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p2y error

https://www.yambo-code.eu/forum/viewtopic.php?t=1903

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p2y error

Posted: Sun Feb 07, 2021 2:09 pm
by gaohan
Dear developers,
When I finished my 'scf' and 'nscf' calculations, I entered the folder '*.save' and run 'p2y'. It shows that error:

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<---> DBs path set to .
 <---> detected QE data format: qexsd
 <---> == PWscf v.6.x generated data (QEXSD fmt) ==
 <---> Header/K-points/Energies...
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     Error in routine qexsd_read_symmetry (2):
     fmt problem
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...
application called MPI_Abort(MPI_COMM_WORLD, 2) - process 0
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=2
:
system msg for write_line failure : Bad file descriptor
My QE edition is 6.7 and my yambo edition is 4.5.2
I will attach my 'scf.inp' and 'nscf.inp'
scf.inp:

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&CONTROL
    calculation='scf', disk_io='low', prefix='alb2',
    pseudo_dir='../../pse', outdir='./tmp', verbosity='high'
    tprnfor=.true., tstress=.true.,
    wf_collect=.true.,nstep = 200,
    etot_conv_thr = 1.0d-6,forc_conv_thr = 1.0d-5
/
&SYSTEM
    ibrav= 4,
    nat= 3, ntyp= 2,
    celldm(1) =5.6211,
    celldm(3) = 6.723,
    occupations = 'smearing', smearing = 'mp', degauss = 0.05,
    ecutwfc= 80, ecutrho = 320,
  !  assume_isolated='2D',
    force_symmorphic=.true.,
/
&ELECTRONS
    conv_thr = 1.0d-9,
    mixing_beta = 0.7d0,
    diagonalization = 'david'
/
&IONS
    ion_dynamics='damp'
/
&CELL
   press = 0.00 ,
   press_conv_thr=0.1
   cell_dynamics = 'bfgs' ,
   cell_dofree = '2Dxy',
/
ATOMIC_SPECIES
 Al  26.981539 Al_ONCV_PBE-1.2.upf
 B   10.811    B_ONCV_PBE-1.2.upf
ATOMIC_POSITIONS (crystal)
Al            0.0000000000       -0.0000000000        0.0306032265
B             0.3333333433        0.6666666866        0.1020700413
B             0.6666666865        0.3333333433        0.1020700413
K_POINTS {automatic}
12 12 1 1 1 1
nscf.inp:

Code: Select all

&CONTROL
    calculation='nscf', disk_io='low', prefix='alb2',
    pseudo_dir='../../pse', outdir='./tmp', verbosity='high'
    tprnfor=.true., tstress=.true.,
    wf_collect=.true.,nstep = 200,
    etot_conv_thr = 1.0d-6,forc_conv_thr = 1.0d-5
/
&SYSTEM
    ibrav= 4,
    nat= 3, ntyp= 2,
    celldm(1) =5.6211,
    celldm(3) = 6.723,
    occupations = 'smearing', smearing = 'mp', degauss = 0.05,
    ecutwfc= 80, ecutrho = 320,
  !  assume_isolated='2D',
    force_symmorphic=.true.,nbnd = 48,
/
&ELECTRONS
    conv_thr = 1.0d-9,
    mixing_beta = 0.7d0,
    diagonalization = 'david'
    diago_thr_init=5.0e-6,
    diago_full_acc=.true.
/
&IONS
    ion_dynamics='damp'
/
&CELL
   press = 0.00 ,
   press_conv_thr=0.1
   cell_dynamics = 'bfgs' ,
   cell_dofree = '2Dxy',
/
ATOMIC_SPECIES
 Al  26.981539 Al_ONCV_PBE-1.2.upf
 B   10.811    B_ONCV_PBE-1.2.upf
ATOMIC_POSITIONS (crystal)
Al            0.0000000000       -0.0000000000        0.0306032265
B             0.3333333433        0.6666666866        0.1020700413
B             0.6666666865        0.3333333433        0.1020700413
K_POINTS {automatic}
48 48 1 1 1 1

Looking forward to your reply.

Re: p2y error

Posted: Sun Feb 07, 2021 2:11 pm
by gaohan
I also should mention. When I run 'yambo' to test my yambo code. It shows:

Code: Select all

yambo: cannot access CORE database (SAVE/*db1 and/or SAVE/*wf)

application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1
:
system msg for write_line failure : Bad file descriptor
I'm not sure that whether the appearance of the last two lines is reasonable.
Looking forward to your help. Thanks very much.

Re: p2y error

Posted: Mon Feb 08, 2021 4:13 pm
by andrea.ferretti
Dea gaohan,

I was able to reproduce the p2y error you report. The problem is due to a small change in the data output format of qe-6.7
(qe-6.6 works fine with y4.5.2/y4.5.3)
This specific problem has already been fixed in yambo v5.0.x, as available on github
https://github.com/yambo-code/yambo/tags

take care
Andrea

Re: p2y error

Posted: Mon Apr 08, 2024 10:09 am
by Jerry
gaohan wrote: ↑Sun Feb 07, 2021 2:11 pm I also should mention. When I run 'yambo' to test my yambo code. It shows:

Code: Select all

yambo: cannot access CORE database (SAVE/*db1 and/or SAVE/*wf)

application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1
:
system msg for write_line failure : Bad file descriptor
I'm not sure that whether the appearance of the last two lines is reasonable.
Looking forward to your help. Thanks very much.
dear GaoHan I have the same problem and I'm using yambo 5.2.0. Do you know how to solve it? :?:

Re: p2y error

Posted: Mon Apr 08, 2024 10:41 am
by Daniele Varsano
Dear Jerry,

please sign your post with your name and affiliation, this is a rule of the forum and you can do once for all by filling the signature in your profile.

The problem you have it happens because you did not generate the SAVE directory using p2y, or you are running in a directory where the SAVE dir is not present. This is indeed what the error message says:

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yambo: cannot access CORE database (SAVE/*db1 and/or SAVE/*wf)
Please have a look at this tutorial:
https://www.yambo-code.eu/wiki/index.php/Initialization

Best,
Daniele

Re: p2y error

Posted: Tue Apr 09, 2024 3:52 pm
by Jerry
Dear Varsano,
I've cahnged my signature. I read the passage you mentioned. I found that I used yambo command in the SAVE directory. So I

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[cd ..
yambo/code]. But I meet new problem. it is said that[code][[ERROR] I/O failed.%  /code]. I don't know how to solve it.

Re: p2y error

Posted: Thu Apr 11, 2024 7:43 am
by Daniele Varsano
Dear Jerry,

it is not clear from your post what you did and what is happening, can you try to explain better and report the entire error message.

Best,
Daniele

Re: p2y error

Posted: Mon Apr 15, 2024 1:03 pm
by Jerry
when i run yambo in bulk_silicon directory. it said that

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[ERROR] I/O failed.%

Re: p2y error

Posted: Tue Apr 16, 2024 7:12 am
by Daniele Varsano
Dear Jerry,
can you attach to the post your report and log files, and also the config.log file of your compilation?

Best,
Daniele

Re: p2y error

Posted: Fri Apr 19, 2024 10:08 am
by Jerry
Dear Versano,
Thank you for your reply!
I ran yambo in yambo-5.2.0/doc/sample/bulk_silicon
and I have yambo-5.2.0/doc/sample/bulk_silicon/SAVE
I jusat get

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[2200011421@wm1-login01]~/yambo520/yambo-5.2.0/doc/sample/bulk_silicon% yambo

[ERROR] I/O failed.%
without any report and logfiles.
Here is my config.log.
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