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TOPIC: Dynamic Geometry not running

Dynamic Geometry not running 1 week 11 hours ago #590

After following the tutorial step by step for the Dynamic Geometry function within mcell I am always unable to actually run the simulation regardless of whether I am using a python script or not. The Fatal error is always the same "On line:22 of file Scene.initialization.mdl" I've attached screenshots of the program and the file in question. Any help would be appreciated.

Thanks!
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Dynamic Geometry not running 1 week 11 hours ago #591

As mentioned in the dynamic geometry tutorial, this feature is only available in an experimental branch of MCell. I'm attaching it here:

File Attachment:

File Name: mcell_2017-09-13.zip
File Size: 340 KB


You'll have to make sure CellBlender points to this version instead of the bundled version (I'm assuming you're using some version of the CellBlender bundle). You can change this under Settings & Preferences -> Set Path to MCell Binary. Let me know if you need any help with this.
Last Edit: 1 week 11 hours ago by jczech. Reason: attachment wouldn't add
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Dynamic Geometry not running 1 week 10 hours ago #592

Thanks for the reply, there doesn't seem to be any link/file I can see within your reply nevermind It just appeared for me. Is the dynamic meshing github file what you're referencing?

Just for clarification, I have Blender 2.78c installed with cellblender 1.1 and mcell 3.4. I set up the mcell binary path, which I just checked in the console although it is indicated as such in Blender (my computer indicates it's running 3.3 when I check in the console, I am not aware if this is an issue or not). I may have the incorrect version.
Last Edit: 1 week 10 hours ago by KatSnow.
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Dynamic Geometry not running 1 week 4 hours ago #593

  • Bob
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I ran the example with an older version of MCell (3.1) to verify the problem and got:

MCell 3.1 (revision 999/2012-10-12 10:02:57 -0700) [unofficial revision]
  Running on ... at Wed Sep 13 17:14:51 2017

  Copyright (C) 2006 - 2010 by
    The Salk Institute for Biological Studies and
    Pittsburgh Supercomputing Center, Carnegie Mellon University

MCell initializing simulation...
MCell[0]: random sequence 1
Fatal error: On line: 22 of file Scene.initialization.mdl

It fails at the same line of the MDL which specifies "LARGE_MOLECULAR_DISPLACEMENT" which I believe was added to support dynamic geometry.

Running with a more current version (3.3, commit 7030a99) works and gives this:

MCell initializing simulation...
MCell[0]: random sequence 1
MCell 3.3 (commit: 7030a99  date: Thu, 19 May 2016 11:14:16 -0400)
  Running on ... at Wed Sep 13 17:25:56 2017

Running an even newer version (3.4, commit: 0e07a94) also works and gives this:

MCell initializing simulation...
MCell[0]: random sequence 1
MCell 3.4 (commit: 0e07a94  date: Thu, 6 Jul 2017 11:42:18 -0400)
  Running on ... at Wed Sep 13 17:21:37 2017

What is the version number (and commit number) reported when you run?
Last Edit: 1 week 4 hours ago by Bob.
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Dynamic Geometry not running 5 days 13 hours ago #594

Thanks for the reply! I get a similar response from a terminal:

MCell: command-line argument syntax error: No MDL file name specified
MCell 3.3 (commit: 49ac0e0 date: Fri, 24 Apr 2015 11:17:22 -0400)
Running on ... at Fri Sep 15 11:42:14 2017

Copyright (C) 2006 - 2014 by
The National Center for Multiscale Modeling of Biological Systems,
The Salk Institute for Biological Studies, and
Pittsburgh Supercomputing Center, Carnegie Mellon University,

After attempting to run the simulation:

MCell initializing simulation...
MCell[0]: random sequence 1
Fatal error: On line: 22 of file Scene.initialization.mdl
Error: syntax error

MCell 3.4 (commit: 275420e date: Thu, 29 Sep 2016 14:07:12 -0400)
Running on . . . at Fri Sep 15 11:47:26 2017

Copyright (C) 2006 - 2016 by
The National Center for Multiscale Modeling of Biological Systems,
The Salk Institute for Biological Studies, and
Pittsburgh Supercomputing Center, Carnegie Mellon University,
Last Edit: 5 days 13 hours ago by KatSnow. Reason: Additional information.
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Dynamic Geometry not running 5 days 8 hours ago #595

  • Bob
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Thanks for posting the commit numbers. That helps me get that exact version.

I pulled that version (275420e) from the repository and I get the exact message you've reported. I believe the problem is that version simply does not support dynamic geometry as Jacob mentioned.

Dynamic geometry support was originally written as a separate branch of our code beginning as early as 2014. So there have been experimental MCell versions supporting dynamic geometry dating at least that far back (maybe further). But I believe the dynamic_meshes branch wasn't merged into our main (master) branch until June 22nd, 2017 (after the date of your version).

As a developer, I usually get my version from the source code repository, and so I'm not sure what has been released to various web sites. I would have expected the mcell.org version to include dynamic meshes by now, but I haven't found it. Let me check and get back to you.

Sorry about the confusion.
Last Edit: 5 days 6 hours ago by Bob.
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Dynamic Geometry not running 2 days 14 hours ago #596

Thank you for clearing that up! Does the version of mcell Jacob linked include the dynamic geometry branch?
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Dynamic Geometry not running 2 days 13 hours ago #597

Yes, the version of MCell I uploaded supports dynamic geometries. Do you need any help using it? Have you gotten it to work from within CellBlender?
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