Author Topic: Error in importing position file using ovito in ubuntu  (Read 104 times)

Dong

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Error in importing position file using ovito in ubuntu
« on: April 21, 2019, 10:48:11 AM »
Hello, I currently have a problem with ovito in ubuntu system.

The attached file"position_error.dat" is the position file I want to visualize using ovito. This file can be successfully read by ovito in windows, but it failed when using ovito (for both 2.9.0 and 3.0.0 version) in ubuntu. In unbuntu, when I import the file, ovito window will close immediately.

Additionally, this file contains 2731 atoms. When I deleted one atom in the file, I found that the file can be imported successfully.

I don't know why. Are there some bugs in ovito code in ubuntu?



Constanze Kalcher

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Re: Error in importing position file using ovito in ubuntu
« Reply #1 on: April 23, 2019, 11:12:44 AM »
Hello,

thanks for letting us know. However, I have difficulties reproducing the error. I can open your file without any trouble with both OVITO 2.9 and the latest developer version. Can you tell us what Ubuntu version you are using?
Also, does this happen with any file?

-Constanze
« Last Edit: April 23, 2019, 02:49:53 PM by Constanze Kalcher »

Dong

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Re: Error in importing position file using ovito in ubuntu
« Reply #2 on: April 25, 2019, 09:15:37 AM »
Dear Constanze,

        Thanks for your reply.

        This error only occurs on some data files. The positions in this file are defected sites detected by Wigner-Seitz method  with ovito 2.9.0 python script. I also use ovito script to output them to the example file (position_error.dat). I have used ovito for many times, as well as the WS method in ovito. Other files with this method are okay, only several files go wrong.

        In the attached files, two error messages are present when I open the position file with ovito execute program in "/data/ovito/bin/ovito".

        My Ubuntu Version is "Ubuntu 16.04.6 LTS", Linux version is "Linux version 4.4.0-143-generic (buildd@lgw01-amd64-041)".

        Thank you for your time!
       
Best wishes,

Dong

Constanze Kalcher

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Re: Error in importing position file using ovito in ubuntu
« Reply #3 on: April 25, 2019, 10:44:54 AM »
Dear Dong,

I assume it has something to do with the graphics card driver you're using. Depending on the number of atoms OVITO switches between different rendering modes, that's why you only get this error in some cases. According to your error message the software renderer swrast fails. It seems like you haven't installed the correct graphics driver for your hardware?
Could you please check that and let me know if that fixes your problem.

-Constanze

Dong

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Re: Error in importing position file using ovito in ubuntu
« Reply #4 on: May 07, 2019, 07:35:19 AM »
Dear Constanze,

    Sorry for replying so late.

    I have tried to re-install the graphic drivers, but the error still exists.

    There are two graphic cards in my computer, ASPEED and NVIDIA. My default graphic card is ASPEED. Re-installing this graphic driver can't fix the error. I tried many times but still can't switch graphics to NVIDIA. So I can't confirm if NVIDIA has the same problem.
   
    Thanks again for your time!

    Best wishes,
    -Dong

Constanze Kalcher

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Re: Error in importing position file using ovito in ubuntu
« Reply #5 on: May 10, 2019, 01:48:21 PM »
Dear Dong,

your best chance is probably to get the NVIDIA driver running, but I'm afraid I cannot help you with that. Does the same problem appear with other programs, like VMD or Paraview?

-Constanze


Dong

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Re: Error in importing position file using ovito in ubuntu
« Reply #6 on: May 14, 2019, 06:46:47 AM »
Dear Constanze,
      I have recently tried vmd and paraview. They can work well. Maybe it is due to my computer drivers. The problem is not easy to fix, so I will use Windows OVITO or other visualization softwares instead. If I fix this error in future, I will tell you.

      Thank you all the same.


Best wishes,
-Dong