Error merging QP database using ypp

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woncheol
Posts: 3
Joined: Mon Mar 15, 2021 3:07 am

Error merging QP database using ypp

Post by woncheol » Mon Mar 22, 2021 3:31 am

Dear developers,

I did GW calculations for each qpoints and tried to merge ndb.QP files using ypp. For 6x6x3, 8x8x4 grids it worked well, but as I increase the density of grid (10x10x5), it failed as below. Could you help me solving this problem ...? I tried two different version (compiled with intel fortran and gfortran) but both failed. I appreciate your help in advance !

Best,
Woncheol

Code: Select all

 ___ __  _____  __ __  _____   _____
|   Y  ||  _  ||  Y  ||  _  \ |  _  |
|   |  ||. |  ||.    ||. |  / |. |  |
 \_  _/ |. _  ||.\_/ ||. _  \ |. |  |
  |: |  |: |  ||: |  ||: |   \|: |  |
  |::|  |:.|:.||:.|:.||::.   /|::.  |
  `--"  `-- --"`-- --"`-----" `-----"


 <---> [01] CPU structure, Files & I/O Directories
 <---> [02] Y(ambo) P(ost)/(re) P(rocessor)
 <---> [03] Core DB
 <---> :: Electrons             : 36.00000
 <---> :: Temperature       [ev]: 0.000000
 <---> :: Lattice factors [a.u.]:  8.61337   7.45940  13.20163
 <---> :: K points              :  58
 <---> :: Bands                 :  500
 <---> :: Symmetries            : 12
 <---> :: RL vectors            :  453025
 <---> [04] K-point grid
 <---> :: Q-points   (IBZ):  58
 <---> :: X K-points (IBZ):  58
 <---> [05] CORE Variables Setup
 <---> [05.01] Unit cells
 <---> [05.02] Symmetries
 <---> [05.03] RL shells
 <---> [05.04] K-grid lattice
 <---> Grid dimensions               : 10  10   5
 <---> [05.05] Energies [ev] & Occupations
 <---> [05.06] QP databases mergering
 <---> -----------------------------
 <---> [DB #1]+ 1.000000 x E < 500_15/q1/ndb.QP
 <---> -----------------------------
 <---> [DB #1] GW solver              : Newton
 <---> [DB #1] == PPA-GN GW ==
 <---> [DB #1]
 <---> [DB #1] PPA imaginary pt   [ev]: 27.21138
 <---> [DB #1] GW SC iterations       :0
 <---> [DB #1] dS/dw steps            : 2
 <---> [DB #1] dS/dw step         [ev]:  0.10000
 <---> [DB #1] X G`s            [used]:  869
 <---> [DB #1] X G`s            [disk]:  869
 <---> [DB #1] X bands                :    1   500
 <---> [DB #1] X poles           [o/o]: 100.0000
 <---> [DB #1] X e/h E range      [ev]:-1.000000 -1.000000
 <---> [DB #1] X xc-Kernel            : none
 <---> [DB #1] X BZ energy Double Grid: no
 <---> [DB #1] X BZ Double Grid points:0
 <---> [DB #1] Sc/G bands             :    1   500
 <---> [DB #1] Sc/G damping       [ev]:  0.10000
 <---> [DB #1] Sc bands terminator    : no
 <---> [DB #1] Sx RL components       :  453025
 <---> [DB #1]
 <---> [DB #1] QP @ K 1 - 1 : b 27 - 44
 <---> -----------------------------
 <---> [DB #2]+ 1.000000 x E < 500_15/q2/ndb.QP
 <---> -----------------------------
 <---> [DB #2] GW solver              : Newton
 <---> [DB #2] == PPA-GN GW ==
 <---> [DB #2]
 <---> [DB #2] PPA imaginary pt   [ev]: 27.21138
 <---> [DB #2] GW SC iterations       :0
 <---> [DB #2] dS/dw steps            : 2
 <---> [DB #2] dS/dw step         [ev]:  0.10000
 <---> [DB #2] X G`s            [used]:  869
 <---> [DB #2] X G`s            [disk]:  869
 <---> [DB #2] X bands                :    1   500
 <---> [DB #2] X poles           [o/o]: 100.0000
 <---> [DB #2] X e/h E range      [ev]:-1.000000 -1.000000
 <---> [DB #2] X xc-Kernel            : none
 <---> [DB #2] X BZ energy Double Grid: no
 <---> [DB #2] X BZ Double Grid points:0
 <---> [DB #2] Sc/G bands             :    1   500
 <---> [DB #2] Sc/G damping       [ev]:  0.10000
 <---> [DB #2] Sc bands terminator    : no
 <---> [DB #2] Sx RL components       :  453025
 <---> [DB #2]
 <---> [DB #2] QP @ K 2 - 2 : b 27 - 44
 <---> -----------------------------
 <---> Merging...detected 1 family(ies) of QP databases...*** Error in `/global/homes/w/woncheol/yambo-4.5.2/bin/ypp': free(): invalid next size (fast): 0x0000000004e1d3e0 ***
[cori11:46046] *** Process received signal ***
[cori11:46046] Signal: Aborted (6)
[cori11:46046] Signal code:  (-6)
[cori11:46046] [ 0] /lib64/libpthread.so.0(+0x132d0)[0x2aaaad09e2d0]
[cori11:46046] [ 1] /lib64/libc.so.6(gsignal+0x110)[0x2aaaad2e3520]
[cori11:46046] [ 2] /lib64/libc.so.6(abort+0x151)[0x2aaaad2e4b01]
[cori11:46046] [ 3] /lib64/libc.so.6(+0x7c957)[0x2aaaad326957]
[cori11:46046] [ 4] /lib64/libc.so.6(+0x83173)[0x2aaaad32d173]
[cori11:46046] [ 5] /lib64/libc.so.6(+0x84a79)[0x2aaaad32ea79]
[cori11:46046] [ 6] /global/homes/w/woncheol/yambo-4.5.2/bin/ypp[0x594b0f]
[cori11:46046] [ 7] /global/homes/w/woncheol/yambo-4.5.2/bin/ypp[0x4a26ec]
[cori11:46046] [ 8] /global/homes/w/woncheol/yambo-4.5.2/bin/ypp[0x49f331]
[cori11:46046] [ 9] /global/homes/w/woncheol/yambo-4.5.2/bin/ypp[0x477309]
[cori11:46046] [10] /global/homes/w/woncheol/yambo-4.5.2/bin/ypp[0x409036]
[cori11:46046] [11] /global/homes/w/woncheol/yambo-4.5.2/bin/ypp[0x405633]
[cori11:46046] [12] /lib64/libc.so.6(__libc_start_main+0xea)[0x2aaaad2ce34a]
[cori11:46046] [13] /global/homes/w/woncheol/yambo-4.5.2/bin/ypp[0x405d9a]
[cori11:46046] *** End of error message ***
Aborted
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Last edited by woncheol on Mon Mar 22, 2021 6:04 pm, edited 1 time in total.
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claudio
Posts: 456
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Location: Marseille
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Re: Error merging QP database using app

Post by claudio » Mon Mar 22, 2021 1:35 pm

Dear Woncheol,

we recently found an error in ypp function that merges ndb.QP databases.
The error was corrected in the github verion of Yambo.

Please download the last version from github and try again

https://github.com/yambo-code/yambo

If the error it still there write us again in this forum

If you are already using the last github version of Yambo, please put the input file
in forum we will try to reproduce your error

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
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woncheol
Posts: 3
Joined: Mon Mar 15, 2021 3:07 am

Re: Error merging QP database using ypp

Post by woncheol » Mon Mar 22, 2021 6:10 pm

Dear Claudio,

Thank you for your help. I tried the latest version using this input script and now I get an error message like below:

Best,
Woncheol

Code: Select all

#                                                                     
#  __  __   ________   ___ __ __    _______   ______                  
# /_/\/_/\ /_______/\ /__//_//_/\ /_______/\ /_____/\                 
# \ \ \ \ \\::: _  \ \\::\| \| \ \\::: _  \ \\:::_ \ \                
#  \:\_\ \ \\::(_)  \ \\:.      \ \\::(_)  \/_\:\ \ \ \               
#   \::::_\/ \:: __  \ \\:.\-/\  \ \\::  _  \ \\:\ \ \ \              
#     \::\ \  \:.\ \  \ \\. \  \  \ \\::(_)  \ \\:\_\ \ \             
#      \__\/   \__\/\__\/ \__\/ \__\/ \_______\/ \_____\/             
#                                                                     
#                                                                     
# GPL Version 4.5.2 Revision 9122. (Based on r.17116 h.2e426da)       
#                                                                     
#                      Serial Build                                   
#                http://www.yambo-code.org                            
#
QPDBs                          # [R] Quasi-particle databases
QPDB_merge                     # [R] Mergering
%Actions_and_names             # [QPDB] Format is "what"|"OP"|"prefactor"|"DB"|. OP can be +/-/x(only for Z)
"E" |"+" |"1" |"ndb.QP1" |
"E" |"+" |"1" |"ndb.QP2" |
%


Code: Select all

____    ____    ___      .___  ___.  .______     ______
\   \  /   /   /   \     |   \/   |  |   _  \   /  __  \
 \   \/   /   /  ^  \    |  \  /  |  |  |_)  | |  |  |  |
  \_    _/   /  /_\  \   |  |\/|  |  |   _  <  |  |  |  |
    |  |    /  _____  \  |  |  |  |  |  |_)  | |  `--"  |
    |__|   /__/     \__\ |__|  |__|  |______/   \______/



 <---> [01] MPI/OPENMP structure, Files & I/O Directories
 <---> [02] Y(ambo) P(ost)/(re) P(rocessor)
 <---> [03] Core DB
 <---> :: Electrons             : 36.00000
 <---> :: Temperature           : 0.000000 [eV]
 <---> :: Lattice factors       :  8.61337   7.45940  13.20163 [a.u.]
 <---> :: K points              :  58
 <---> :: Bands                 :  500
 <---> :: Symmetries            : 12
 <---> :: RL vectors            :  453025
 <---> [04] K-point grid
 <---> :: Q-points   (IBZ):  58
 <---> :: X K-points (IBZ):  58
 <---> [05] CORE Variables Setup
 <---> [05.01] Unit cells
 <---> [05.02] Symmetries
 <---> [05.03] Reciprocal space
 <---> [05.04] K-grid lattice
 <---> Grid dimensions      :  10  10   5
 <---> [05.05] Energies & Occupations

[ERROR] STOP signal received while in[05.05] Energies & Occupations
[ERROR] Reading File ./500_15/k1/ndb.QP; Variable PARS; NetCDF: Index exceeds dimension bound
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claudio
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Re: Error merging QP database using ypp

Post by claudio » Sat Mar 27, 2021 7:57 am

Dear Woncheol,

I will try to reproduce your bug and contact you again in few days

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
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woncheol
Posts: 3
Joined: Mon Mar 15, 2021 3:07 am

Re: Error merging QP database using ypp

Post by woncheol » Fri Apr 23, 2021 2:12 am

Hi Claudio,

May I ask how it is going ? I appreciate your help.

Sincerely,
Woncheol
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claudio
Posts: 456
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Location: Marseille
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Re: Error merging QP database using ypp

Post by claudio » Sat Apr 24, 2021 7:47 pm

Dear Woncheol

all bugs in the QP merging have been fixed, please download the last version from github

https://github.com/yambo-code/yambo/arc ... master.zip

and try again

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
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Dean
Posts: 102
Joined: Thu Oct 10, 2019 7:03 am

Re: Error merging QP database using ypp

Post by Dean » Thu Aug 12, 2021 3:01 am

Dear Claudio,
I met the same merge problem when I used the last version of yambo from github.

The error is followed as:
...........

Code: Select all

<---> Merging...detected 1 family(ies) of QP databases...*** Error in `./ypp': double free or corruption (!prev): 0x0000000007ab14a0 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81299)[0x2b74f287b299]
./ypp[0xfd89ad]
./ypp[0x64608a]
Can you give me some help?
Thanks in advances.
Dr. Yimin Ding
Soochow University, China.
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