NetCDF: Numeric conversion not representable when BSE

Deals with issues related to computation of optical spectra, in RPA (-o c) or by solving the Bethe-Salpeter equation (-o b). Includes local field effects, excitons, etc.

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chwolf
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NetCDF: Numeric conversion not representable when BSE

Post by chwolf » Sun Jul 14, 2019 9:01 am

Dear all,

I have MgO with 72 k-points and 200 KS bands. I can run IPA, RPA and GW but when attempting to do BSE I get the following error:

Code: Select all

 [03] Transferred momenta grid
 =============================

 [RD./SAVE//ndb.kindx]---------------------------------------
  Fragmentation                    :no
  Polarization last K   :  72
  QP states             :   1   72
  X grid is uniform     :yes
  BS scattering         :yes
  COLL scattering       :no
 - S/N 000495 -------------------------- v.04.02.01 r.00110 -

 [ERROR] STOP signal received while in :[03] Transferred momenta grid

 [ERROR] File ./SAVE//ndb.kindx; Variable Bindx; NetCDF: Numeric conversion not representable
Does anyone know what the problem might be? Apparently this is not a common problem and I could not find anything related to it in the forum.

I have compiled QE 6.4.1 and Yambo 4.3.2 on Intel 19, if you need any specifics regarding the compilation please let me know.

Thanks in advance and have a nice Sunday everyone!
Chris
Christoph Wolf

Postech university, South Korea
chwolf@postech.ac.kr

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Daniele Varsano
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Re: NetCDF: Numeric conversion not representable when BSE

Post by Daniele Varsano » Mon Jul 15, 2019 11:55 am

Dear Christoph,
indeed it is the first time I see this kind of error. In order to spot the problem, we need to reproduce your error.
Can you please provide us you qe input/pseudo and yambo input file?

Many thanks,
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/

chwolf
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Re: NetCDF: Numeric conversion not representable when BSE

Post by chwolf » Tue Jul 16, 2019 8:53 am

Dear Daniele,

I attached the input in the zip file - I now think this might be related to the memory issue in my other thread which I should investigate in more details first I guess...

the pseudopotentials used are from the ONCV library
inputs.zip
PP.zip
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Christoph Wolf

Postech university, South Korea
chwolf@postech.ac.kr

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Daniele Varsano
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Re: NetCDF: Numeric conversion not representable when BSE

Post by Daniele Varsano » Tue Jul 16, 2019 9:56 am

Dear Christoph,
I now think this might be related to the memory issue
did you spot some messages in the LOG files? If so, can you post it?

Thanks,
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/

chwolf
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Re: NetCDF: Numeric conversion not representable when BSE

Post by chwolf » Tue Jul 16, 2019 11:57 am

Dear Daniele,

there is no warning in the logs but a single process of yambo keeps eating up to 190 GB of Ram (max RAM per node on the cluster) and then crashes. Sorry that I made another post as I initially thought those two are unrelated

viewtopic.php?f=13&t=1604

Best,
Chris
Christoph Wolf

Postech university, South Korea
chwolf@postech.ac.kr

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Daniele Varsano
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Re: NetCDF: Numeric conversion not representable when BSE

Post by Daniele Varsano » Tue Jul 16, 2019 12:16 pm

Dear Christoph,
thanks for reporting, I'm not sure the probems are related.
Looking at the point where yambo stops:

Code: Select all

STOP signal received while in :[03] Transferred momenta grid
this part should be not memory intensive.
Actually I never tested before Intel 19 and I do not have it available in any machine.

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/

chwolf
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Re: NetCDF: Numeric conversion not representable when BSE

Post by chwolf » Tue Jul 16, 2019 4:28 pm

Dear Daniele,

thanks for your swift reply - is there any compiler set you can recommend other than intel19?

Does Yambo usually play nice with gfortran?

Thanks for your continuous support!

Chris
Christoph Wolf

Postech university, South Korea
chwolf@postech.ac.kr

chwolf
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Re: NetCDF: Numeric conversion not representable when BSE

Post by chwolf » Wed Jul 17, 2019 4:21 am

Sorry, I guess that my mistake was to use Ry instead of RL for BSENGBlk :shock: :shock:

I must have copied the input over from the previous attempt without noticing. It seems to be working (for the very small values of BSENGBlk I tried) - I will try to run a more realistic calculation and let you know.

Best,
Chris
Christoph Wolf

Postech university, South Korea
chwolf@postech.ac.kr

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Daniele Varsano
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Re: NetCDF: Numeric conversion not representable when BSE

Post by Daniele Varsano » Wed Jul 17, 2019 9:18 am

Dear Christoph,
ok let us know if you encounter problems.
I think that different problems are mixing. Inputs in Ry for BSENGBlk should also work.
The netcdf problem you encountered at the beginning contrary to what I said you in my first reply was already spotted in the past and fixed in the devel version of the code, but it appeared for very large k point samplings and this is not your case.

About gfortran, this is also an option for Yambo.

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/

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