warning pending errors

[Stephan]

Hello,

I try to work with Yambo on a cluster. The input is computed with Quantum Espresso.
Yambo was installed on the cluster due to my recommendation.
Unfortunately the p2y-routine is not working. Before I complain to the administrator I want to know what's the problem.
I receive the following message:
# WARNING: there are pending errors
# PENDING ERROR (ierr=1)
# ERROR IN: iotk_open_read (iotk_files.spp:487)
# CVS Revision: 1.20
# unit
file=./Ca.pbe-sp-hgh.UPF
binary=F
iostat=29
# PENDING ERROR (ierr=2)
# ERROR IN: iotk_close_read (iotk_files.spp:575)
# CVS Revision: 1.20
# FROM IOTK LIBRARY, VERSION 1.2.0
# UNRECOVERABLE ERROR (ierr=3)
# ERROR IN: iotk_getline (iotk_scan.spp:814)
# CVS Revision: 1.23
#
iostat=29
# ERROR IN: iotk_scan_tag (iotk_scan.spp:518)
# CVS Revision: 1.23
# ERROR IN: iotk_scan (iotk_scan.spp:712)
# CVS Revision: 1.23
# ERROR IN: iotk_scan_begin (iotk_scan.spp:94)
# CVS Revision: 1.23
########################################################################################################################

Is this because the programm is not linked correctly to the iotk-library of Quantum Espresso?
Or is there any other reason for the error?

Thanks and Regards

Stephan

[andrea.ferretti]

Hi Stephan,

usually linking different versions of iotk is not a problem
(though, if different versions have different bugs, and your case is showing one of them, there could be a role of the lib version...)

since espresso has run properly, I would rather start searching for a problem in the p2y parsing of the pseudo file at hand (the problem could also be in the pseudofile itself)
Did you modify the pseudo file ?

If not, looking at the content of the pseudo file I do not see any major problems (in the past, a comment like "generation date: < 1984" use to break the parsing of the pseudo file)

now: can you post a simple example (e.g. Ca bulk or anything quick to run) showing the problem (ideally a scf input file would do) ?

take care
Andrea

[Stephan]

Hi Andrea,
I don't know why but the pseudo-files were not saved in the .save directory of the QE-output.
Maybe thats the simple reason for my problem.
I'll try again..

Thanks and reagards,

Stephan

[Stephan]

Hi,
I copied the pseudo files in the .save-directory and p2y works fine now.
Here the output l_stderr:

__ __ ______ ____ _____
/\ \ /\ \\ _ \ /"\_/`\/\ _`\ /\ __`\
\ `\`\\/"/ \ \L\ \/\ \ \ \L\ \ \ \/\ \
`\ `\ /" \ \ __ \ \ \__\ \ \ _ <" \ \ \ \
`\ \ \ \ \ \/\ \ \ \_/\ \ \ \L\ \ \ \_\ \
\ \_\ \ \_\ \_\ \_\\ \_\ \____/\ \_____\
\/_/ \/_/\/_/\/_/ \/_/\/___/ \/_____/


<---> DBs path set to .
<---> Index file set to data-file.xml
<03s> Header/K-points/Energies...
<14s> Cell data...
<17s> Atomic data...
<17s> Symmetries...
<20s> XC functional...Perdew, Burke & Ernzerhof(X)+Perdew, Burke & Ernzerhof(C)
<20s> EXX fraction... 0.000000
<20s> EXX screening... 0.000000
<20s> K-points mesh...
<21s> RL vectors...
<23s> IGK arrays...
<24s> Energies...
<25s> :: Electrons : 52.00000
<25s> :: Temperature [ev]: 0.000000
<25s> :: Lattice factors [a.u.]: 11.08324 11.08324 11.08324
<25s> :: K-points : 288
<25s> :: Bands : 70
<25s> :: Spinor components : 1
<25s> :: Spin polarizations : 1
<25s> :: Spin orbit coupling : no
<25s> :: Symmetries [spatial]: 16
<25s> :: [T-rev]: no
<25s> :: Max WF components : 42067
<25s> :: RL vectors (WF): 48202
<25s> :: RL vectors (CHARGE): 336209
<25s> :: XC potential : Perdew, Burke & Ernzerhof(X)+Perdew, Burke & Ernzerhof(C)
<25s> :: Atomic species : 3
<25s> :: Max atoms/species : 2
<25s> == DB1 (Gvecs and more) ...
<25s> ... Database done
<25s> == DB2 (wavefunctions) ...
<25s> [M 0.044 Gb] Alloc wf_disk ( 0.044)
<02m-16s> [M 0.000 Gb] Free wf_disk ( 0.044)
<02m-16s> == DB3 (PseudoPotential) ...
<02m-19s> [M 0.011 Gb] Alloc pp_kbs pp_kb pp_kbd ( 0.011)
<03m-40s> [M 0.000 Gb] Free pp_kbs pp_kb pp_kbd ( 0.011)
<03m-41s> == P2Y completed ==

But now I have a problem with the generation of the input file.
The command yambo -o c results in the following yambo.in file:
#
# __ __ ________ ___ __ __ _______ ______
# /_/\/_/\ /_______/\ /__//_//_/\ /_______/\ /_____/\
# \ \ \ \ \\::: _ \ \\::\| \| \ \\::: _ \ \\:::_ \ \
# \:\_\ \ \\::(_) \ \\:. \ \\::(_) \/_\:\ \ \ \
# \::::_\/ \:: __ \ \\:.\-/\ \ \\:: _ \ \\:\ \ \ \
# \::\ \ \:.\ \ \ \\. \ \ \ \\::(_) \ \\:\_\ \ \
# \__\/ \__\/\__\/ \__\/ \__\/ \_______\/ \_____\/
#
#
# GPL Version 4.0.1 Revision 88
# OpenMPI Build
# http://www.yambo-code.org
#
setup # [R INI] Initialization

I do not receive further error messages.

Have you any idea whats wrong?

Thanks and regards

Stephan

[andrea.ferretti]

hi Stefan,
I think this just means that first you have to run the setup (which is the input you have just generated),
and, after that, you can generate the input for any other calculations of yambo...
am I missing something ?

ciao ciao
Andrea

[Stephan]

Hi Andrea,
of course you are right. I just forgot one step in the input preparation.

Thanks and regards

Stephan