NETCDF error

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NETCDF error

Postby vjhalani » Mon Apr 29, 2019 6:43 pm

Hi all,

I'd like to check RPA on a 50^3 k-grid in GaAs to check convergence, but am running into an issue. To get the yambo setup to run, I had to add the DBsFRAGpm= "+QINDX" option. When I then run an RPA calculation, I get the following error:

P0001: [ERROR] File ./SAVE//ndb.kindx; Variable Sindx; NetCDF: Variable not found

This was the second time I tried, the first time I got an error related to "Variable Sindx; NetCDF: One or more variable sizes violate format constraints"

Looking in the forum, I saw that this was related to NetCDF databases being >2Gb in size and the solution was to compile with large file support, or recommended was to add the -S option to yambo to fragment the database. The -S option doesn't seem to be a supported feature anymore right?

To clarify, I ran yambo initialization successfully only after adding DBsFRAGpm= "+QINDX". Then doing an RPA I get the format constraint error. Then I tried adding "-S" which obviously didn't work, then trying to run RPA again to reproduce the error I got the variable not found error.

Thanks,
Vatsal
Vatsal A. Jhalani
Postdoctoral Scholar | Department of Applied Physics
California Institute of Technology
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Re: NETCDF error

Postby Davide Sangalli » Mon Apr 29, 2019 8:34 pm

Ciao Vatsal,
you are really pushing yambo using big k-points grids.

First, as you noticed, the -S option does not exist anymore and it was replaced by the option
Code: Select all
DBsFRAGpm= "+QINDX"

which is DB specific and thus more flexible.

The QINDX db is needed for any run, thus if you put such option in the input for the setup, you need to keep it in all the subsequent input files.
Otherwise yambo checks the ndb.kindx, finds that it is fragmented while the input file does not want it fragmented and tries to recompute it.

Accordingly, this is my guess for what is happening.
a) you generate the ndb.kindx with fragments
b) run the RPA calculation, without specifically asking for fragmentation. yambo tries to re-generate the ndb.kindx and fails for the violation of the formal constraints
c) then running RPA again, yambo finds the corrupted ndb.kindx and gives the message Variable not found

In summary just erase all ndb.kindx and run first the setup and the subsequent RPA calculation with
Code: Select all
DBsFRAGpm= "+QINDX"

in input in both cases.

An alternative is to recompile yambo using netcdf v4, adding to the configure the option
Code: Select all
--enable-netcdf-hdf5

It has less formal constraints and should work also without the fragmentation.
Yambo should still be able to read all the databases in older format, but will generate all dew databases in HDF5 format.

Both solutions are fine for your case from what I understand.
If you push yambo even further you may need the netcdf v4 and the fragmentation together.

Best,
D.
Davide Sangalli, PhD
CNR-ISM, Division of Ultrafast Processes in Materials (FLASHit) and MaX Centre
http://www.ism.cnr.it/en/davide-sangalli-cv/
http://www.max-centre.eu/
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Re: NETCDF error

Postby vjhalani » Wed May 01, 2019 7:34 pm

Ciao,

Yeah, I can tell I am pushing yambo, but I know it can do it!!!! :D

Anyways, thanks for the suggestion, I did both fragmentation and compiling with netcdf v4 and was able to get past the error.

However... now I get another one. Yambo crashes at the dipoles, and some of the log files end with the error:
P0303: [ERROR] STOP signal received while in :[04] Dipoles
P0303: [ERROR]Allocation attempt of DIP_S of negative size.

I seem to get this type of negative allocation attempt a lot when pushing to big k-point grids for different variables. Note I am using the Covariant dipole approach.

Grazie!
Vatsal
Vatsal A. Jhalani
Postdoctoral Scholar | Department of Applied Physics
California Institute of Technology
vjhalani
 
Posts: 18
Joined: Mon Jan 22, 2018 8:23 pm


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