Author Topic: run ovitos on HPC  (Read 387 times)

zfan

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run ovitos on HPC
« on: January 16, 2019, 11:01:33 PM »
Dear OVITOS users,

When I run ovitos to calculate atomic strain on HPC, it always failed after run several seconds or ~10 minutes seems when it was trying to use a X11 window.
My job just calculate atomic strain for many different configurations. Computing atomic strain for a single configuration just need at most one minute, which I tested it login node.
It could run ~10 minutes means the function of ovitos should be fine. The failure may be due to that it wants to try a X11 window in batch job on HPC?
Is there any option to prevent it to try X11 window on HPC when run ovitos?

Thanks,
Zhao

Alexander Stukowski

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Re: run ovitos on HPC
« Reply #1 on: January 17, 2019, 08:44:30 AM »
Dear Zhao,

You can prevent "ovitos" from connecting to the X server by clearing the DISPLAY environment variable before executing "ovitos":

   export DISPLAY=
   ./ovitos yourscript.py

Or even simpler:

  DISPLAY= ./ovitos yourscript.py

-Alex

Xtof

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Re: run ovitos on HPC
« Reply #2 on: January 17, 2019, 01:27:09 PM »
Possible reason:

When you use ovitos on the HPC, do you launch it from the command line or do you launch a job to the queue?
I work on the HPC Marconi and if I launch ovitos (or any code) from the command line, I have max 2 min. After that, the HPC Marconi stops the program. I guess it is made to avoid people running programs on the login node.
If I want to make an analysis with ovitos and I know it will take more than 2 min, then I launch it via a job.

Best regards,
Christophe

zfan

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Re: run ovitos on HPC
« Reply #3 on: January 17, 2019, 06:17:49 PM »
Dear Alex,

Thanks very much for your solution. It works for me.

And I compiled ovitos from source code on another HPC. It could run without any error and I could get correct results. But each time I run ovitos, I would get a warning:
QStandardPaths: XDG_RUNTIME_DIR points to non-existing path '/run/user/2174', please create it with 0700 permissions.

Could you please give me some suggestions to fix it?

Best,
Zhao

zfan

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Re: run ovitos on HPC
« Reply #4 on: January 17, 2019, 06:20:21 PM »
Thanks, Christophe, for your suggestion. But I run my job in batch jobs rather than on login node. And the issue was resolved with Alex's solution. Thanks anyway.

Best,
Zhao