Problem running a simulation

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Siting Li

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Mar 16, 2021, 8:26:22 AM3/16/21
to CRIMSON Users

Dear developers, 

I tried to use a CustomizeHeartModel.py on the latest version of CRIMSON. Initially, I used my own model, but I kept encountering the same problem while trying to start the simulation: “orterun has exited due to process rank 1 with PID 0”. I changed into the “example A” model from your tutorial and followed every step. The problem remained and could not work on another computer, either. I was wondering if this was due to the heart model or other reasons.

Looking forward to your guidance. Thanks!

 Best regards,

Siting

error1.png
error2.png
model.png

Chris Arthurs

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Mar 16, 2021, 5:08:45 PM3/16/21
to Siting Li, CRIMSON Users
Hi Siting,

I'm not sure what's going on here - it's very unusual not to get a stack trace from Python if it's a Python scripting problem, but I can take a look. Are you able to share your simulation files with me? Zip them up into a single file, and I'll take a look.

Best,
Chris

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Siting Li

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Mar 16, 2021, 11:40:50 PM3/16/21
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Hi Chris,

I've uploaded my model files:

Thank you for your help!

Best regards,
Siting

Chris Arthurs

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Apr 27, 2021, 5:59:29 PM4/27/21
to Siting Li, CRIMSON Users
Hi Siting,

I just got a moment to look at your problem.

The issue is that the structure of your heart model is wrong. See the attached image - it's made in two disconnected parts for some reason. Take a look at the netlist_surfaces.xml that gets generated when you write out the simulation files. You can adjust this (look at the startNodeIndex and endNodeIndex XML tags), or you can remake the heart model in the boundary condition toolbox (this is what I'd recommend.

Best,
Chris

Sent from my phone

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