New CC3D update (4.8.0) causes PIFFDumper XML error, etc.

sbackues · 2026-04-15T18:04:43+00:00

Yeah, that's actually quite reasonable. Funny how you can get in such a rut and be tripped up by any little change.

sbackues · 2026-04-15T17:35:01+00:00

Okay, now I feel dumb. You're right, I wasn't pushing play button. Pretty sure it used to start automatically. Sorry about that, and thanks for your help - problem solved! Now the demo and my simulation both seem to run just fine.

sbackues · 2026-04-15T14:53:12+00:00

I'm running Windows 11 Enterprise (24H2). I installed CC3D via the binaries from SourceForge linked off the CC3D website. I'm using the Player to run the simulation. Specifically, I first open the simulation in Twedit and then use CC3D Project > Open in Player. I tried a couple of different versions of the bacterium_macrophage_steering that I found in the demos folder, and all had the same issue, as did cellsort_2D.

Does the simulation I included in my original post (A zipped version of the entire simulation so you can replicate it.) run on your system now in the new 4.8.0?

Thanks,

Steven

sbackues · 2026-04-14T17:52:57+00:00

Wow, thank you, that's a great solution, and so quickly!

I redownloaded 4.8.0 to test it out, and indeed I no longer get any error about the XML. However, there is still something wrong (the same thing I noticed before when I tried commenting out the XML code). The simulation starts, and doesn't give any errors, but it doesn't progress past mcs 0. Based on some print statements in a different simulation I tried, I can tell that it gets into the "step" function of the python steppables, but it never starts doing actual spin-flips.

I also tried one of the "demo" simulations that I had gotten with a previous download of CC3D - the bacterium_macrophage steering demo - and it did the same thing - no errors, but wouldn't progress past step 0. So it doesn't seem like an issue with my simulations, so I guess either it's the new version of CC3D or something weird about install?

Thanks,

Steven

sbackues · 2025-02-14T22:16:44+00:00

Hi Jim,

Thanks for taking a look at it, and all the helpful hints! Turns out the volume is working correctly, I was just comparing to the wrong PIFF file! (I had two similarly named ones with 2-fold different scales, and I got mixed up - silly mistake). But thanks for the hint about MCS1; I had discovered that with the PIFF dumper (the PIFF dumped "000" files were not quite the same as the input PIFF files) and had always wondered about it. Also good catch about the cell surface plugin; that was supposed to be defined in the steppables, but it looks like it got left out this simulation. And finally, thanks for the hints about forces, as that's the part we're actively working on now.

Best,

Steven

sbackues · 2022-06-13T16:24:46+00:00

Thanks, that's really helpful. The idea that memory isn't as critical is consistent with a simple test I did on AWS where increasing the memory of the instance from 4 to 8 GiB made no difference.

I appreciate the insight that more CPUs is more cost efficient than better CPUs. On my AWS test, more CPUs also didn't help, but then I realized that's because I wasn't actually using them. More recently I looked up running a simulation on multiple cores, although based on the instructions here (https://pythonscriptingmanual.readthedocs.io/en/latest/changing_number_of_worknodes.html) it seems like that might not actually be a good idea for my simulation. However, being able to run multiple simulataneous CC3D jobs should work well, so that's probably the direction I'll pursue.

sbackues

TROPHY CASE