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61
General Questions and Answers / Issue on running MTP training simulation
« Last post by Lim changmin on November 18, 2025, 06:52 »
Hello, I am trying to train MTP with GeTe doped with C and N.
However, I have encountered an error that I have never seen.
This is the error script below.

node01
Tue Nov 18 10:59:59 KST 2025
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
zipdir/NL/Study/Study.py:788: UserWarning: The original file of the Study object 'GeTeCN_amor_train_2.hdf5' no longer exists.This means no task results will be saved to the new file.
srun: Job step aborted: Waiting up to 32 seconds for job step to finish.
slurmstepd: error: *** JOB 4041 ON node01 CANCELLED AT 2025-11-18T11:05:56 ***
slurmstepd: error: *** STEP 4041.0 ON node01 CANCELLED AT 2025-11-18T11:05:56 ***

I don't know why the hdf5 no longer exist.
Can anyone help me to solve the error?

Thank you.
I have also attached a py file that I used
62
General Questions and Answers / Re: Parallelization issues with OrbitalMoment() in QuantumATK
« Last post by corsicATK on November 4, 2025, 23:02 »
Thank you very much for your reply! That really confirms what I was thinking.
I actually did something similar (running several independent jobs), and it works. Thanks for your help.
63
Plugin Development / Bondhistogram plugin
« Last post by Anders Blom on November 4, 2025, 20:47 »
A BondHistogram plugin I made. Currently tested and works for X-2025.06 but should also be fine for slightly older versions.
64
General Questions and Answers / Re: Unexpected Transmission Channel in Monolayer Graphene DFT Transport CalculationD
« Last post by Anders Blom on November 4, 2025, 20:44 »
You may need to go up to 100-300 k-points in the periodic direction to resolve artefacts related to the very specific band structure of graphene.
65
General Questions and Answers / Re: Whenever trying to open Current density .hdf5 file after execution isnot opening
« Last post by Anders Blom on November 4, 2025, 20:42 »
You don't open the file itself, you select it in the Data View in NanoLab and then you can access the individual objects inside the file. For more assistance, you need to be more specific what exactly you do, with screenshots ideally.
66
General Questions and Answers / Re: Connection to Cluster
« Last post by Anders Blom on November 4, 2025, 20:41 »
I think the warning message is quite clear, check your script for absolute paths to files that may not be available on the cluster in the same location. In general, always use relative paths to reference files you need from within a script that gets submitted to a different machine.
67
Future Releases / Re: Machine Learning potential that can also predict density of state
« Last post by Anders Blom on November 4, 2025, 20:39 »
I have yet to see a predefined ML model (we should not call them potentials) that can accurately predict DOS across many applications, but training a specific one for a given problem space is something we are working on.
68
General Questions and Answers / Re: DFT Phonon Transmission
« Last post by Anders Blom on November 4, 2025, 01:16 »
No, does not sound normal, I'd expect the whole thing to take a few minutes only, even on CPU. OK maybe an hour on CPU, as MACE is slow on CPU.

Maybe do a simple test calculation first on CPU for MoS2 with a similar number of atoms (make some distortion in the center to make it interesting) using the built-in ReaxFF potential in QuantumATK, just to get a feeling for the calculation time.
69
Future Releases / Machine Learning potential that can also predict density of state
« Last post by Lim changmin on November 3, 2025, 06:32 »
I understand that machine learning potentials have many advantages and are receiving a lot of attention. However, in the current version of ATK, the provided potentials can only compute force, stress, and energy. Meanwhile, several recent studies have shown the possibility of predicting the density of states (DOS) using machine learning. Therefore, it would be great if ATK could be updated to include ML potentials capable of calculating DOS as well.
70
General Questions and Answers / Re: DFT Phonon Transmission
« Last post by AsifShah on November 2, 2025, 09:18 »
Hi
I fine tuned MACE with additional data as per my requirement and when run on GPU, it is very very slow. It has been one day it shows only two progress cells in phonon transmission. The total size is 928 atoms

Is this normal?
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