Complexation hangs with certain sim seeds

[tahorst]

I've noticed some of my sims can hang during complexation - the process becomes unresponsive and will eventually run out of memory. It has happened for multiple seeds and different sim options (same seed but very different cell states). I've pushed a branch with a script to reproduce this error here.

It appears to be a sporadic arrow issue and only happens with certain seeds and numbers of molecules. The system can evolve with the same number of molecule counts for 7179 iterations before it reaches a random state that causes the hang. Adding 1 to all of the molecules causes it to happen at an earlier iteration.

Running this from the arrow-hang branch should reproduce the error (after 7100 displays you'll have to ctrl+z to get out of it since ctrl+c is unresponsive):

python arrow_hang.py

Is there a way to handle this in this repo (doesn't seem like we can pass signals to the arrow c extension to nicely handle it with a timeout) or do we need to debug the c code in arrow?

[1fish2]

I think we'll need to debug the C code in the arrow repo. Great work reproducing it and narrowing that down to a small test case!

There is a newer release, stochastic-arrow==0.4.3, but it just adds the ability to pickle arrow instances.

[1fish2]

Oops. The new release is stochastic-arrow==0.4.4.

[tahorst]

Forgot to mention that I tested it on both 0.4.3 and 0.4.4 with the same result

[1fish2]

Test case copied to a stochastic-arrow unit test.

Issue copied to CovertLab/arrow#48