Error in routine qexsd_read_planewaves

Come here to discuss issues with using the p2y converter from PWscf to Yambo, how to best run PWscf , link with the IOTK library, and so on.

Moderator: Conor Hogan

Forum rules
Before posting, make sure to first read carefully all the detailed steps and suggestions given in the main documentation:
http://www.yambo-code.org/doc/databases/index.php
Post Reply
Conrard
Posts: 4
Joined: Tue May 21, 2019 8:06 pm

Error in routine qexsd_read_planewaves

Post by 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

User avatar
Daniele Varsano
Posts: 2097
Joined: Tue Mar 17, 2009 2:23 pm
Contact:

Re: Error in routine qexsd_read_planewaves

Post by 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/

Conrard
Posts: 4
Joined: Tue May 21, 2019 8:06 pm

Re: Error in routine qexsd_read_planewaves

Post by 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

andrea.ferretti
Posts: 102
Joined: Fri Jan 31, 2014 11:13 am

Re: Error in routine qexsd_read_planewaves

Post by 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: 102
Joined: Fri Jan 31, 2014 11:13 am

Re: Error in routine qexsd_read_planewaves

Post by 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

Conrard
Posts: 4
Joined: Tue May 21, 2019 8:06 pm

Re: Error in routine qexsd_read_planewaves

Post by 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

andrea.ferretti
Posts: 102
Joined: Fri Jan 31, 2014 11:13 am

Re: Error in routine qexsd_read_planewaves

Post by 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

Conrard
Posts: 4
Joined: Tue May 21, 2019 8:06 pm

Re: Error in routine qexsd_read_planewaves

Post by 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

Post Reply