000 00:00 0 
14573c16c000-14573c27b000 rw-p 00000000 00:00 0 
14573c37f000-14573c780000 rw-s 00000000 00:2c 1104782552                 /dev/shm/vader_segment.e2358.a5440001.6


Hammouri, M.
Assistant Professor of Physics
University of Wisconsin
USA

User avatar
Daniele Varsano
Posts: 3773
Joined: Tue Mar 17, 2009 2:23 pm
Contact:

Re: GW yambo error

Post by Daniele Varsano » Fri Apr 01, 2022 6:49 am

Dear Hammouri,
it does not seem you went out of memory.
In order to spot the problem can you attach your report, input and log files?
Please attach the entire files (probably you need to rename them with an allowed suffix e.g. .txt).

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/

User avatar
hammouri
Posts: 34
Joined: Fri Feb 09, 2018 11:25 pm

Re: GW yambo error

Post by hammouri » Fri Apr 01, 2022 12:42 pm

Here 3 files:
r_setup.txt
hf_in.txt
gw_ppa_in.txt
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Hammouri, M.
Assistant Professor of Physics
University of Wisconsin
USA

User avatar
hammouri
Posts: 34
Joined: Fri Feb 09, 2018 11:25 pm

Re: GW yambo error

Post by hammouri » Fri Apr 01, 2022 12:43 pm

another 2:
r-10b_1Ry_HF_and_locXC_gw0_em1d_ppa.txt
gw_ppa_log.txt
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Hammouri, M.
Assistant Professor of Physics
University of Wisconsin
USA

User avatar
Daniele Varsano
Posts: 3773
Joined: Tue Mar 17, 2009 2:23 pm
Contact:

Re: GW yambo error

Post by Daniele Varsano » Sat Apr 02, 2022 1:11 pm

Dear Hammouri,

your system has 30 filled bands:

Code: Select all

[X] Filled Bands                                  :  30
 [X] Empty Bands                                   :   31   44
and you are including only 10 bands in the polarization function:

Code: Select all

% BndsRnXp
  1 | 10 |                 # [Xp] Polarization function bands
%
There are no transitions to be included, so the calculation cannot be performed. You need to include at least one empty band. Of course then the number of empty bands needs to be converged.

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/

User avatar
hammouri
Posts: 34
Joined: Fri Feb 09, 2018 11:25 pm

Re: GW yambo error

Post by hammouri » Mon Apr 04, 2022 1:02 pm

Thank you!
It worked when I use:
% BndsRnXp
1 | 35 |
but when I change it to 45 I got this error:

Code: Select all

--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 7 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
[e343.chtc.wisc.edu:13424] 15 more processes have sent help message help-mpi-api.txt / mpi-abort
[e343.chtc.wisc.edu:13424] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
The run remains idle for hours then goes on hold.
Hammouri, M.
Assistant Professor of Physics
University of Wisconsin
USA

User avatar
hammouri
Posts: 34
Joined: Fri Feb 09, 2018 11:25 pm

Re: GW yambo error

Post by hammouri » Mon Apr 04, 2022 1:18 pm

I think I found the problem here, please correct me if I'm wrong.
I've been trying to use more bands than the # of empty bands I have (40). So, if I need more bands I need to redo the scf/nscf calcs and include more bands so I can go over 40 bands to convergence testing.
Now, are the 40 bands enough for a system of 30 filled bands?
Hammouri, M.
Assistant Professor of Physics
University of Wisconsin
USA

User avatar
hammouri
Posts: 34
Joined: Fri Feb 09, 2018 11:25 pm

Re: GW yambo error

Post by hammouri » Tue Apr 05, 2022 6:12 am

I am doing Hartree convergence test for the cut off energy but noticed in the Hartree-Fock occupations report the Indirect Gap between k-points: 84 84 and [X] Indirect Gap between k-points :83 1, for all EXXRLvcs from 20-60 Ry.
But for EXXRLvcs = 10 Ry,
[X] Indirect Gap between k-points : 83 1
and [Hartree-Fock] Indirect Gap between k-points : 83 1

Why the k points locations are not same?
Last edited by hammouri on Tue Apr 05, 2022 8:55 pm, edited 1 time in total.
Hammouri, M.
Assistant Professor of Physics
University of Wisconsin
USA

User avatar
hammouri
Posts: 34
Joined: Fri Feb 09, 2018 11:25 pm

Re: GW yambo error

Post by hammouri » Tue Apr 05, 2022 5:25 pm

Now I tried to use the full k points, i.e. 84 and this is what I got for cut off energy 50 Ry:

Hartree-Fock occupations report
=======================================

[Hartree-Fock] === General ===
[Hartree-Fock] Electronic Temperature : 0.000000 0.000000 [eV K]
[Hartree-Fock] Bosonic Temperature : 0.000000 0.000000 [eV K]
[Hartree-Fock] Finite Temperature mode : no
[Hartree-Fock] El. density : 0.95891E+24 [cm-3]
[Hartree-Fock] Fermi Level : 7.902941 [eV]

[Hartree-Fock] === Gaps and Widths ===
[Hartree-Fock] Conduction Band Min : 5.790139 [eV]
[Hartree-Fock] Valence Band Max : -6.835408 [eV]
[Hartree-Fock] Filled Bands : 30
[Hartree-Fock] Empty Bands : 31 44
[Hartree-Fock] Direct Gap : 13.24154 [eV]
[Hartree-Fock] Direct Gap localized at k-point : 1
[Hartree-Fock] Indirect Gap : 12.62555 [eV]
[Hartree-Fock] Indirect Gap between k-points : 25 1
[Hartree-Fock] Last valence band width : 0.677345 [eV]
[Hartree-Fock] 1st conduction band width : 5.004027 [eV]
And this is what I got for 60 Ry

Code: Select all

  [04.01] Hartree-Fock occupations report
  =======================================

  [Hartree-Fock] === General ===
  [Hartree-Fock] Electronic Temperature             :  0.000000  0.000000 [eV K]
  [Hartree-Fock] Bosonic    Temperature             :  0.000000  0.000000 [eV K]
  [Hartree-Fock] Finite Temperature mode            : no
  [Hartree-Fock] El. density                        :  0.95891E+24 [cm-3]
  [Hartree-Fock] Fermi Level                        :  7.902941 [eV]

  [Hartree-Fock] === Gaps and Widths ===
  [Hartree-Fock] Conduction Band Min                :  5.785617 [eV]
  [Hartree-Fock] Valence Band Max                   : -6.863066 [eV]
  [Hartree-Fock] Filled Bands                       :  30
  [Hartree-Fock] Empty Bands                        :   31   44
  [Hartree-Fock] Direct Gap                         :  13.26058 [eV]
  [Hartree-Fock] Direct Gap localized at k-point    :  1
  [Hartree-Fock] Indirect Gap                       :  12.64868 [eV]
  [Hartree-Fock] Indirect Gap between k-points      :  22   1
  [Hartree-Fock] Last valence band width            :  0.827222 [eV]
  [Hartree-Fock] 1st conduction band width          :  4.998238 [eV][/quote]

And this is for 70 Ry
[code]  [04.01] Hartree-Fock occupations report
  =======================================

  [Hartree-Fock] === General ===
  [Hartree-Fock] Electronic Temperature             :  0.000000  0.000000 [eV K]
  [Hartree-Fock] Bosonic    Temperature             :  0.000000  0.000000 [eV K]
  [Hartree-Fock] Finite Temperature mode            : no
  [Hartree-Fock] El. density                        :  0.95891E+24 [cm-3]
  [Hartree-Fock] Fermi Level                        :  7.902941 [eV]

  [Hartree-Fock] === Gaps and Widths ===
  [Hartree-Fock] Conduction Band Min                :  5.784584 [eV]
  [Hartree-Fock] Valence Band Max                   : -6.869387 [eV]
  [Hartree-Fock] Filled Bands                       :  30
  [Hartree-Fock] Empty Bands                        :   31   44
  [Hartree-Fock] Direct Gap                         :  13.26507 [eV]
  [Hartree-Fock] Direct Gap localized at k-point    :  1
  [Hartree-Fock] Indirect Gap                       :  12.65397 [eV]
  [Hartree-Fock] Indirect Gap between k-points      :  13   1
  [Hartree-Fock] Last valence band width            :  0.883430 [eV]
  [Hartree-Fock] 1st conduction band width          :  4.996186 
Now my question: where does the indirect band gap located at?
Hammouri, M.
Assistant Professor of Physics
University of Wisconsin
USA

User avatar
Daniele Varsano
Posts: 3773
Joined: Tue Mar 17, 2009 2:23 pm
Contact:

Re: GW yambo error

Post by Daniele Varsano » Fri Apr 08, 2022 9:46 am

Dear Hammouri,
So, if I need more bands I need to redo the scf/nscf calcs and include more bands so I can go over 40 bands to convergence testing.
Now, are the 40 bands enough for a system of 30 filled bands?
Exact, you need to perform an nscf calculation including more bands (no need to repeat scf).
40 bands probably are not enough, in general, you need to check, in order to save time it is suggested to include many bands in nscf calculation in order to avoid to repeat it.
Why the k points locations are not same?
Because different convergence parameters can give different corrections and it is not guaranteed the shift in energy is uniform, You can inspect the output and realize what is happening.
Now my question: where does the indirect band gap located at?
You need to check the converged results to answer this question.

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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