When GUI crashes it locks the hdf5 files

[manuelmelle]

Hello,

I have been recently using QATK to do DFT calculations on 1D and 2D systems and I have been very impressied about the quality of the results and the performance of the software.

That said, the GUI interface is not that stable in our workstations, and when it crashes it seems to lock the hdf5 file that is being analyzed turning it unreadable by the GUI after restart. Somehow I understood the origin of the problem (the error message does not mention the hdf5 file), and I found a way to recover from it, but it is a common nuisance. Any comments on this (I run the 2022.12 version)?

I think it is a nice idea to save everything in the hdf5 file, but is there an straightforward way to inspect/extract information hdf5 files from command line?.

regards

Manuel

[Anders Blom]

You can extract all info from HDF5 files using commands like nlread and then query functions for each class. This is all documented in the API, https://docs.quantumatk.com

I am sorry to hear the GUI crashes (and locks the files), it is not my own experience that it is unstable, and we have not heard from other users about similar problems. You mentioned an error message, can you share that?

[manuelmelle]

Thanks for your prompt answer and sorry for my lack of reply, busy times.

My workstation has a dated Ubuntu OS which could well be the cause of the instabilities of the GUI, another major suite software has also GUI instabilities there.

In fact, probably related, now I am unable to run locally jobs from the GUI anymore. On the good side now I run the calculations from command line the lock problems does not happen anymore. Once/if it happens again I will send it to you.

I do use nlread to read data from the hdf5 file and use it to monitor the evolution of the lattice parameter of the calculations, but that is somewhat cumbersome at the moment. Is there any way to adjust the output in the log file, as it is quite terse, to also include the lattice parameters and angles?

thanks in advance,

manuel 

 

It would be more convinient though to have a bit more verbose log file,


 cannot run jobs locally

[Anders Blom]

The default verbosity is on purpose a but lower to avoid too much output. It can be increased by removing, if you have, the command setVerbosity(MinimalLog) in the Python file.

Lattice parameters etc are most easily output with nlprint(configuration) statements at relevant points in your script.

[manuelmelle]

The default verbosity is on purpose a but lower to avoid too much output. It can be increased by removing, if you have, the command setVerbosity(MinimalLog) in the Python file.


Lattice parameters etc are most easily output with nlprint(configuration) statements at relevant points in your script.

Thanks, yes, about the verbosity of the log it figured.

Yes, I was testing using nlprint to extract the information from hdf5 files, but it is clearly easier to put it in the script, thanks!.

About the error you asked from my first message,  it just happened again:
"Source scanning error 'frozenset' object has no attribute 'add' "


regards, and thanks for the support,

Manuel

[manuelmelle]

Update, the error in the message before did not come from a crashed GUI but from the fact that I had one of the hdf5 files opened in an atkpython interactive session.

regards

Manuel

[Anders Blom]

Ok, I guess we consider it all solved for now then?

[manuelmelle]

That actually referred only to the cause of the last error message, as in that case, it was not caused by the GUI crashing.
The hdf5 file lock due to GUI crashing still should be there.

[Anders Blom]

Ok, but it's more of a operating system thing, than anything we can control in our code