Show Posts

This section allows you to view all posts made by this member. Note that you can only see posts made in areas you currently have access to.

Messages - Pieter Vancraeyveld

Pages: [1] 2
The workaround posted in will solve your issue.

Questions and Answers / Re: Job Manager won't work
« on: August 7, 2020, 14:22 »
The procedure on Windows is the same.

You can create your device configuration by pasting the following code snippet at the bottom of the script that defines your bulk configuration:

Code: [Select]
from NL.CommonConcepts.Configurations.DeviceFromBulk import deviceFromBulk, findBothElectrodeLengths
device_configuration = deviceFromBulk(
    electrode_lengths=findBothElectrodeLengths(bulk_configuration) * Angstrom,

The issue in Nanolab will be resolved in the R-2020.09 release scheduled for September 8.

You have discovered a bug in the Q-2019.12 version of QuantumATK that has been fixed for the upcoming R-2020.09 release.

As a workaround, you can select the option 'Set up electrode cross-section as a supercell' in the 'Device from Bulk' widget as indicated in the attached screenshot.

Can you share your script? Perhaps we can give you some suggestions based on what you have written already.

Based on your input, it appears that one of your bash startup scripts (.profile, .bashrc, .bash_profile) contains an error. After you have fixed it, you should be able to execute

ssh liuxiaolin@ 'echo $0; echo $SHELL; env'

as a single command without getting error messages.

Please ssh to your login node and execute the following command:

bash -c 'echo $0; echo $-; env'

What output do you get?

Your output contains a lot of "command not found" errors. This indicates errors in the scripts being sourced at login. Can you check or share ~/.bashrc on your login node? It is likely that PATH is set incorrectly.

I can see that my instructions were not 100% clear. Can you also execute

ssh liuxiaolin@ 'echo $0; echo $SHELL; env'

as a single command and provide the output?

Can you execute the following commands one by one and share the output?

ssh liuxiaolin@ 'echo $0; echo $SHELL; env'
ssh liuxiaolin@
echo $0
echo $SHELL

Thanks, Pieter

It is not clear why the diagnostic check fails if you can manually execute 'which bash'.

Can you empty the 'Scripts to source' field in the 'Environment' tab of the machine settings and submit a new script using the job manager?

Hi Aanand,

The reason that you can run some, but not all of the configurations, is related to the electrodes. Some of your devices have transverse electrode repetitions, while others don't. DeviceDensityOfStates does not support all definitions in Q-2019.12 and we will address this for the R-2020.09 release.

For now, you can pass method=LocalDeviceDensityOfStates to the ProjectedLocalDensityOfStates definition in your scripts. You might considering lowering the density_mesh_cutoff passed to ProjectedLocalDensityOfStates to improve performance.


It appears that 'bash' is not available on the server. Can you manually login and execute the command 'which bash'?

Hi Nayab,

Where are you running Nanolab? On Linux or Windows, inside a virtual machine or not? Please share the script of a structure that cannot be dropped and a screenshot of the About box under Help > About.


Pages: [1] 2