Error in routine qexsd_read_planewaves

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Error in routine qexsd_read_planewaves

Postby Conrard » Tue May 21, 2019 9:26 pm

Hi everyone,

I am a new yambo user. I am using yambo/4.3.2.

I followed the SiH4 Tutorials (http://www.yambo-code.org/tutorials/index.php).

First I ran the "scf" and the "nscf" calculations on the 'pw_scf.in' file in 'Pwscf' directory, using q-e/6.4.1.

Then I moved in the 'SiH4.save' directory to generate the database.

I used the command line: p2y -N -b 40 -F data-file-schema.xml and I got this error message
___ __ _____ __ __ _____ _____
| Y || _ || Y || _ \ | _ |
| | ||. | ||. ||. | / |. | |
\_ _/ |. _ ||.\_/ ||. _ \ |. | |
|: | |: | ||: | ||: | \|: | |
|::| |:.|:.||:.|:.||::. /|::. |
`--" `-- --"`-- --"`-----" `-----"
<---> DBs path set to .
<---> detected QE data format: qexsd-hdf5
<---> == PWscf v.6.x generated data (QEXSD-HDF5 fmt) ==
<---> Header/K-points/Energies...
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error in routine qexsd_read_planewaves (2):
fmt problem I
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
stopping ...
Attempting to use an MPI routine before initializing MPI
Kind regards,

Conrard TETSASSI
----------------------------------------------------------
Conrard Giresse Tetsassi Feugmo, PhD
Post-Doctoral Associate
SoftSimu Group - Maths & Physics of Complex Systems
Department of Chemistry
Chemistry Building, Room 003, Dock II
University of Western Ontario
1151 Richmond Street N,
London, ON Canada, N6A 5B7
Conrard
 
Posts: 4
Joined: Tue May 21, 2019 8:06 pm

Re: Error in routine qexsd_read_planewaves

Postby Daniele Varsano » Wed May 22, 2019 2:05 pm

Dear Conrard,
what happen if you run a simpe
> p2y
without any option?
p2y should automatically read the QEXSD format.

May be you will need to recompile p2y by adding this line in your configure command:
Code: Select all
--enable-hdf5-p2y-support



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
Daniele Varsano
 
Posts: 1973
Joined: Tue Mar 17, 2009 2:23 pm

Re: Error in routine qexsd_read_planewaves

Postby Conrard » Wed May 22, 2019 3:56 pm

Hi Daniele

During the compilation we used " --enable-hdf5-p2y-support".

When I run simple p2y I got this

[dragon2-ctrl0:~/UWO/Test/Yambo/YAMBO_TUTORIALS_SiH4/SiH4/Pwscf/SiH4.save :]$p2y

<---> DBs path set to .
<---> detected QE data format: qexsd-hdf5
<---> == PWscf v.6.x generated data (QEXSD-HDF5 fmt) ==
<---> Header/K-points/Energies...
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error in routine qexsd_read_planewaves (2):
fmt problem I
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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


kind regards,

Conrard TETSASSI
----------------------------------------------------------
Conrard Giresse Tetsassi Feugmo, PhD
Post-Doctoral Associate
SoftSimu Group - Maths & Physics of Complex Systems
Department of Chemistry
Chemistry Building, Room 003, Dock II
University of Western Ontario
1151 Richmond Street N,
London, ON Canada, N6A 5B7
Conrard
 
Posts: 4
Joined: Tue May 21, 2019 8:06 pm

Re: Error in routine qexsd_read_planewaves

Postby andrea.ferretti » Thu May 23, 2019 9:57 am

dear Conrard,

following the description o the problem that you provided I was able to reproduce the problem locally.
I'll investigate and let you know.
Andrea
Andrea Ferretti, PhD
CNR-NANO-S3 and MaX Centre
via Campi 213/A, 41125, Modena, Italy
Tel: +39 059 2055322; Skype: andrea_ferretti
URL: http://www.nano.cnr.it
andrea.ferretti
 
Posts: 96
Joined: Fri Jan 31, 2014 11:13 am

Re: Error in routine qexsd_read_planewaves

Postby andrea.ferretti » Thu May 23, 2019 11:32 am

Hi again,

I've just figured out that the problem relies in a small change to the data-file-schema.xml file occurred with QE-6.4.1 (surely not there in qe-6.3.x).
The offending lines are

Code: Select all
 
      <fft_grid nr1="120" nr2="120" nr3="120"></fft_grid>
      <fft_smooth nr1="120" nr2="120" nr3="120"></fft_smooth>
      <fft_box nr1="120" nr2="120" nr3="120"></fft_box>


In order to have yambo working, a simply fix is to change the above into:

Code: Select all
 
      <fft_grid nr1="120" nr2="120" nr3="120"/>
      <fft_smooth nr1="120" nr2="120" nr3="120"/>
      <fft_box nr1="120" nr2="120" nr3="120"/>


In the meantime we'll put together a proper fix to be later released.
thanks for reporting
Andrea
Andrea Ferretti, PhD
CNR-NANO-S3 and MaX Centre
via Campi 213/A, 41125, Modena, Italy
Tel: +39 059 2055322; Skype: andrea_ferretti
URL: http://www.nano.cnr.it
andrea.ferretti
 
Posts: 96
Joined: Fri Jan 31, 2014 11:13 am

Re: Error in routine qexsd_read_planewaves

Postby Conrard » Thu May 23, 2019 1:58 pm

Hi Andrea,

I change manually the three and its work.

Thank you


Kind regards

Conrard TETSASSI
----------------------------------------------------------
Conrard Giresse Tetsassi Feugmo, PhD
Post-Doctoral Associate
SoftSimu Group - Maths & Physics of Complex Systems
Department of Chemistry
Chemistry Building, Room 003, Dock II
University of Western Ontario
1151 Richmond Street N,
London, ON Canada, N6A 5B7
Tel: 519 661 2111 ext. 83793
Conrard
 
Posts: 4
Joined: Tue May 21, 2019 8:06 pm

Re: Error in routine qexsd_read_planewaves

Postby andrea.ferretti » Thu May 23, 2019 2:34 pm

here is a patch to apply to
yambo/interfaces/p2y/qexsd_p2y.F
to fix the problem on the yambo side without any need to hack the QE database.

Andrea


Code: Select all
979c979
<       CHARACTER(256) :: filename
---
>       CHARACTER(256) :: filename, str_tmp
1003a1004
>          attr=""
1005c1006,1010
<          if (ierr/=0) return
---
>          !if (ierr/=0) return
>          if (ierr/=0) then
>            call iotk_scan_dat( iunit, "fft_grid", str_tmp, ATTR=attr, IERR=ierr )
>            if (ierr/=0) return
>          endif
1023a1029
>          attr=""
1025c1031,1035
<          if (ierr/=0) return
---
>          !if (ierr/=0) return
>          if (ierr/=0) then
>             call iotk_scan_dat( iunit, "fft_smooth",str_tmp, ATTR=attr, IERR=ierr )
>             if (ierr/=0) return
>          endif
Andrea Ferretti, PhD
CNR-NANO-S3 and MaX Centre
via Campi 213/A, 41125, Modena, Italy
Tel: +39 059 2055322; Skype: andrea_ferretti
URL: http://www.nano.cnr.it
andrea.ferretti
 
Posts: 96
Joined: Fri Jan 31, 2014 11:13 am

Re: Error in routine qexsd_read_planewaves

Postby Conrard » Tue May 28, 2019 3:30 pm

I Andrea,

Just to thank you.

The patch works

Kind regards

Conrard TETSASSI
----------------------------------------------------------
Conrard Giresse Tetsassi Feugmo, PhD
Post-Doctoral Associate
SoftSimu Group - Maths & Physics of Complex Systems
Department of Chemistry
Chemistry Building, Room 003, Dock II
University of Western Ontario
1151 Richmond Street N,
London, ON Canada, N6A 5B7
Conrard
 
Posts: 4
Joined: Tue May 21, 2019 8:06 pm


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